1 Single cell expression data

Source:
High-throughput single-cell functional elucidation of neurodevelopmental disease-associated genes reveals convergent mechanisms altering neuronal differentiation, GEO accession: GSE142078.

Perturbations:
CRISPR knock-down of 14 autism spectrum disorder (ASD)–associated genes (3 gRNAs per gene) + 5 non-targeting gRNAs.

Cells:
Lund human mesencephalic (LUHMES) neural progenitor cell line.
Cells from 3 batches were merged together into 1 analysis. All cells have only a single type of gRNA readout. Quality control resulted in 8708 cells.

Genes:
Only genes detected in > 10% of cells were kept, resulted in 6213 genes.

Normalization:
Seurat “LogNormalize”: log(count per 10K + 1).
Batch effect, unique UMI count, library size, and mitochondria percentage were all corrected for. The corrected and scaled expression data were used as input for subsequent factor analysis.

2 Guided results

Here, our “guide”, \(G\) matrix, consists of 15 types (14 genes + NTC) of gene-level knock-down conditions across cells.

In each case, Gibbs sampling was conducted for 2000 iterations, and the posterior mean estimates were averaged over the last 500 iterations.

2.1 SVD Initialization

2.1.1 Local False Sign Rate (LFSR)

For a given GSFA inference result, we can estimate the effect a certain KO condition \(m\) has on the expression of gene \(j\) by computing the LFSR of \(\beta_{m\cdot} \cdot W_{j\cdot}\).

GSFA, # of genes that passed LFSR cutoff of 0.05:
KO ADNP ARID1B ASH1L CHD2 CHD8
Num_genes 2092 434 789 1938 0
KO CTNND2 DYRK1A HDAC5 MECP2 MYT1L
Num_genes 0 0 0 0 0
KO Nontargeting POGZ PTEN RELN SETD5
Num_genes 0 0 2099 0 987

2.1.2 Estimate of Factor ~ Perturbation Associations (\(\beta\))

2.1.3 Factor ~ Perturbation Association P Values

2.1.4 Beta PIP vs P-Value

2.1.5 Correlation btw Factors

2.2 Alternative Initializations and Chain Convergence

Other than initializing GSFA using truncated SVD, we also ran 2 chains with random initialization.

2.2.1 Association results for 2 randomly initialized GSFA runs

2.2.2 Chain mixing and convergence evaluation

Min. 1st Qu. Median Mean 3rd Qu. Max.
ADNP 0.999 1.03 1.06 1.09 1.13 1.70
ARID1B 1.000 1.03 1.06 1.07 1.10 1.55
ASH1L 0.999 1.02 1.04 1.06 1.08 1.52
CHD2 0.999 1.01 1.03 1.06 1.07 1.98
CHD8 0.999 1.00 1.00 1.00 1.01 1.04
CTNND2 0.999 1.00 1.00 1.00 1.00 1.02
DYRK1A 0.999 1.01 1.02 1.02 1.02 1.08
HDAC5 0.999 1.00 1.00 1.01 1.01 1.11
MECP2 0.999 1.00 1.00 1.00 1.00 1.02
MYT1L 0.999 1.00 1.00 1.00 1.00 1.02
Nontargeting 0.999 1.00 1.01 1.03 1.03 1.23
POGZ 0.999 1.00 1.00 1.00 1.00 1.05
PTEN 0.999 1.02 1.04 1.07 1.09 1.60
RELN 0.999 1.00 1.01 1.01 1.01 1.07
SETD5 1.000 1.03 1.06 1.08 1.11 1.64
offset 0.999 1.01 1.03 1.13 1.14 2.69

2.2.3 Difference btw methods in factor estimation

For a pair of \(Z\) estimations from 2 inference methods, \(Z_1, Z_2\), we quantify the pairwise estimation difference as \(||Z_1Z_1^T - Z_2Z_2^T||_F/N\), where \(||\cdot||\) is the Frobenius norm of a matrix, and \(N\) is the number of rows (samples) in \(Z\).

Guided SVD vs Rand_01: 0.752

Guided SVD vs Rand_02: 0.56

Rand_01 vs Rand_02: 0.611

3 Unguided Result

In contrast to the guided version, here we provide no guidance (\(G = \vec{0}\)) to our sparse factor analysis model to serve as a comparison.

3.1 Factor ~ KO Beta PIP

3.2 Factor ~ KO Posterior Association

3.3 Unguided vs Guided

4 FLASH

4.1 Factor ~ KO Posterior Association

4.2 FLASH vs GSFA

We matched the factors obtained from GFSA with those from FLASH, and conducted pairwise comparisons for both factors and gene loadings.

In the following heatmaps, factors are labeled by the KO condition(s) that they have an association p-value < 1e-4 with.

5 Gene Set Enrichment Analysis

Target genes: Genes w/ non-zero loadings in each factor (PIP cutoff at 0.95);
Backgroud genes: all 6213 genes used in factor analysis;
Statistical test: hypergeometric test (over-representation test);
Only GO terms/pathways that satisfy fold change \(\geq\) 2 and test FDR \(<\) 0.05 are shown below.

5.1 GO Slim Over-Representation Analysis

Gene sets: Gene ontology “Biological Process” (non-redundant).

Factor 2 : 16 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0070972 protein localization to endoplasmic reticulum 14.715942 0.0000000 0.0000000 82/123
GO:0006413 translational initiation 12.434040 0.0000000 0.0000000 89/158
GO:0002181 cytoplasmic translation 11.633549 0.0000000 0.0000000 39/74
GO:0090150 establishment of protein localization to membrane 8.702216 0.0000000 0.0000000 82/208
GO:0006401 RNA catabolic process 7.780150 0.0000000 0.0000000 86/244
GO:0006605 protein targeting 6.622174 0.0000000 0.0000000 81/270
GO:1902600 proton transmembrane transport 4.810981 0.0000000 0.0000031 17/78
GO:0071826 ribonucleoprotein complex subunit organization 4.153693 0.0000000 0.0000000 35/186
GO:0016072 rRNA metabolic process 3.511759 0.0000000 0.0000003 28/176
GO:0022613 ribonucleoprotein complex biogenesis 3.416201 0.0000000 0.0000000 52/336
GO:0034470 ncRNA processing 2.607889 0.0000021 0.0001404 28/237
GO:0009141 nucleoside triphosphate metabolic process 2.401825 0.0001437 0.0075622 21/193
GO:0034248 regulation of cellular amide metabolic process 2.378654 0.0000384 0.0023576 25/232
GO:0009636 response to toxic substance 2.337238 0.0006037 0.0278085 18/170
GO:0009123 nucleoside monophosphate metabolic process 2.317761 0.0002378 0.0116841 21/200
GO:0010608 posttranscriptional regulation of gene expression 2.169978 0.0000507 0.0028769 29/295
Factor 5 : 1 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0015844 monoamine transport 2.308212 0.0003117 0.0208834 13/17
Factor 7 : 4 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0090662 ATP hydrolysis coupled transmembrane transport 2.457081 0.0009878 0.0345378 11/17
GO:0010257 NADH dehydrogenase complex assembly 2.215096 0.0000001 0.0000132 35/60
GO:0070972 protein localization to endoplasmic reticulum 2.130197 0.0000000 0.0000000 69/123
GO:0033108 mitochondrial respiratory chain complex assembly 2.051419 0.0000000 0.0000044 47/87
Factor 8 : 11 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0070972 protein localization to endoplasmic reticulum 3.008760 0.0000000 0.0000000 96/123
GO:0006413 translational initiation 2.513052 0.0000000 0.0000000 103/158
GO:1903513 endoplasmic reticulum to cytosol transport 2.386412 0.0005341 0.0196828 13/21
GO:0036260 RNA capping 2.372291 0.0001327 0.0054332 16/26
GO:0002181 cytoplasmic translation 2.344241 0.0000000 0.0000000 45/74
GO:0090150 establishment of protein localization to membrane 2.075755 0.0000000 0.0000000 112/208
GO:1902600 proton transmembrane transport 2.075755 0.0000001 0.0000096 42/78
GO:0017004 cytochrome complex assembly 2.065164 0.0016318 0.0400884 15/28
GO:0010257 NADH dehydrogenase complex assembly 2.055986 0.0000050 0.0002465 32/60
GO:0032527 protein exit from endoplasmic reticulum 2.040868 0.0006833 0.0239810 18/34
GO:0006401 RNA catabolic process 2.038080 0.0000000 0.0000000 129/244
Factor 9 : 2 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0070972 protein localization to endoplasmic reticulum 2.472091 4.00e-07 0.0003286 33/123
GO:0006413 translational initiation 2.041110 2.28e-05 0.0056108 35/158
Factor 10 : 16 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0035924 cellular response to vascular endothelial growth factor stimulus 4.296474 0.0009241 0.0387893 6/10
GO:0048645 animal organ formation 3.905885 0.0017941 0.0473867 6/11
GO:0048483 autonomic nervous system development 3.855810 0.0008017 0.0369303 7/13
GO:0015844 monoamine transport 3.369784 0.0010526 0.0387893 8/17
GO:0021675 nerve development 3.113387 0.0005418 0.0332771 10/23
GO:2001023 regulation of response to drug 2.963086 0.0002656 0.0195762 12/29
GO:0043583 ear development 2.685296 0.0000394 0.0072662 18/48
GO:0002576 platelet degranulation 2.515953 0.0009652 0.0387893 13/37
GO:0045165 cell fate commitment 2.437716 0.0003880 0.0259967 16/47
GO:0008202 steroid metabolic process 2.412875 0.0000011 0.0002607 31/92
GO:0090596 sensory organ morphogenesis 2.345776 0.0002008 0.0185011 19/58
GO:0070972 protein localization to endoplasmic reticulum 2.270494 0.0000003 0.0001978 39/123
GO:2000027 regulation of animal organ morphogenesis 2.254323 0.0007250 0.0369303 17/54
GO:1901615 organic hydroxy compound metabolic process 2.164890 0.0000011 0.0002607 39/129
GO:0015850 organic hydroxy compound transport 2.161748 0.0016990 0.0473867 16/53
GO:0003007 heart morphogenesis 2.045940 0.0018003 0.0473867 18/63
Factor 11 : 10 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0034453 microtubule anchoring 3.133951 0.0015751 0.0408236 8/16
GO:0061842 microtubule organizing center localization 3.133951 0.0015751 0.0408236 8/16
GO:0002200 somatic diversification of immune receptors 2.872788 0.0005354 0.0232132 11/24
GO:0006338 chromatin remodeling 2.537008 0.0000000 0.0000361 34/84
GO:0014074 response to purine-containing compound 2.250016 0.0018649 0.0429519 14/39
GO:0030048 actin filament-based movement 2.186477 0.0018064 0.0429466 15/43
GO:0032200 telomere organization 2.169658 0.0000368 0.0031555 27/78
GO:0006310 DNA recombination 2.129869 0.0000043 0.0007892 35/103
GO:0006333 chromatin assembly or disassembly 2.117534 0.0001118 0.0063396 25/74
GO:0071103 DNA conformation change 2.027850 0.0000258 0.0031555 33/102
Factor 12 : 6 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0070972 protein localization to endoplasmic reticulum 3.389851 0.0000000 0.0000000 68/123
GO:0002065 columnar/cuboidal epithelial cell differentiation 2.952272 0.0001124 0.0118336 13/27
GO:0006413 translational initiation 2.871782 0.0000000 0.0000000 74/158
GO:0090150 establishment of protein localization to membrane 2.505719 0.0000000 0.0000000 85/208
GO:0002181 cytoplasmic translation 2.237221 0.0000186 0.0022818 27/74
GO:0006605 protein targeting 2.112010 0.0000000 0.0000000 93/270
Factor 13 : 46 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0010644 cell communication by electrical coupling 5.659978 0.0002965 0.0102778 6/13
GO:0046683 response to organophosphorus 3.967533 0.0000474 0.0034922 11/34
GO:0060191 regulation of lipase activity 3.872616 0.0030728 0.0415358 6/19
GO:0014074 response to purine-containing compound 3.773318 0.0000377 0.0030890 12/39
GO:0002576 platelet degranulation 3.645841 0.0001131 0.0060883 11/37
GO:0035270 endocrine system development 3.449049 0.0007511 0.0185936 9/32
GO:0007422 peripheral nervous system development 3.433720 0.0030030 0.0415358 7/25
GO:0046847 filopodium assembly 3.301654 0.0038268 0.0492304 7/26
GO:0008277 regulation of G protein-coupled receptor signaling pathway 3.199118 0.0002217 0.0090771 12/46
GO:0035418 protein localization to synapse 3.153416 0.0015176 0.0279626 9/35
GO:0071241 cellular response to inorganic substance 2.978226 0.0000309 0.0028465 17/70
GO:0032103 positive regulation of response to external stimulus 2.885479 0.0006217 0.0163645 12/51
GO:0035637 multicellular organismal signaling 2.870131 0.0010930 0.0230158 11/47
GO:0045165 cell fate commitment 2.870131 0.0010930 0.0230158 11/47
GO:0007159 leukocyte cell-cell adhesion 2.829989 0.0001682 0.0072921 15/65
GO:0032409 regulation of transporter activity 2.819146 0.0000150 0.0018428 20/87
GO:0010959 regulation of metal ion transport 2.803037 0.0000023 0.0005730 24/105
GO:0043270 positive regulation of ion transport 2.803037 0.0001157 0.0060883 16/70
GO:0006814 sodium ion transport 2.796890 0.0005140 0.0145707 13/57
GO:0034765 regulation of ion transmembrane transport 2.791642 0.0000004 0.0002654 28/123
GO:0050920 regulation of chemotaxis 2.725174 0.0027650 0.0412477 10/45
GO:0034764 positive regulation of transmembrane transport 2.705136 0.0002866 0.0102778 15/68
GO:0010038 response to metal ion 2.702080 0.0000019 0.0005730 26/118
GO:1902600 proton transmembrane transport 2.672767 0.0001335 0.0061502 17/78
GO:0050803 regulation of synapse structure or activity 2.627847 0.0001074 0.0060883 18/84
GO:0060541 respiratory system development 2.609210 0.0038743 0.0492304 10/47
GO:0021953 central nervous system neuron differentiation 2.581744 0.0017689 0.0310391 12/57
GO:1901654 response to ketone 2.494228 0.0024118 0.0408742 12/59
GO:0042391 regulation of membrane potential 2.452657 0.0000180 0.0018969 25/125
GO:0010257 NADH dehydrogenase complex assembly 2.452657 0.0027983 0.0412477 12/60
GO:0099177 regulation of trans-synaptic signaling 2.358324 0.0000060 0.0011038 30/156
GO:0051271 negative regulation of cellular component movement 2.353560 0.0003220 0.0102778 19/99
GO:1901342 regulation of vasculature development 2.289147 0.0025478 0.0408742 14/75
GO:0090130 tissue migration 2.266042 0.0010329 0.0230158 17/92
GO:0060560 developmental growth involved in morphogenesis 2.241676 0.0011714 0.0233327 17/93
GO:0001667 ameboidal-type cell migration 2.211412 0.0002828 0.0102778 22/122
GO:0002521 leukocyte differentiation 2.189872 0.0006058 0.0163645 20/112
GO:0040013 negative regulation of locomotion 2.185536 0.0011514 0.0233327 18/101
GO:0001525 angiogenesis 2.118204 0.0012520 0.0242815 19/110
GO:0019932 second-messenger-mediated signaling 2.109812 0.0030997 0.0415358 16/93
GO:0002009 morphogenesis of an epithelium 2.102277 0.0003347 0.0102778 24/140
GO:0061564 axon development 2.092314 0.0000124 0.0018245 36/211
GO:0072511 divalent inorganic cation transport 2.043881 0.0014838 0.0279626 20/120
GO:0048638 regulation of developmental growth 2.043881 0.0025227 0.0408742 18/108
GO:0009141 nucleoside triphosphate metabolic process 2.033291 0.0000683 0.0045787 32/193
GO:0050808 synapse organization 2.030345 0.0004382 0.0129185 25/151
Factor 15 : 55 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0015844 monoamine transport 5.501393 0.0001253 0.0046187 7/17
GO:0106030 neuron projection fasciculation 5.344210 0.0045114 0.0496258 4/10
GO:0034109 homotypic cell-cell adhesion 4.922299 0.0002847 0.0083923 7/19
GO:0014812 muscle cell migration 3.597065 0.0023499 0.0320713 7/26
GO:0043062 extracellular structure organization 3.396744 0.0000185 0.0013647 15/59
GO:0001763 morphogenesis of a branching structure 3.340132 0.0010241 0.0203992 9/36
GO:0035270 endocrine system development 3.340132 0.0019450 0.0286696 8/32
GO:0055088 lipid homeostasis 3.340132 0.0037132 0.0427598 7/28
GO:0098742 cell-cell adhesion via plasma-membrane adhesion molecules 3.258665 0.0006691 0.0149440 10/41
GO:2001023 regulation of response to drug 3.224955 0.0045866 0.0497112 7/29
GO:0030048 actin filament-based movement 3.107099 0.0009998 0.0203992 10/43
GO:0001764 neuron migration 3.083198 0.0000635 0.0029229 15/65
GO:0043270 positive regulation of ion transport 3.053835 0.0000411 0.0021620 16/70
GO:0009612 response to mechanical stimulus 3.025025 0.0004144 0.0108254 12/53
GO:0051271 negative regulation of cellular component movement 2.969006 0.0000025 0.0006055 22/99
GO:0003007 heart morphogenesis 2.969006 0.0001715 0.0054946 14/63
GO:0032409 regulation of transporter activity 2.917816 0.0000158 0.0012921 19/87
GO:0040013 negative regulation of locomotion 2.910214 0.0000035 0.0006468 22/101
GO:0090130 tissue migration 2.904462 0.0000101 0.0009337 20/92
GO:0035637 multicellular organismal signaling 2.842665 0.0020623 0.0292284 10/47
GO:0045165 cell fate commitment 2.842665 0.0020623 0.0292284 10/47
GO:0010038 response to metal ion 2.830620 0.0000013 0.0006055 25/118
GO:0006814 sodium ion transport 2.812742 0.0008358 0.0175996 12/57
GO:0048568 embryonic organ development 2.799348 0.0000069 0.0008471 22/105
GO:0061448 connective tissue development 2.783443 0.0024355 0.0326358 10/48
GO:0015850 organic hydroxy compound transport 2.772939 0.0015468 0.0242547 11/53
GO:0003012 muscle system process 2.717395 0.0000045 0.0006702 24/118
GO:0010959 regulation of metal ion transport 2.672105 0.0000237 0.0015907 21/105
GO:0031589 cell-substrate adhesion 2.672105 0.0001423 0.0047678 17/85
GO:0001667 ameboidal-type cell migration 2.628300 0.0000083 0.0008789 24/122
GO:0060560 developmental growth involved in morphogenesis 2.585908 0.0001418 0.0047678 18/93
GO:0051056 regulation of small GTPase mediated signal transduction 2.578347 0.0000274 0.0016306 22/114
GO:0021953 central nervous system neuron differentiation 2.578347 0.0028558 0.0369252 11/57
GO:0061351 neural precursor cell proliferation 2.578347 0.0028558 0.0369252 11/57
GO:0034764 positive regulation of transmembrane transport 2.554218 0.0013341 0.0223461 13/68
GO:0034330 cell junction organization 2.544862 0.0000771 0.0033413 20/105
GO:0001655 urogenital system development 2.493965 0.0011243 0.0212469 14/75
GO:0010721 negative regulation of cell development 2.490946 0.0000477 0.0023459 22/118
GO:1901654 response to ketone 2.490946 0.0037842 0.0429069 11/59
GO:0097305 response to alcohol 2.481241 0.0017604 0.0264776 13/70
GO:0019932 second-messenger-mediated signaling 2.442247 0.0004407 0.0108254 17/93
GO:0003013 circulatory system process 2.429187 0.0003222 0.0091337 18/99
GO:0034765 regulation of ion transmembrane transport 2.389688 0.0000917 0.0037558 22/123
GO:0097485 neuron projection guidance 2.365927 0.0006464 0.0148875 17/96
GO:0042391 regulation of membrane potential 2.351453 0.0001176 0.0045629 22/125
GO:0001525 angiogenesis 2.307727 0.0004373 0.0108254 19/110
GO:0001503 ossification 2.298585 0.0012783 0.0223461 16/93
GO:0070972 protein localization to endoplasmic reticulum 2.281065 0.0002606 0.0080021 21/123
GO:0061564 axon development 2.279521 0.0000017 0.0006055 36/211
GO:0050890 cognition 2.274132 0.0014376 0.0230333 16/94
GO:0051961 negative regulation of nervous system development 2.206325 0.0010659 0.0206729 18/109
GO:0007389 pattern specification process 2.186268 0.0011889 0.0219053 18/110
GO:0022604 regulation of cell morphogenesis 2.157168 0.0000288 0.0016306 31/192
GO:0050808 synapse organization 2.035047 0.0007381 0.0159993 23/151
GO:0090066 regulation of anatomical structure size 2.007940 0.0004178 0.0108254 26/173
Factor 16 : 25 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0042558 pteridine-containing compound metabolic process 4.570345 0.0002369 0.0093214 7/12
GO:0051156 glucose 6-phosphate metabolic process 4.273569 0.0011054 0.0271548 6/11
GO:0070670 response to interleukin-4 4.273569 0.0011054 0.0271548 6/11
GO:0051187 cofactor catabolic process 3.482167 0.0009100 0.0239536 8/18
GO:0006081 cellular aldehyde metabolic process 3.191987 0.0002530 0.0093214 11/27
GO:0072524 pyridine-containing compound metabolic process 2.651804 0.0000085 0.0006022 22/65
GO:0009123 nucleoside monophosphate metabolic process 2.624684 0.0000000 0.0000000 67/200
GO:0099132 ATP hydrolysis coupled cation transmembrane transport 2.611626 0.0018242 0.0388436 11/33
GO:0046939 nucleotide phosphorylation 2.554851 0.0003708 0.0109672 15/46
GO:0046390 ribose phosphate biosynthetic process 2.550890 0.0000000 0.0000004 42/129
GO:0072522 purine-containing compound biosynthetic process 2.531268 0.0000000 0.0000004 42/130
GO:0009141 nucleoside triphosphate metabolic process 2.516903 0.0000000 0.0000000 62/193
GO:0070972 protein localization to endoplasmic reticulum 2.484229 0.0000000 0.0000024 39/123
GO:0006090 pyruvate metabolic process 2.458000 0.0003912 0.0110879 16/51
GO:1902600 proton transmembrane transport 2.410731 0.0000211 0.0011110 24/78
GO:0014074 response to purine-containing compound 2.410731 0.0024825 0.0457408 12/39
GO:0002181 cytoplasmic translation 2.223411 0.0002477 0.0093214 21/74
GO:0009259 ribonucleotide metabolic process 2.217418 0.0000000 0.0000000 75/265
GO:1901293 nucleoside phosphate biosynthetic process 2.181864 0.0000002 0.0000189 44/158
GO:0016999 antibiotic metabolic process 2.161345 0.0018447 0.0388436 16/58
GO:0009132 nucleoside diphosphate metabolic process 2.136785 0.0028661 0.0491240 15/55
GO:0006413 translational initiation 2.132277 0.0000006 0.0000467 43/158
GO:0006091 generation of precursor metabolites and energy 2.131086 0.0000000 0.0000000 68/250
GO:0010257 NADH dehydrogenase complex assembly 2.089300 0.0027016 0.0485626 16/60
GO:1901615 organic hydroxy compound metabolic process 2.004271 0.0000482 0.0023678 33/129
Factor 17 : 15 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0006413 translational initiation 6.550170 0.0000000 0.0000000 53/158
GO:0070972 protein localization to endoplasmic reticulum 6.508974 0.0000000 0.0000000 41/123
GO:0002181 cytoplasmic translation 6.333056 0.0000000 0.0000000 24/74
GO:0034109 homotypic cell-cell adhesion 6.166397 0.0002625 0.0161240 6/19
GO:1902600 proton transmembrane transport 4.756558 0.0000000 0.0000007 19/78
GO:0090150 establishment of protein localization to membrane 4.130695 0.0000000 0.0000000 44/208
GO:0006401 RNA catabolic process 4.001419 0.0000000 0.0000000 50/244
GO:0006605 protein targeting 3.326809 0.0000000 0.0000000 46/270
GO:0010257 NADH dehydrogenase complex assembly 3.254487 0.0008106 0.0398268 10/60
GO:0009141 nucleoside triphosphate metabolic process 2.934097 0.0000001 0.0000096 29/193
GO:0009123 nucleoside monophosphate metabolic process 2.733769 0.0000008 0.0000645 28/200
GO:0006091 generation of precursor metabolites and energy 2.343231 0.0000083 0.0006087 30/250
GO:0009636 response to toxic substance 2.297285 0.0003725 0.0211170 20/170
GO:0009259 ribonucleotide metabolic process 2.210595 0.0000263 0.0017637 30/265
GO:0071826 ribonucleoprotein complex subunit organization 2.204653 0.0004685 0.0246629 21/186
Factor 18 : 81 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0048483 autonomic nervous system development 8.710895 0.0000262 0.0016095 6/13
GO:0014075 response to amine 8.578912 0.0001428 0.0037591 5/11
GO:0050886 endocrine process 7.259079 0.0003643 0.0078973 5/13
GO:0010737 protein kinase A signaling 6.863129 0.0018914 0.0225976 4/11
GO:0021953 central nervous system neuron differentiation 5.960086 0.0000000 0.0000002 18/57
GO:0021675 nerve development 5.744141 0.0001277 0.0036187 7/23
GO:0015844 monoamine transport 5.551061 0.0014700 0.0193462 5/17
GO:0048706 embryonic skeletal system development 5.392459 0.0000688 0.0028606 8/28
GO:0097366 response to bronchodilator 5.392459 0.0050566 0.0465839 4/14
GO:0006959 humoral immune response 5.284610 0.0002284 0.0052607 7/25
GO:1904888 cranial skeletal system development 5.242668 0.0019484 0.0225976 5/18
GO:2001023 regulation of response to drug 5.206512 0.0000906 0.0030365 8/29
GO:0021510 spinal cord development 4.853213 0.0000601 0.0027696 9/35
GO:0001655 urogenital system development 4.781314 0.0000000 0.0000015 19/75
GO:0001763 morphogenesis of a branching structure 4.718401 0.0000765 0.0028606 9/36
GO:0015837 amine transport 4.718401 0.0032312 0.0329662 5/20
GO:0038179 neurotrophin signaling pathway 4.493716 0.0040603 0.0383650 5/21
GO:0042982 amyloid precursor protein metabolic process 4.355448 0.0019599 0.0225976 6/26
GO:0031644 regulation of neurological system process 4.261782 0.0009502 0.0142914 7/31
GO:0035270 endocrine system development 4.128601 0.0011621 0.0161597 7/32
GO:0043270 positive regulation of ion transport 4.044344 0.0000026 0.0003134 15/70
GO:0097305 response to alcohol 4.044344 0.0000026 0.0003134 15/70
GO:0003007 heart morphogenesis 3.894554 0.0000187 0.0013384 13/63
GO:0046683 response to organophosphorus 3.885742 0.0016959 0.0215499 7/34
GO:0014074 response to purine-containing compound 3.871509 0.0008182 0.0128295 8/39
GO:0035418 protein localization to synapse 3.774721 0.0020258 0.0226213 7/35
GO:0015893 drug transport 3.692662 0.0005612 0.0100885 9/46
GO:0042445 hormone metabolic process 3.669868 0.0024032 0.0256691 7/36
GO:0003205 cardiac chamber development 3.614095 0.0006626 0.0110980 9/47
GO:0045165 cell fate commitment 3.614095 0.0006626 0.0110980 9/47
GO:2000027 regulation of animal organ morphogenesis 3.495112 0.0004436 0.0090807 10/54
GO:0060560 developmental growth involved in morphogenesis 3.450014 0.0000055 0.0005837 17/93
GO:0035148 tube formation 3.431565 0.0005173 0.0095308 10/55
GO:0034764 positive regulation of transmembrane transport 3.330636 0.0001940 0.0047662 12/68
GO:0030902 hindbrain development 3.254070 0.0008017 0.0128295 10/58
GO:0090596 sensory organ morphogenesis 3.254070 0.0008017 0.0128295 10/58
GO:0060541 respiratory system development 3.212529 0.0028944 0.0300450 8/47
GO:0015850 organic hydroxy compound transport 3.204952 0.0016303 0.0210791 9/53
GO:0043583 ear development 3.145601 0.0033176 0.0329662 8/48
GO:0060485 mesenchyme development 3.102511 0.0003863 0.0081354 12/73
GO:0048705 skeletal system morphogenesis 3.081405 0.0037874 0.0362508 8/49
GO:0061564 axon development 3.041245 0.0000000 0.0000010 34/211
GO:0050673 epithelial cell proliferation 2.980043 0.0001175 0.0036095 15/95
GO:0046677 response to antibiotic 2.915435 0.0000200 0.0013384 19/123
GO:0009636 response to toxic substance 2.886551 0.0000007 0.0001257 26/170
GO:0010038 response to metal ion 2.879025 0.0000395 0.0019838 18/118
GO:0010721 negative regulation of cell development 2.879025 0.0000395 0.0019838 18/118
GO:0048568 embryonic organ development 2.875978 0.0001080 0.0034611 16/105
GO:0030900 forebrain development 2.872070 0.0000092 0.0008473 21/138
GO:0060537 muscle tissue development 2.839392 0.0000776 0.0028606 17/113
GO:0048880 sensory system development 2.831041 0.0002123 0.0050473 15/100
GO:0007517 muscle organ development 2.822221 0.0001359 0.0037092 16/107
GO:0051961 negative regulation of nervous system development 2.770438 0.0001698 0.0043164 16/109
GO:0097485 neuron projection guidance 2.752401 0.0004637 0.0092359 14/96
GO:0048732 gland development 2.739717 0.0000774 0.0028606 18/124
GO:0021915 neural tube development 2.739717 0.0049195 0.0458947 9/62
GO:0001503 ossification 2.638246 0.0011078 0.0157666 13/93
GO:0048638 regulation of developmental growth 2.621334 0.0005004 0.0095308 15/108
GO:0050890 cognition 2.610180 0.0012260 0.0167324 13/94
GO:0050769 positive regulation of neurogenesis 2.603256 0.0000119 0.0009735 24/174
GO:0032409 regulation of transporter activity 2.603256 0.0019211 0.0225976 12/87
GO:0002009 morphogenesis of an epithelium 2.561418 0.0001241 0.0036187 19/140
GO:0042063 gliogenesis 2.544756 0.0023394 0.0253550 12/89
GO:0042692 muscle cell differentiation 2.483369 0.0008938 0.0137241 15/114
GO:0002683 negative regulation of immune system process 2.435304 0.0033995 0.0329662 12/93
GO:0019932 second-messenger-mediated signaling 2.435304 0.0033995 0.0329662 12/93
GO:0016049 cell growth 2.422281 0.0000404 0.0019838 24/187
GO:0007389 pattern specification process 2.402095 0.0018265 0.0225976 14/110
GO:0003012 muscle system process 2.399187 0.0012815 0.0171723 15/118
GO:0007568 aging 2.380455 0.0019930 0.0225976 14/111
GO:0035690 cellular response to drug 2.380455 0.0019930 0.0225976 14/111
GO:0048545 response to steroid hormone 2.377777 0.0009809 0.0144590 16/127
GO:0050808 synapse organization 2.374825 0.0003389 0.0075695 19/151
GO:0010959 regulation of metal ion transport 2.336732 0.0033732 0.0329662 13/105
GO:0099177 regulation of trans-synaptic signaling 2.298708 0.0005146 0.0095308 19/156
GO:0010975 regulation of neuron projection development 2.268462 0.0000840 0.0029492 25/208
GO:0051098 regulation of binding 2.220424 0.0005799 0.0101753 20/170
GO:0031346 positive regulation of cell projection organization 2.160232 0.0011124 0.0157666 19/166
GO:0034765 regulation of ion transmembrane transport 2.148215 0.0051731 0.0470689 14/123
GO:0070997 neuron death 2.110864 0.0025855 0.0272219 17/152
GO:0071900 regulation of protein serine/threonine kinase activity 2.037492 0.0022262 0.0244877 19/176
Factor 19 : 4 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0001655 urogenital system development 3.709224 0.0000721 0.0268350 12/75
GO:0006413 translational initiation 2.641061 0.0001316 0.0323235 18/158
GO:0090150 establishment of protein localization to membrane 2.452011 0.0000728 0.0268350 22/208
GO:0061564 axon development 2.307278 0.0002538 0.0467578 21/211
Factor 20 : 52 significant GO terms
GeneSet description enrichmentRatio pValue FDR GeneRatio
GO:0042116 macrophage activation 12.692500 0.0000035 0.0019767 6/15
GO:0050918 positive chemotaxis 12.692500 0.0001720 0.0138834 4/10
GO:0014075 response to amine 11.538636 0.0002637 0.0138834 4/11
GO:0050919 negative chemotaxis 11.538636 0.0002637 0.0138834 4/11
GO:0048483 autonomic nervous system development 9.763462 0.0005438 0.0169411 4/13
GO:0035924 cellular response to vascular endothelial growth factor stimulus 9.519375 0.0031313 0.0461551 3/10
GO:0015844 monoamine transport 9.332721 0.0001329 0.0138834 5/17
GO:0097366 response to bronchodilator 9.066071 0.0007428 0.0188770 4/14
GO:0021675 nerve development 6.898098 0.0006200 0.0169411 5/23
GO:0015837 amine transport 6.346250 0.0031015 0.0461551 4/20
GO:0021953 central nervous system neuron differentiation 5.566886 0.0000088 0.0021578 10/57
GO:2001023 regulation of response to drug 5.470905 0.0018781 0.0345845 5/29
GO:0035270 endocrine system development 4.958008 0.0029512 0.0453129 5/32
GO:0050920 regulation of chemotaxis 4.935972 0.0004479 0.0165056 7/45
GO:0008277 regulation of G protein-coupled receptor signaling pathway 4.828669 0.0005145 0.0169411 7/46
GO:0009612 response to mechanical stimulus 4.789623 0.0002163 0.0138834 8/53
GO:0045165 cell fate commitment 4.725931 0.0005888 0.0169411 7/47
GO:0061351 neural precursor cell proliferation 4.453509 0.0003624 0.0155891 8/57
GO:0032103 positive regulation of response to external stimulus 4.355270 0.0009752 0.0224600 7/51
GO:0015850 organic hydroxy compound transport 4.190920 0.0012316 0.0259348 7/53
GO:0015893 drug transport 4.138859 0.0029407 0.0453129 6/46
GO:0043270 positive regulation of ion transport 4.079732 0.0003062 0.0150465 9/70
GO:0003205 cardiac chamber development 4.050798 0.0032849 0.0474698 6/47
GO:0003007 heart morphogenesis 4.029365 0.0007236 0.0188770 8/63
GO:0019932 second-messenger-mediated signaling 3.753159 0.0001409 0.0138834 11/93
GO:0050890 cognition 3.713231 0.0001553 0.0138834 11/94
GO:0030900 forebrain development 3.678986 0.0000054 0.0019767 16/138
GO:0032409 regulation of transporter activity 3.647270 0.0003606 0.0155891 10/87
GO:0006836 neurotransmitter transport 3.525694 0.0002474 0.0138834 11/99
GO:0070371 ERK1 and ERK2 cascade 3.525694 0.0033977 0.0481553 7/63
GO:0060485 mesenchyme development 3.477397 0.0019240 0.0345845 8/73
GO:0060560 developmental growth involved in morphogenesis 3.411962 0.0006190 0.0169411 10/93
GO:0050803 regulation of synapse structure or activity 3.399777 0.0011895 0.0257844 9/84
GO:0001655 urogenital system development 3.384667 0.0022896 0.0383512 8/75
GO:0009410 response to xenobiotic stimulus 3.254487 0.0029381 0.0453129 8/78
GO:0099504 synaptic vesicle cycle 3.208778 0.0017958 0.0345845 9/89
GO:0007389 pattern specification process 3.173125 0.0006206 0.0169411 11/110
GO:0051235 maintenance of location 3.173125 0.0006206 0.0169411 11/110
GO:0001505 regulation of neurotransmitter levels 3.121107 0.0004092 0.0158736 12/122
GO:0031098 stress-activated protein kinase signaling cascade 3.022024 0.0015980 0.0318312 10/105
GO:0023061 signal release 2.993514 0.0001235 0.0138834 15/159
GO:0050808 synapse organization 2.941970 0.0002515 0.0138834 14/151
GO:0032147 activation of protein kinase activity 2.911124 0.0021200 0.0372014 10/109
GO:0072511 divalent inorganic cation transport 2.908698 0.0012879 0.0263666 11/120
GO:0072507 divalent inorganic cation homeostasis 2.884659 0.0022700 0.0383512 10/110
GO:0061564 axon development 2.857316 0.0000286 0.0052617 19/211
GO:0061458 reproductive system development 2.770189 0.0019158 0.0345845 11/126
GO:0071900 regulation of protein serine/threonine kinase activity 2.704368 0.0003807 0.0155891 15/176
GO:0099177 regulation of trans-synaptic signaling 2.644271 0.0011606 0.0257844 13/156
GO:0009636 response to toxic substance 2.613162 0.0008441 0.0207362 14/170
GO:0042326 negative regulation of phosphorylation 2.582776 0.0009475 0.0224600 14/172
GO:0022604 regulation of cell morphogenesis 2.313737 0.0027111 0.0444022 14/192
Summary:
Factor 1 2 3 4 5 6 7 8 9 10
Signif_GO_terms 0 16 0 0 1 0 4 11 2 16
Factor 11 12 13 14 15 16 17 18 19 20
Signif_GO_terms 10 6 46 0 55 25 15 81 4 52

5.1.1 Factors of interest

10: (nerve development, cell fate commitment);
11: chromatin remodeling, DNA recombination;
13: regulation of metal ion transport, axon development, …;
15: neuron migration, response to metal ion, CNS neuron development, …;
18: CNS neuron differentiation, xxx tissue development, …;
19: axon development;
20: nerve development, neurotransmitter transport, ….

5.2 Reactome Pathway Over-Representation Analysis

Gene sets: The Reactome pathway database.

Factor 2 : 43 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-156902 Peptide chain elongation 16.822537 0.0000000 0.0000000 79/84
R-HSA-156842 Eukaryotic Translation Elongation 16.653651 0.0000000 0.0000000 81/87
R-HSA-192823 Viral mRNA Translation 16.594200 0.0000000 0.0000000 77/83
R-HSA-2408557 Selenocysteine synthesis 16.203749 0.0000000 0.0000000 77/85
R-HSA-72764 Eukaryotic Translation Termination 16.015333 0.0000000 0.0000000 77/86
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 15.854612 0.0000000 0.0000000 78/88
R-HSA-72689 Formation of a pool of free 40S subunits 15.816099 0.0000000 0.0000000 84/95
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 14.820868 0.0000000 0.0000000 87/105
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 14.681049 0.0000000 0.0000000 87/106
R-HSA-2408522 Selenoamino acid metabolism 14.092989 0.0000000 0.0000000 78/99
R-HSA-72613 Eukaryotic Translation Initiation 13.929898 0.0000000 0.0000000 88/113
R-HSA-72737 Cap-dependent Translation Initiation 13.929898 0.0000000 0.0000000 88/113
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 13.788092 0.0000000 0.0000000 37/48
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 13.458030 0.0000000 0.0000000 79/105
R-HSA-927802 Nonsense-Mediated Decay (NMD) 13.287675 0.0000000 0.0000000 78/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 13.287675 0.0000000 0.0000000 78/105
R-HSA-72649 Translation initiation complex formation 13.008913 0.0000000 0.0000000 40/55
R-HSA-72702 Ribosomal scanning and start codon recognition 13.008913 0.0000000 0.0000000 40/55
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 12.776611 0.0000000 0.0000000 40/56
R-HSA-168273 Influenza Viral RNA Transcription and Replication 11.771954 0.0000000 0.0000000 77/117
R-HSA-168255 Influenza Life Cycle 11.161647 0.0000000 0.0000000 78/125
R-HSA-168254 Influenza Infection 10.624760 0.0000000 0.0000000 79/133
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 9.603895 0.0000000 0.0000000 80/149
R-HSA-8876725 Protein methylation 8.943627 0.0000198 0.0005040 6/12
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol 8.886662 0.0000000 0.0000000 78/157
R-HSA-8868773 rRNA processing in the nucleus and cytosol 8.559545 0.0000000 0.0000000 78/163
R-HSA-72312 rRNA processing 8.354526 0.0000000 0.0000000 78/167
R-HSA-376176 Signaling by ROBO receptors 7.994304 0.0000000 0.0000000 80/179
R-HSA-2514856 The phototransduction cascade 7.154902 0.0015257 0.0330685 4/10
R-HSA-2514859 Inactivation, recovery and regulation of the phototransduction cascade 7.154902 0.0015257 0.0330685 4/10
R-HSA-71291 Metabolism of amino acids and derivatives 6.749907 0.0000000 0.0000000 80/212
R-HSA-72766 Translation 6.560962 0.0000000 0.0000000 95/259
R-HSA-8982491 Glycogen metabolism 6.388305 0.0006875 0.0156870 5/14
R-HSA-5626467 RHO GTPases activate IQGAPs 5.962418 0.0002989 0.0070741 6/18
R-HSA-5663205 Infectious disease 5.668496 0.0000000 0.0000000 90/284
R-HSA-5339562 Uptake and actions of bacterial toxins 5.260957 0.0018512 0.0391458 5/17
R-HSA-163210 Formation of ATP by chemiosmotic coupling 4.968682 0.0024482 0.0493631 5/18
R-HSA-422475 Axon guidance 4.730064 0.0000000 0.0000000 87/329
R-HSA-1266738 Developmental Biology 3.698039 0.0000000 0.0000000 92/445
R-HSA-1643685 Disease 3.472891 0.0000000 0.0000000 93/479
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 2.824303 0.0000453 0.0011231 18/114
R-HSA-611105 Respiratory electron transport 2.447730 0.0021058 0.0434700 13/95
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 2.376628 0.0003019 0.0070741 19/143
Factor 5 : 17 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis 2.295113 0.0016976 0.0358973 10/13
R-HSA-445355 Smooth Muscle Contraction 2.281612 0.0003521 0.0080343 13/17
R-HSA-156902 Peptide chain elongation 2.131176 0.0000000 0.0000000 60/84
R-HSA-156842 Eukaryotic Translation Elongation 2.126277 0.0000000 0.0000000 62/87
R-HSA-192823 Viral mRNA Translation 2.084958 0.0000000 0.0000000 58/83
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 2.077897 0.0000000 0.0000010 39/56
R-HSA-72649 Translation initiation complex formation 2.061429 0.0000001 0.0000019 38/55
R-HSA-72702 Ribosomal scanning and start codon recognition 2.061429 0.0000001 0.0000019 38/55
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.054776 0.0000000 0.0000000 73/106
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 2.051257 0.0000006 0.0000150 33/48
R-HSA-72764 Eukaryotic Translation Termination 2.046921 0.0000000 0.0000000 59/86
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.045929 0.0000000 0.0000000 72/105
R-HSA-72689 Formation of a pool of free 40S subunits 2.041443 0.0000000 0.0000000 65/95
R-HSA-2408557 Selenocysteine synthesis 2.035900 0.0000000 0.0000000 58/85
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC 2.034305 0.0009064 0.0201493 15/22
R-HSA-72613 Eukaryotic Translation Initiation 2.006700 0.0000000 0.0000000 76/113
R-HSA-72737 Cap-dependent Translation Initiation 2.006700 0.0000000 0.0000000 76/113
Factor 6 : 30 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-5663084 Diseases of carbohydrate metabolism 2.547295 0.0021880 0.0321526 8/10
R-HSA-912631 Regulation of signaling by CBL 2.547295 0.0021880 0.0321526 8/10
R-HSA-512988 Interleukin-3, Interleukin-5 and GM-CSF signaling 2.388089 0.0004166 0.0079667 12/16
R-HSA-8876725 Protein methylation 2.388089 0.0023879 0.0326641 9/12
R-HSA-157858 Gap junction trafficking and regulation 2.346193 0.0001808 0.0039181 14/19
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism 2.335020 0.0010127 0.0168852 11/15
R-HSA-190828 Gap junction trafficking 2.299641 0.0004319 0.0079667 13/18
R-HSA-5626467 RHO GTPases activate IQGAPs 2.299641 0.0004319 0.0079667 13/18
R-HSA-1296071 Potassium Channels 2.274370 0.0024112 0.0326641 10/14
R-HSA-163359 Glucagon signaling in metabolic regulation 2.274370 0.0024112 0.0326641 10/14
R-HSA-8982491 Glycogen metabolism 2.274370 0.0024112 0.0326641 10/14
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC 2.189082 0.0023242 0.0326641 11/16
R-HSA-72702 Ribosomal scanning and start codon recognition 2.142044 0.0000000 0.0000021 37/55
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 2.122746 0.0000005 0.0000183 32/48
R-HSA-156842 Eukaryotic Translation Elongation 2.086147 0.0000000 0.0000000 57/87
R-HSA-437239 Recycling pathway of L1 2.086147 0.0001548 0.0034410 19/29
R-HSA-156902 Peptide chain elongation 2.084840 0.0000000 0.0000000 55/84
R-HSA-72649 Translation initiation complex formation 2.084150 0.0000002 0.0000077 36/55
R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 2.065374 0.0000266 0.0008527 24/37
R-HSA-432040 Vasopressin regulates renal water homeostasis via Aquaporins 2.060312 0.0047289 0.0482351 11/17
R-HSA-445717 Aquaporin-mediated transport 2.060312 0.0047289 0.0482351 11/17
R-HSA-186797 Signaling by PDGF 2.060312 0.0047289 0.0482351 11/17
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 2.046933 0.0000003 0.0000143 36/56
R-HSA-375165 NCAM signaling for neurite out-growth 2.037836 0.0007689 0.0133330 16/25
R-HSA-72764 Eukaryotic Translation Termination 2.036355 0.0000000 0.0000000 55/86
R-HSA-192823 Viral mRNA Translation 2.033232 0.0000000 0.0000001 53/83
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.026257 0.0000000 0.0000000 56/88
R-HSA-5654736 Signaling by FGFR1 2.011022 0.0042276 0.0452512 12/19
R-HSA-5654741 Signaling by FGFR3 2.011022 0.0042276 0.0452512 12/19
R-HSA-5654743 Signaling by FGFR4 2.011022 0.0042276 0.0452512 12/19
Factor 7 : 45 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-73780 RNA Polymerase III Chain Elongation 2.835276 0.0002581 0.0054113 10/13
R-HSA-156902 Peptide chain elongation 2.544998 0.0000000 0.0000000 58/84
R-HSA-73980 RNA Polymerase III Transcription Termination 2.534028 0.0006007 0.0115731 11/16
R-HSA-156842 Eukaryotic Translation Elongation 2.499605 0.0000000 0.0000000 59/87
R-HSA-192823 Viral mRNA Translation 2.486844 0.0000000 0.0000000 56/83
R-HSA-2408557 Selenocysteine synthesis 2.471693 0.0000000 0.0000000 57/85
R-HSA-76061 RNA Polymerase III Transcription Initiation From Type 1 Promoter 2.457239 0.0001705 0.0037908 14/21
R-HSA-72764 Eukaryotic Translation Termination 2.442953 0.0000000 0.0000000 57/86
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.429316 0.0000000 0.0000000 58/88
R-HSA-76066 RNA Polymerase III Transcription Initiation From Type 2 Promoter 2.395808 0.0004281 0.0084350 13/20
R-HSA-72689 Formation of a pool of free 40S subunits 2.366709 0.0000000 0.0000000 61/95
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.351929 0.0000000 0.0000000 67/105
R-HSA-2408522 Selenoamino acid metabolism 2.345546 0.0000000 0.0000000 63/99
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.329741 0.0000000 0.0000000 67/106
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.316825 0.0000000 0.0000000 66/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.316825 0.0000000 0.0000000 66/105
R-HSA-5205685 Pink/Parkin Mediated Mitophagy 2.303662 0.0031443 0.0470017 10/16
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.281722 0.0000000 0.0000000 65/105
R-HSA-6799198 Complex I biogenesis 2.268221 0.0000002 0.0000050 32/52
R-HSA-73863 RNA Polymerase I Transcription Termination 2.252469 0.0025040 0.0380871 11/18
R-HSA-73772 RNA Polymerase I Promoter Escape 2.252469 0.0025040 0.0380871 11/18
R-HSA-72613 Eukaryotic Translation Initiation 2.250657 0.0000000 0.0000000 69/113
R-HSA-72737 Cap-dependent Translation Initiation 2.250657 0.0000000 0.0000000 69/113
R-HSA-983189 Kinesins 2.243566 0.0006779 0.0127764 14/23
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 2.237843 0.0000001 0.0000034 34/56
R-HSA-73777 RNA Polymerase I Chain Elongation 2.237843 0.0001865 0.0040429 17/28
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 2.226873 0.0000011 0.0000292 29/48
R-HSA-72649 Translation initiation complex formation 2.211515 0.0000003 0.0000072 33/55
R-HSA-76071 RNA Polymerase III Transcription Initiation From Type 3 Promoter 2.211515 0.0019811 0.0324790 12/20
R-HSA-5250924 B-WICH complex positively regulates rRNA expression 2.211515 0.0001491 0.0034010 18/30
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.173712 0.0000000 0.0000000 69/117
R-HSA-168255 Influenza Life Cycle 2.152541 0.0000000 0.0000000 73/125
R-HSA-72702 Ribosomal scanning and start codon recognition 2.144499 0.0000010 0.0000275 32/55
R-HSA-917937 Iron uptake and transport 2.140176 0.0002663 0.0054113 18/31
R-HSA-427413 NoRC negatively regulates rRNA expression 2.133918 0.0000588 0.0014560 22/38
R-HSA-69231 Cyclin D associated events in G1 2.106205 0.0034937 0.0496562 12/21
R-HSA-69236 G1 Phase 2.106205 0.0034937 0.0496562 12/21
R-HSA-5250941 Negative epigenetic regulation of rRNA expression 2.079202 0.0001007 0.0023602 22/39
R-HSA-168254 Influenza Infection 2.078492 0.0000000 0.0000000 75/133
R-HSA-6790901 rRNA modification in the nucleus and cytosol 2.057223 0.0000615 0.0014811 24/43
R-HSA-76046 RNA Polymerase III Transcription Initiation 2.047699 0.0016229 0.0287148 15/27
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 2.036922 0.0000000 0.0000000 63/114
R-HSA-8868773 rRNA processing in the nucleus and cytosol 2.035137 0.0000000 0.0000000 90/163
R-HSA-611105 Respiratory electron transport 2.017523 0.0000000 0.0000003 52/95
R-HSA-72312 rRNA processing 2.008462 0.0000000 0.0000000 91/167
Factor 8 : 89 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-156902 Peptide chain elongation 3.518679 0.0000000 0.0000000 81/84
R-HSA-192823 Viral mRNA Translation 3.473145 0.0000000 0.0000000 79/83
R-HSA-156842 Eukaryotic Translation Elongation 3.439287 0.0000000 0.0000000 82/87
R-HSA-2408557 Selenocysteine synthesis 3.391424 0.0000000 0.0000000 79/85
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 3.358739 0.0000000 0.0000000 81/88
R-HSA-72764 Eukaryotic Translation Termination 3.351988 0.0000000 0.0000000 79/86
R-HSA-72689 Formation of a pool of free 40S subunits 3.188074 0.0000000 0.0000000 83/95
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 3.162467 0.0000000 0.0000000 91/105
R-HSA-2408522 Selenoamino acid metabolism 3.096121 0.0000000 0.0000000 84/99
R-HSA-927802 Nonsense-Mediated Decay (NMD) 3.023457 0.0000000 0.0000000 87/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 3.023457 0.0000000 0.0000000 87/105
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.988705 0.0000000 0.0000000 86/105
R-HSA-983170 Antigen Presentation: Folding, assembly and peptide loading of class I MHC 2.985546 0.0002665 0.0018785 9/11
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC 2.964812 0.0000109 0.0002055 13/16
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.960509 0.0000000 0.0000000 86/106
R-HSA-72613 Eukaryotic Translation Initiation 2.841699 0.0000000 0.0000000 88/113
R-HSA-72737 Cap-dependent Translation Initiation 2.841699 0.0000000 0.0000000 88/113
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.838111 0.0000000 0.0000000 91/117
R-HSA-5601884 PIWI-interacting RNA (piRNA) biogenesis 2.806923 0.0002827 0.0019451 10/13
R-HSA-168255 Influenza Life Cycle 2.802432 0.0000000 0.0000000 96/125
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 2.767362 0.0000000 0.0000000 113/149
R-HSA-8876725 Protein methylation 2.736750 0.0008064 0.0048554 9/12
R-HSA-167160 RNA Pol II CTD phosphorylation and interaction with CE during HIV infection 2.736750 0.0000123 0.0002110 15/20
R-HSA-77075 RNA Pol II CTD phosphorylation and interaction with CE 2.736750 0.0000123 0.0002110 15/20
R-HSA-168254 Influenza Infection 2.688737 0.0000000 0.0000000 98/133
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 2.660729 0.0000000 0.0000000 35/48
R-HSA-72086 mRNA Capping 2.653818 0.0000119 0.0002110 16/22
R-HSA-163210 Formation of ATP by chemiosmotic coupling 2.635389 0.0000936 0.0008572 13/18
R-HSA-5620922 BBSome-mediated cargo-targeting to cilium 2.554300 0.0060839 0.0293041 7/10
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 2.541268 0.0000000 0.0000000 39/56
R-HSA-389977 Post-chaperonin tubulin folding pathway 2.526231 0.0019849 0.0107554 9/13
R-HSA-72649 Translation initiation complex formation 2.521127 0.0000000 0.0000000 38/55
R-HSA-72702 Ribosomal scanning and start codon recognition 2.521127 0.0000000 0.0000000 38/55
R-HSA-1839126 FGFR2 mutant receptor activation 2.508688 0.0006603 0.0040889 11/16
R-HSA-8851708 Signaling by FGFR2 IIIa TM 2.508688 0.0006603 0.0040889 11/16
R-HSA-376176 Signaling by ROBO receptors 2.385101 0.0000000 0.0000000 117/179
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding 2.379783 0.0001625 0.0012866 15/23
R-HSA-445355 Smooth Muscle Contraction 2.361118 0.0014099 0.0078862 11/17
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC 2.322091 0.0003954 0.0025774 14/22
R-HSA-8949613 Cristae formation 2.311033 0.0000389 0.0004621 19/30
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint 2.297518 0.0000000 0.0000009 34/54
R-HSA-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA 2.251511 0.0000008 0.0000162 29/47
R-HSA-1236975 Antigen processing-Cross presentation 2.245538 0.0000002 0.0000051 32/52
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 2.240614 0.0000000 0.0000000 70/114
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol 2.231236 0.0000000 0.0000000 96/157
R-HSA-5626467 RHO GTPases activate IQGAPs 2.229944 0.0027347 0.0143693 11/18
R-HSA-5578775 Ion homeostasis 2.221130 0.0007577 0.0046259 14/23
R-HSA-1236974 ER-Phagosome pathway 2.218020 0.0000005 0.0000114 31/51
R-HSA-72312 rRNA processing 2.206880 0.0000000 0.0000000 101/167
R-HSA-8868773 rRNA processing in the nucleus and cytosol 2.193877 0.0000000 0.0000000 98/163
R-HSA-611105 Respiratory electron transport 2.189400 0.0000000 0.0000000 57/95
R-HSA-71291 Metabolism of amino acids and derivatives 2.168745 0.0000000 0.0000000 126/212
R-HSA-180534 Vpu mediated degradation of CD4 2.156227 0.0000091 0.0001786 26/44
R-HSA-187577 SCF(Skp2)-mediated degradation of p27/p21 2.141804 0.0000073 0.0001462 27/46
R-HSA-211733 Regulation of activated PAK-2p34 by proteasome mediated degradation 2.121512 0.0000200 0.0002849 25/43
R-HSA-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A 2.121512 0.0000200 0.0002849 25/43
R-HSA-69610 p53-Independent DNA Damage Response 2.121512 0.0000200 0.0002849 25/43
R-HSA-69613 p53-Independent G1/S DNA damage checkpoint 2.121512 0.0000200 0.0002849 25/43
R-HSA-174113 SCF-beta-TrCP mediated degradation of Emi1 2.108311 0.0000159 0.0002468 26/45
R-HSA-349425 Autodegradation of the E3 ubiquitin ligase COP1 2.108311 0.0000159 0.0002468 26/45
R-HSA-68827 CDT1 association with the CDC6:ORC:origin complex 2.108311 0.0000159 0.0002468 26/45
R-HSA-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis 2.108311 0.0000159 0.0002468 26/45
R-HSA-113418 Formation of the Early Elongation Complex 2.105192 0.0010754 0.0062995 15/26
R-HSA-167158 Formation of the HIV-1 Early Elongation Complex 2.105192 0.0010754 0.0062995 15/26
R-HSA-5362768 Hh mutants that don’t undergo autocatalytic processing are degraded by ERAD 2.096234 0.0000127 0.0002110 27/47
R-HSA-5387390 Hh mutants abrogate ligand secretion 2.096234 0.0000127 0.0002110 27/47
R-HSA-9604323 Negative regulation of NOTCH4 signaling 2.096234 0.0000127 0.0002110 27/47
R-HSA-5678895 Defective CFTR causes cystic fibrosis 2.085143 0.0000100 0.0001932 28/49
R-HSA-69229 Ubiquitin-dependent degradation of Cyclin D1 2.073295 0.0000345 0.0004212 25/44
R-HSA-75815 Ubiquitin-dependent degradation of Cyclin D 2.073295 0.0000345 0.0004212 25/44
R-HSA-169911 Regulation of Apoptosis 2.073295 0.0000345 0.0004212 25/44
R-HSA-180585 Vif-mediated degradation of APOBEC3G 2.062478 0.0000272 0.0003551 26/46
R-HSA-5655253 Signaling by FGFR2 in disease 2.062478 0.0029863 0.0154161 13/23
R-HSA-1236978 Cross-presentation of soluble exogenous antigens (endosomes) 2.058410 0.0001187 0.0010212 22/39
R-HSA-6814122 Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding 2.043440 0.0023279 0.0124583 14/25
R-HSA-72766 Translation 2.042876 0.0000000 0.0000000 145/259
R-HSA-350562 Regulation of ornithine decarboxylase (ODC) 2.036651 0.0000734 0.0007073 24/43
R-HSA-5663205 Infectious disease 2.030077 0.0000000 0.0000000 158/284
R-HSA-4641258 Degradation of DVL 2.027222 0.0000577 0.0006099 25/45
R-HSA-8941858 Regulation of RUNX3 expression and activity 2.027222 0.0000577 0.0006099 25/45
R-HSA-68867 Assembly of the pre-replicative complex 2.018596 0.0000453 0.0005234 26/47
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 2.015881 0.0000000 0.0000000 79/143
R-HSA-1168372 Downstream signaling events of B Cell Receptor (BCR) 2.006950 0.0000051 0.0001048 33/60
R-HSA-162588 Budding and maturation of HIV virion 2.006950 0.0082347 0.0385920 11/20
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements 2.004380 0.0000007 0.0000157 39/71
R-HSA-5619084 ABC transporter disorders 2.003372 0.0000279 0.0003551 28/51
R-HSA-69563 p53-Dependent G1 DNA Damage Response 2.003372 0.0000279 0.0003551 28/51
R-HSA-69580 p53-Dependent G1/S DNA damage checkpoint 2.003372 0.0000279 0.0003551 28/51
R-HSA-69615 G1/S DNA Damage Checkpoints 2.003372 0.0000279 0.0003551 28/51
Factor 9 : 31 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-5576892 Phase 0 - rapid depolarisation 4.875549 0.0001806 0.0057987 7/13
R-HSA-445355 Smooth Muscle Contraction 4.793607 0.0000242 0.0009131 9/17
R-HSA-5626467 RHO GTPases activate IQGAPs 4.527295 0.0000438 0.0015177 9/18
R-HSA-389977 Post-chaperonin tubulin folding pathway 4.179042 0.0015226 0.0366702 6/13
R-HSA-425393 Transport of inorganic cations/anions and amino acids/oligopeptides 3.621836 0.0007824 0.0205546 8/20
R-HSA-192823 Viral mRNA Translation 3.163652 0.0000000 0.0000019 29/83
R-HSA-156902 Peptide chain elongation 3.125990 0.0000000 0.0000019 29/84
R-HSA-2408557 Selenocysteine synthesis 3.089213 0.0000000 0.0000019 29/85
R-HSA-72764 Eukaryotic Translation Termination 3.053292 0.0000000 0.0000020 29/86
R-HSA-156842 Eukaryotic Translation Elongation 3.018197 0.0000000 0.0000023 29/87
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.983899 0.0000000 0.0000026 29/88
R-HSA-397014 Muscle contraction 2.963321 0.0000122 0.0004825 18/55
R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 2.936624 0.0003923 0.0113369 12/37
R-HSA-425407 SLC-mediated transmembrane transport 2.929426 0.0007018 0.0190140 11/34
R-HSA-2408522 Selenoamino acid metabolism 2.926736 0.0000000 0.0000019 32/99
R-HSA-5576891 Cardiac conduction 2.766681 0.0012011 0.0297533 11/36
R-HSA-72689 Formation of a pool of free 40S subunits 2.764033 0.0000001 0.0000088 29/95
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.673260 0.0000001 0.0000082 31/105
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.673260 0.0000001 0.0000082 31/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.673260 0.0000001 0.0000082 31/105
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.648041 0.0000002 0.0000090 31/106
R-HSA-72613 Eukaryotic Translation Initiation 2.644261 0.0000001 0.0000055 33/113
R-HSA-72737 Cap-dependent Translation Initiation 2.644261 0.0000001 0.0000055 33/113
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.500792 0.0000015 0.0000762 29/105
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.321690 0.0000053 0.0002420 30/117
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 2.309224 0.0000003 0.0000174 38/149
R-HSA-168255 Influenza Life Cycle 2.245538 0.0000078 0.0003213 31/125
R-HSA-168254 Influenza Infection 2.110469 0.0000298 0.0010751 31/133
R-HSA-112316 Neuronal System 2.076741 0.0002337 0.0072372 25/109
R-HSA-376176 Signaling by ROBO receptors 2.073956 0.0000024 0.0001134 41/179
R-HSA-112315 Transmission across Chemical Synapses 2.023967 0.0018041 0.0422734 19/85
Factor 10 : 29 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-191273 Cholesterol biosynthesis 5.350440 0.0000000 0.0000003 16/22
R-HSA-445355 Smooth Muscle Contraction 4.327562 0.0000157 0.0005300 10/17
R-HSA-2426168 Activation of gene expression by SREBF (SREBP) 3.433199 0.0000111 0.0004002 14/30
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF) 3.269713 0.0000057 0.0002143 16/36
R-HSA-70263 Gluconeogenesis 3.097623 0.0021020 0.0467282 8/19
R-HSA-8957322 Metabolism of steroids 3.055924 0.0000000 0.0000021 27/65
R-HSA-192823 Viral mRNA Translation 2.925015 0.0000000 0.0000005 33/83
R-HSA-72764 Eukaryotic Translation Termination 2.908524 0.0000000 0.0000005 34/86
R-HSA-156902 Peptide chain elongation 2.890193 0.0000000 0.0000006 33/84
R-HSA-2408557 Selenocysteine synthesis 2.856191 0.0000000 0.0000007 33/85
R-HSA-156842 Eukaryotic Translation Elongation 2.790531 0.0000000 0.0000011 33/87
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.758821 0.0000000 0.0000013 33/88
R-HSA-977225 Amyloid fiber formation 2.724761 0.0018953 0.0432429 10/27
R-HSA-114608 Platelet degranulation 2.675220 0.0001131 0.0031622 16/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 2.675220 0.0001131 0.0031622 16/44
R-HSA-72689 Formation of a pool of free 40S subunits 2.555539 0.0000001 0.0000083 33/95
R-HSA-397014 Muscle contraction 2.541459 0.0000590 0.0018282 19/55
R-HSA-2408522 Selenoamino acid metabolism 2.526597 0.0000001 0.0000080 34/99
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.452285 0.0000001 0.0000099 35/105
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.326527 0.0000003 0.0000168 37/117
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.312154 0.0000013 0.0000616 33/105
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.312154 0.0000013 0.0000616 33/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.312154 0.0000013 0.0000616 33/105
R-HSA-168255 Influenza Life Cycle 2.295339 0.0000002 0.0000127 39/125
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.290342 0.0000017 0.0000743 33/106
R-HSA-72613 Eukaryotic Translation Initiation 2.213567 0.0000028 0.0001117 34/113
R-HSA-72737 Cap-dependent Translation Initiation 2.213567 0.0000028 0.0001117 34/113
R-HSA-168254 Influenza Infection 2.212588 0.0000004 0.0000227 40/133
R-HSA-373760 L1CAM interactions 2.055592 0.0012682 0.0323389 19/68
Factor 11 : 20 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-445095 Interaction between L1 and Ankyrins 3.326724 0.0009379 0.0262297 8/15
R-HSA-5627123 RHO GTPases activate PAKs 3.282951 0.0002423 0.0084014 10/19
R-HSA-163210 Formation of ATP by chemiosmotic coupling 3.118803 0.0008176 0.0236293 9/18
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC 3.118803 0.0016151 0.0371583 8/16
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC 2.835276 0.0010720 0.0281647 10/22
R-HSA-983189 Kinesins 2.712003 0.0016286 0.0371583 10/23
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding 2.712003 0.0016286 0.0371583 10/23
R-HSA-156902 Peptide chain elongation 2.376231 0.0000006 0.0001893 32/84
R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 2.360176 0.0010633 0.0281647 14/37
R-HSA-2408557 Selenocysteine synthesis 2.348276 0.0000009 0.0001893 32/85
R-HSA-192823 Viral mRNA Translation 2.329709 0.0000016 0.0001975 31/83
R-HSA-156842 Eukaryotic Translation Elongation 2.294292 0.0000016 0.0001975 32/87
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.268221 0.0000021 0.0002312 32/88
R-HSA-72764 Eukaryotic Translation Termination 2.248440 0.0000038 0.0003685 31/86
R-HSA-2408522 Selenoamino acid metabolism 2.205214 0.0000015 0.0001975 35/99
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.198014 0.0000008 0.0001893 37/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.198014 0.0000008 0.0001893 37/105
R-HSA-72689 Formation of a pool of free 40S subunits 2.166748 0.0000047 0.0004116 33/95
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.079202 0.0000071 0.0005175 35/105
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 2.079202 0.0022836 0.0460444 16/48
Factor 12 : 47 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-156902 Peptide chain elongation 4.407005 0.0000000 0.0000000 63/84
R-HSA-192823 Viral mRNA Translation 4.389306 0.0000000 0.0000000 62/83
R-HSA-2408557 Selenocysteine synthesis 4.355158 0.0000000 0.0000000 63/85
R-HSA-72764 Eukaryotic Translation Termination 4.304516 0.0000000 0.0000000 63/86
R-HSA-156842 Eukaryotic Translation Elongation 4.255039 0.0000000 0.0000000 63/87
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 4.139914 0.0000000 0.0000000 62/88
R-HSA-2408522 Selenoamino acid metabolism 3.976691 0.0000000 0.0000000 67/99
R-HSA-5626467 RHO GTPases activate IQGAPs 3.917338 0.0000037 0.0000936 12/18
R-HSA-72689 Formation of a pool of free 40S subunits 3.896720 0.0000000 0.0000000 63/95
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 3.794921 0.0000000 0.0000000 31/48
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 3.749452 0.0000000 0.0000000 67/105
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 3.658645 0.0000000 0.0000000 66/106
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 3.637528 0.0000000 0.0000000 65/105
R-HSA-373080 Class B/2 (Secretin family receptors) 3.616004 0.0003892 0.0086511 8/13
R-HSA-190828 Gap junction trafficking 3.590893 0.0000320 0.0007927 11/18
R-HSA-5218921 VEGFR2 mediated cell proliferation 3.525604 0.0026850 0.0415698 6/10
R-HSA-927802 Nonsense-Mediated Decay (NMD) 3.525604 0.0000000 0.0000000 63/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 3.525604 0.0000000 0.0000000 63/105
R-HSA-72613 Eukaryotic Translation Initiation 3.484004 0.0000000 0.0000000 67/113
R-HSA-72737 Cap-dependent Translation Initiation 3.484004 0.0000000 0.0000000 67/113
R-HSA-427359 SIRT1 negatively regulates rRNA expression 3.427670 0.0014398 0.0290298 7/12
R-HSA-72702 Ribosomal scanning and start codon recognition 3.418767 0.0000000 0.0000000 32/55
R-HSA-157858 Gap junction trafficking and regulation 3.401899 0.0000644 0.0015380 11/19
R-HSA-168273 Influenza Viral RNA Transcription and Replication 3.364893 0.0000000 0.0000000 67/117
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 3.357718 0.0000000 0.0000000 32/56
R-HSA-72649 Translation initiation complex formation 3.311931 0.0000000 0.0000000 31/55
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC 3.205094 0.0000656 0.0015380 12/22
R-HSA-389977 Post-chaperonin tubulin folding pathway 3.164004 0.0026655 0.0415698 7/13
R-HSA-168255 Influenza Life Cycle 3.149539 0.0000000 0.0000000 67/125
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding 3.065742 0.0001162 0.0026519 12/23
R-HSA-168254 Influenza Infection 3.004274 0.0000000 0.0000000 68/133
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC 2.938003 0.0024089 0.0401646 8/16
R-HSA-451326 Activation of kainate receptors upon glutamate binding 2.938003 0.0024089 0.0401646 8/16
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 2.878849 0.0000000 0.0000000 73/149
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression 2.810264 0.0005958 0.0129150 11/23
R-HSA-977225 Amyloid fiber formation 2.611558 0.0007705 0.0162924 12/27
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol 2.582449 0.0000000 0.0000000 69/157
R-HSA-376176 Signaling by ROBO receptors 2.527668 0.0000000 0.0000000 77/179
R-HSA-8868773 rRNA processing in the nucleus and cytosol 2.523438 0.0000000 0.0000000 70/163
R-HSA-72312 rRNA processing 2.462997 0.0000000 0.0000000 70/167
R-HSA-71291 Metabolism of amino acids and derivatives 2.439097 0.0000000 0.0000000 88/212
R-HSA-3214858 RMTs methylate histone arginines 2.431451 0.0016538 0.0318624 12/29
R-HSA-500792 GPCR ligand binding 2.393929 0.0029834 0.0453790 11/27
R-HSA-72766 Translation 2.382165 0.0000000 0.0000000 105/259
R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 2.223354 0.0019383 0.0355181 14/37
R-HSA-1445148 Translocation of SLC2A4 (GLUT4) to the plasma membrane 2.043828 0.0026191 0.0415698 16/46
R-HSA-422475 Axon guidance 2.036063 0.0000000 0.0000000 114/329
Factor 13 : 45 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-442729 CREB phosphorylation through the activation of CaMKII 6.701561 0.0000900 0.0043352 6/11
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 6.701561 0.0000900 0.0043352 6/11
R-HSA-5576892 Phase 0 - rapid depolarisation 6.615644 0.0000247 0.0017836 7/13
R-HSA-5218921 VEGFR2 mediated cell proliferation 6.143098 0.0006185 0.0191500 5/10
R-HSA-114604 GPVI-mediated activation cascade 5.584634 0.0010588 0.0245060 5/11
R-HSA-442742 CREB phosphorylation through the activation of Ras 5.375210 0.0001327 0.0052305 7/16
R-HSA-5578775 Ion homeostasis 5.341824 0.0000048 0.0005237 10/23
R-HSA-445355 Smooth Muscle Contraction 5.059022 0.0002101 0.0075881 7/17
R-HSA-5576891 Cardiac conduction 4.777965 0.0000003 0.0000660 14/36
R-HSA-5626467 RHO GTPases activate IQGAPs 4.777965 0.0003200 0.0110983 7/18
R-HSA-451326 Activation of kainate receptors upon glutamate binding 4.607323 0.0010981 0.0245060 6/16
R-HSA-438064 Post NMDA receptor activation events 4.300168 0.0006759 0.0201960 7/20
R-HSA-936837 Ion transport by P-type ATPases 4.252914 0.0001254 0.0051783 9/26
R-HSA-397014 Muscle contraction 4.244322 0.0000000 0.0000093 19/55
R-HSA-114608 Platelet degranulation 4.188476 0.0000008 0.0001220 15/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 4.188476 0.0000008 0.0001220 15/44
R-HSA-418346 Platelet homeostasis 4.095398 0.0000757 0.0041015 10/30
R-HSA-442755 Activation of NMDA receptors and postsynaptic events 4.095398 0.0009442 0.0238917 7/21
R-HSA-2672351 Stimuli-sensing channels 3.780368 0.0007454 0.0201960 8/26
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) 3.723089 0.0001870 0.0070481 10/33
R-HSA-4086398 Ca2+ pathway 3.583474 0.0022711 0.0418938 7/24
R-HSA-8957275 Post-translational protein phosphorylation 3.455492 0.0007269 0.0201960 9/32
R-HSA-76002 Platelet activation, signaling and aggregation 3.412832 0.0000000 0.0000093 25/90
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission 2.948687 0.0004884 0.0158333 12/50
R-HSA-983712 Ion channel transport 2.925285 0.0001075 0.0049037 15/63
R-HSA-373760 L1CAM interactions 2.890869 0.0000738 0.0041015 16/68
R-HSA-6799198 Complex I biogenesis 2.835276 0.0007159 0.0201960 12/52
R-HSA-1474244 Extracellular matrix organization 2.730266 0.0010260 0.0245060 12/54
R-HSA-611105 Respiratory electron transport 2.715896 0.0000155 0.0012209 21/95
R-HSA-194138 Signaling by VEGF 2.680624 0.0012188 0.0264170 12/55
R-HSA-112315 Transmission across Chemical Synapses 2.601783 0.0001156 0.0050119 18/85
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 2.586567 0.0000092 0.0008880 24/114
R-HSA-112316 Neuronal System 2.479782 0.0000441 0.0029396 22/109
R-HSA-109582 Hemostasis 2.470594 0.0000001 0.0000299 37/184
R-HSA-156842 Eukaryotic Translation Elongation 2.400751 0.0004931 0.0158333 17/87
R-HSA-192823 Viral mRNA Translation 2.368423 0.0008416 0.0221100 16/83
R-HSA-156902 Peptide chain elongation 2.340228 0.0009645 0.0238917 16/84
R-HSA-2408557 Selenocysteine synthesis 2.312696 0.0011023 0.0245060 16/85
R-HSA-72764 Eukaryotic Translation Termination 2.285804 0.0012565 0.0265714 16/86
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 2.233854 0.0000600 0.0037153 26/143
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.233854 0.0016201 0.0321045 16/88
R-HSA-72689 Formation of a pool of free 40S subunits 2.198582 0.0014015 0.0289311 17/95
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.106205 0.0017034 0.0321045 18/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.106205 0.0017034 0.0321045 18/105
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.106205 0.0017034 0.0321045 18/105
Factor 14 : 2 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex 9.80914 0.0001106 0.0479298 5/20
R-HSA-195258 RHO GTPase Effectors 3.46990 0.0000693 0.0479298 13/147
Factor 15 : 67 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-5626467 RHO GTPases activate IQGAPs 7.327309 0.0000008 0.0001702 9/18
R-HSA-418990 Adherens junctions interactions 7.327309 0.0000620 0.0021880 6/12
R-HSA-373076 Class A/1 (Rhodopsin-like receptors) 6.661190 0.0004671 0.0094172 5/11
R-HSA-442729 CREB phosphorylation through the activation of CaMKII 6.661190 0.0004671 0.0094172 5/11
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 6.661190 0.0004671 0.0094172 5/11
R-HSA-451326 Activation of kainate receptors upon glutamate binding 6.411396 0.0000425 0.0017260 7/16
R-HSA-8978934 Metabolism of cofactors 6.106091 0.0007564 0.0121444 5/12
R-HSA-202131 Metabolism of nitric oxide 6.106091 0.0007564 0.0121444 5/12
R-HSA-203765 eNOS activation and regulation 6.106091 0.0007564 0.0121444 5/12
R-HSA-445355 Smooth Muscle Contraction 6.034255 0.0000681 0.0021880 7/17
R-HSA-445095 Interaction between L1 and Ankyrins 5.861847 0.0002818 0.0066023 6/15
R-HSA-5576892 Phase 0 - rapid depolarisation 5.636392 0.0011613 0.0167806 5/13
R-HSA-421270 Cell-cell junction organization 5.495482 0.0004253 0.0092182 6/16
R-HSA-4086398 Ca2+ pathway 5.495482 0.0000147 0.0016228 9/24
R-HSA-5578775 Ion homeostasis 5.097259 0.0000838 0.0025736 8/23
R-HSA-446728 Cell junction organization 5.072752 0.0000310 0.0017260 9/26
R-HSA-500792 GPCR ligand binding 4.884873 0.0000438 0.0017260 9/27
R-HSA-442755 Activation of NMDA receptors and postsynaptic events 4.884873 0.0003213 0.0071434 7/21
R-HSA-190828 Gap junction trafficking 4.884873 0.0008776 0.0130845 6/18
R-HSA-157858 Gap junction trafficking and regulation 4.627774 0.0012103 0.0172024 6/19
R-HSA-442742 CREB phosphorylation through the activation of Ras 4.579568 0.0033259 0.0424051 5/16
R-HSA-936837 Ion transport by P-type ATPases 4.509113 0.0002230 0.0055248 8/26
R-HSA-381426 Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) 4.440793 0.0000417 0.0017260 10/33
R-HSA-438064 Post NMDA receptor activation events 4.396386 0.0016316 0.0228163 6/20
R-HSA-397014 Muscle contraction 4.263162 0.0000004 0.0001058 16/55
R-HSA-1500931 Cell-Cell communication 4.133354 0.0000362 0.0017260 11/39
R-HSA-8957275 Post-translational protein phosphorylation 4.121611 0.0001936 0.0049368 9/32
R-HSA-5576891 Cardiac conduction 4.070727 0.0000953 0.0026648 10/36
R-HSA-114608 Platelet degranulation 3.996714 0.0000231 0.0016318 12/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 3.996714 0.0000231 0.0016318 12/44
R-HSA-5218920 VEGFR2 mediated vascular permeability 3.996714 0.0027975 0.0367496 6/22
R-HSA-418346 Platelet homeostasis 3.907898 0.0006576 0.0114027 8/30
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission 3.810201 0.0000185 0.0016318 13/50
R-HSA-1474244 Extracellular matrix organization 3.799345 0.0000091 0.0013088 14/54
R-HSA-416482 G alpha (12/13) signalling events 3.781837 0.0008349 0.0126993 8/31
R-HSA-373760 L1CAM interactions 3.663655 0.0000017 0.0002913 17/68
R-HSA-194840 Rho GTPase cycle 3.256582 0.0006914 0.0117546 10/45
R-HSA-1445148 Translocation of SLC2A4 (GLUT4) to the plasma membrane 3.185787 0.0008315 0.0126993 10/46
R-HSA-418594 G alpha (i) signalling events 3.156379 0.0000861 0.0025736 14/65
R-HSA-156842 Eukaryotic Translation Elongation 3.031990 0.0000150 0.0016228 18/87
R-HSA-192823 Viral mRNA Translation 3.001548 0.0000299 0.0017260 17/83
R-HSA-156902 Peptide chain elongation 2.965816 0.0000353 0.0017260 17/84
R-HSA-2408557 Selenocysteine synthesis 2.930924 0.0000414 0.0017260 17/85
R-HSA-76002 Platelet activation, signaling and aggregation 2.930924 0.0000245 0.0016318 18/90
R-HSA-72764 Eukaryotic Translation Termination 2.896843 0.0000485 0.0018280 17/86
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.831006 0.0000660 0.0021880 17/88
R-HSA-194138 Signaling by VEGF 2.664476 0.0034594 0.0434687 10/55
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.651788 0.0000631 0.0021880 19/105
R-HSA-72689 Formation of a pool of free 40S subunits 2.622405 0.0001785 0.0046893 17/95
R-HSA-372790 Signaling by GPCR 2.621151 0.0000198 0.0016318 22/123
R-HSA-388396 GPCR downstream signalling 2.586109 0.0000380 0.0017260 21/119
R-HSA-112315 Transmission across Chemical Synapses 2.586109 0.0005025 0.0098043 15/85
R-HSA-983712 Ion channel transport 2.558743 0.0030651 0.0396631 11/63
R-HSA-2408522 Selenoamino acid metabolism 2.516450 0.0002996 0.0068346 17/99
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.488520 0.0002301 0.0055412 18/106
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.372653 0.0006127 0.0108412 17/105
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.372653 0.0006127 0.0108412 17/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.372653 0.0006127 0.0108412 17/105
R-HSA-72613 Eukaryotic Translation Initiation 2.334364 0.0005202 0.0098043 18/113
R-HSA-72737 Cap-dependent Translation Initiation 2.334364 0.0005202 0.0098043 18/113
R-HSA-422475 Axon guidance 2.316232 0.0000000 0.0000008 52/329
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.254557 0.0007988 0.0125925 18/117
R-HSA-1266738 Developmental Biology 2.173494 0.0000000 0.0000001 66/445
R-HSA-112316 Neuronal System 2.151137 0.0025651 0.0342145 16/109
R-HSA-109582 Hemostasis 2.150406 0.0000910 0.0026301 27/184
R-HSA-194315 Signaling by Rho GTPases 2.138782 0.0001001 0.0027125 27/185
R-HSA-168255 Influenza Life Cycle 2.110265 0.0017532 0.0241276 18/125
Factor 16 : 62 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-389960 Formation of tubulin folding intermediates by CCT/TriC 4.402751 0.0000110 0.0002500 10/16
R-HSA-389977 Post-chaperonin tubulin folding pathway 4.335016 0.0001044 0.0020577 8/13
R-HSA-5626467 RHO GTPases activate IQGAPs 4.304912 0.0000053 0.0001429 11/18
R-HSA-163210 Formation of ATP by chemiosmotic coupling 4.304912 0.0000053 0.0001429 11/18
R-HSA-389958 Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding 4.287897 0.0000003 0.0000091 14/23
R-HSA-389957 Prefoldin mediated transfer of substrate to CCT/TriC 4.162601 0.0000012 0.0000372 13/22
R-HSA-8876725 Protein methylation 4.109234 0.0004629 0.0071660 7/12
R-HSA-8978934 Metabolism of cofactors 4.109234 0.0004629 0.0071660 7/12
R-HSA-70263 Gluconeogenesis 4.078338 0.0000109 0.0002500 11/19
R-HSA-191273 Cholesterol biosynthesis 3.842401 0.0000099 0.0002373 12/22
R-HSA-190828 Gap junction trafficking 3.522201 0.0003216 0.0054672 9/18
R-HSA-157858 Gap junction trafficking and regulation 3.336822 0.0005351 0.0081388 9/19
R-HSA-8949613 Cristae formation 3.287387 0.0000185 0.0004011 14/30
R-HSA-3299685 Detoxification of Reactive Oxygen Species 3.130845 0.0018414 0.0238288 8/18
R-HSA-70614 Amino acid synthesis and interconversion (transamination) 3.081926 0.0039901 0.0437904 7/16
R-HSA-3371497 HSP90 chaperone cycle for steroid hormone receptors (SHR) 3.046228 0.0000155 0.0003448 16/37
R-HSA-156902 Peptide chain elongation 2.935167 0.0000000 0.0000001 35/84
R-HSA-379716 Cytosolic tRNA aminoacylation 2.935167 0.0009173 0.0130371 10/24
R-HSA-437239 Recycling pathway of L1 2.914925 0.0003052 0.0052916 12/29
R-HSA-2408557 Selenocysteine synthesis 2.900636 0.0000000 0.0000001 35/85
R-HSA-192823 Viral mRNA Translation 2.885658 0.0000000 0.0000001 34/83
R-HSA-156842 Eukaryotic Translation Elongation 2.833955 0.0000000 0.0000001 35/87
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.801751 0.0000000 0.0000002 35/88
R-HSA-72764 Eukaryotic Translation Termination 2.784996 0.0000000 0.0000003 34/86
R-HSA-2408522 Selenoamino acid metabolism 2.775067 0.0000000 0.0000001 39/99
R-HSA-1655829 Regulation of cholesterol biosynthesis by SREBP (SREBF) 2.739489 0.0002122 0.0037543 14/36
R-HSA-72689 Formation of a pool of free 40S subunits 2.669457 0.0000000 0.0000004 36/95
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 2.657099 0.0000000 0.0000001 43/114
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.616492 0.0000000 0.0000002 39/105
R-HSA-2426168 Activation of gene expression by SREBF (SREBP) 2.582947 0.0017916 0.0235355 11/30
R-HSA-114608 Platelet degranulation 2.561601 0.0001911 0.0036019 16/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 2.561601 0.0001911 0.0036019 16/44
R-HSA-391251 Protein folding 2.550559 0.0000208 0.0004404 21/58
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.549402 0.0000000 0.0000005 38/105
R-HSA-379724 tRNA Aminoacylation 2.515858 0.0036043 0.0411169 10/28
R-HSA-72613 Eukaryotic Translation Initiation 2.493593 0.0000000 0.0000004 40/113
R-HSA-72737 Cap-dependent Translation Initiation 2.493593 0.0000000 0.0000004 40/113
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.458895 0.0000000 0.0000019 37/106
R-HSA-1445148 Translocation of SLC2A4 (GLUT4) to the plasma membrane 2.450227 0.0003453 0.0057571 16/46
R-HSA-168255 Influenza Life Cycle 2.423274 0.0000000 0.0000004 43/125
R-HSA-927802 Nonsense-Mediated Decay (NMD) 2.415223 0.0000001 0.0000045 36/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 2.415223 0.0000001 0.0000045 36/105
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 2.413816 0.0000000 0.0000001 49/143
R-HSA-390466 Chaperonin-mediated protein folding 2.392438 0.0002099 0.0037543 18/53
R-HSA-611105 Respiratory electron transport 2.372851 0.0000009 0.0000299 32/95
R-HSA-168254 Influenza Infection 2.330479 0.0000000 0.0000007 44/133
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.287925 0.0000003 0.0000088 38/117
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic 2.284671 0.0036998 0.0411243 12/37
R-HSA-1592230 Mitochondrial biogenesis 2.272388 0.0002101 0.0037543 20/62
R-HSA-15869 Metabolism of nucleotides 2.241401 0.0021578 0.0275119 14/44
R-HSA-2565942 Regulation of PLK1 Activity at G2/M Transition 2.224548 0.0005800 0.0086706 18/57
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 2.222059 0.0000000 0.0000011 47/149
R-HSA-71291 Metabolism of amino acids and derivatives 2.193068 0.0000000 0.0000000 66/212
R-HSA-380259 Loss of Nlp from mitotic centrosomes 2.191592 0.0027344 0.0324760 14/45
R-HSA-380284 Loss of proteins required for interphase microtubule organization from the centrosome 2.191592 0.0027344 0.0324760 14/45
R-HSA-8854518 AURKA Activation by TPX2 2.191592 0.0027344 0.0324760 14/45
R-HSA-8957322 Metabolism of steroids 2.167508 0.0004267 0.0068504 20/65
R-HSA-6799198 Complex I biogenesis 2.167508 0.0015839 0.0214571 16/52
R-HSA-5628897 TP53 Regulates Metabolic Genes 2.102806 0.0006614 0.0095579 20/67
R-HSA-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint 2.087230 0.0024521 0.0304056 16/54
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 2.012686 0.0036836 0.0411243 16/56
R-HSA-376176 Signaling by ROBO receptors 2.007064 0.0000003 0.0000088 51/179
Factor 17 : 39 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-156902 Peptide chain elongation 8.313967 0.0000000 0.0000000 40/84
R-HSA-72689 Formation of a pool of free 40S subunits 8.270209 0.0000000 0.0000000 45/95
R-HSA-156842 Eukaryotic Translation Elongation 8.027278 0.0000000 0.0000000 40/87
R-HSA-2408557 Selenocysteine synthesis 8.010751 0.0000000 0.0000000 39/85
R-HSA-192823 Viral mRNA Translation 7.993428 0.0000000 0.0000000 38/83
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 7.981408 0.0000000 0.0000000 48/105
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 7.741401 0.0000000 0.0000000 47/106
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 7.737658 0.0000000 0.0000000 39/88
R-HSA-72764 Eukaryotic Translation Termination 7.714588 0.0000000 0.0000000 38/86
R-HSA-72613 Eukaryotic Translation Initiation 7.416353 0.0000000 0.0000000 48/113
R-HSA-72737 Cap-dependent Translation Initiation 7.416353 0.0000000 0.0000000 48/113
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 6.910985 0.0000000 0.0000000 19/48
R-HSA-2408522 Selenoamino acid metabolism 6.877918 0.0000000 0.0000000 39/99
R-HSA-72649 Translation initiation complex formation 6.666290 0.0000000 0.0000000 21/55
R-HSA-927802 Nonsense-Mediated Decay (NMD) 6.651173 0.0000000 0.0000000 40/105
R-HSA-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 6.651173 0.0000000 0.0000000 40/105
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 6.651173 0.0000000 0.0000000 40/105
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 6.547249 0.0000000 0.0000000 21/56
R-HSA-72702 Ribosomal scanning and start codon recognition 6.348847 0.0000000 0.0000000 20/55
R-HSA-168273 Influenza Viral RNA Transcription and Replication 5.819777 0.0000000 0.0000000 39/117
R-HSA-163210 Formation of ATP by chemiosmotic coupling 5.819777 0.0003412 0.0079950 6/18
R-HSA-168255 Influenza Life Cycle 5.586986 0.0000000 0.0000000 40/125
R-HSA-168254 Influenza Infection 5.382199 0.0000000 0.0000000 41/133
R-HSA-9010553 Regulation of expression of SLITs and ROBOs 4.569892 0.0000000 0.0000000 39/149
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol 4.225825 0.0000000 0.0000000 38/157
R-HSA-437239 Recycling pathway of L1 4.214321 0.0009670 0.0214970 7/29
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 4.135104 0.0000000 0.0000000 27/114
R-HSA-8868773 rRNA processing in the nucleus and cytosol 4.070273 0.0000000 0.0000000 38/163
R-HSA-376176 Signaling by ROBO receptors 3.999064 0.0000000 0.0000000 41/179
R-HSA-72312 rRNA processing 3.972782 0.0000000 0.0000000 38/167
R-HSA-611105 Respiratory electron transport 3.859431 0.0000000 0.0000010 21/95
R-HSA-72766 Translation 3.774990 0.0000000 0.0000000 56/259
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport 3.540703 0.0000000 0.0000000 29/143
R-HSA-71291 Metabolism of amino acids and derivatives 3.458924 0.0000000 0.0000000 42/212
R-HSA-6799198 Complex I biogenesis 3.357563 0.0005806 0.0132472 10/52
R-HSA-5663205 Infectious disease 3.135302 0.0000000 0.0000000 51/284
R-HSA-422475 Axon guidance 2.865665 0.0000000 0.0000000 54/329
R-HSA-1266738 Developmental Biology 2.354067 0.0000000 0.0000000 60/445
R-HSA-1643685 Disease 2.077624 0.0000000 0.0000003 57/479
Factor 19 : 50 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-983695 Antigen activates B Cell Receptor (BCR) leading to generation of second messengers 9.296815 0.0005654 0.0196096 4/10
R-HSA-5626467 RHO GTPases activate IQGAPs 9.038570 0.0000051 0.0022100 7/18
R-HSA-111447 Activation of BAD and translocation to mitochondria 8.451650 0.0008589 0.0240227 4/11
R-HSA-442729 CREB phosphorylation through the activation of CaMKII 8.451650 0.0008589 0.0240227 4/11
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 8.451650 0.0008589 0.0240227 4/11
R-HSA-5339562 Uptake and actions of bacterial toxins 8.203072 0.0000481 0.0069546 6/17
R-HSA-8978934 Metabolism of cofactors 7.747346 0.0012455 0.0281957 4/12
R-HSA-202131 Metabolism of nitric oxide 7.747346 0.0012455 0.0281957 4/12
R-HSA-203765 eNOS activation and regulation 7.747346 0.0012455 0.0281957 4/12
R-HSA-5576892 Phase 0 - rapid depolarisation 7.151396 0.0017393 0.0327819 4/13
R-HSA-389977 Post-chaperonin tubulin folding pathway 7.151396 0.0017393 0.0327819 4/13
R-HSA-1483249 Inositol phosphate metabolism 7.151396 0.0017393 0.0327819 4/13
R-HSA-425393 Transport of inorganic cations/anions and amino acids/oligopeptides 5.810510 0.0012683 0.0281957 5/20
R-HSA-1445148 Translocation of SLC2A4 (GLUT4) to the plasma membrane 5.557879 0.0000024 0.0020686 11/46
R-HSA-442755 Activation of NMDA receptors and postsynaptic events 5.533819 0.0016075 0.0324126 5/21
R-HSA-5218920 VEGFR2 mediated vascular permeability 5.282281 0.0020090 0.0355477 5/22
R-HSA-72662 Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 4.565400 0.0000183 0.0039708 11/56
R-HSA-72695 Formation of the ternary complex, and subsequently, the 43S complex 4.357882 0.0001591 0.0153238 9/48
R-HSA-72649 Translation initiation complex formation 4.225825 0.0000895 0.0097047 10/55
R-HSA-72702 Ribosomal scanning and start codon recognition 4.225825 0.0000895 0.0097047 10/55
R-HSA-114608 Platelet degranulation 4.225825 0.0004639 0.0194565 8/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 4.225825 0.0004639 0.0194565 8/44
R-HSA-425407 SLC-mediated transmembrane transport 4.101536 0.0028476 0.0457205 6/34
R-HSA-373760 L1CAM interactions 3.417947 0.0005490 0.0196096 10/68
R-HSA-156842 Eukaryotic Translation Elongation 3.205798 0.0002840 0.0166676 12/87
R-HSA-192823 Viral mRNA Translation 3.080270 0.0007248 0.0232739 11/83
R-HSA-2408522 Selenoamino acid metabolism 3.051985 0.0002608 0.0166676 13/99
R-HSA-156902 Peptide chain elongation 3.043600 0.0008035 0.0240227 11/84
R-HSA-2408557 Selenocysteine synthesis 3.007793 0.0008892 0.0240917 11/85
R-HSA-195258 RHO GTPase Effectors 3.004073 0.0000117 0.0033928 19/147
R-HSA-72764 Eukaryotic Translation Termination 2.972819 0.0009823 0.0258087 11/86
R-HSA-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) 2.905255 0.0011929 0.0281957 11/88
R-HSA-72613 Eukaryotic Translation Initiation 2.879545 0.0002812 0.0166676 14/113
R-HSA-72737 Cap-dependent Translation Initiation 2.879545 0.0002812 0.0166676 14/113
R-HSA-156827 L13a-mediated translational silencing of Ceruloplasmin expression 2.877586 0.0004701 0.0194565 13/105
R-HSA-72706 GTP hydrolysis and joining of the 60S ribosomal subunit 2.850439 0.0005161 0.0194565 13/106
R-HSA-168255 Influenza Life Cycle 2.789045 0.0002427 0.0166676 15/125
R-HSA-168273 Influenza Viral RNA Transcription and Replication 2.781099 0.0004058 0.0194565 14/117
R-HSA-72689 Formation of a pool of free 40S subunits 2.691183 0.0022431 0.0373988 11/95
R-HSA-1799339 SRP-dependent cotranslational protein targeting to membrane 2.656233 0.0015947 0.0324126 12/105
R-HSA-168254 Influenza Infection 2.621282 0.0004814 0.0194565 15/133
R-HSA-68877 Mitotic Prometaphase 2.606584 0.0018797 0.0346740 12/107
R-HSA-71291 Metabolism of amino acids and derivatives 2.521542 0.0000259 0.0044839 23/212
R-HSA-2555396 Mitotic Metaphase and Anaphase 2.456476 0.0021076 0.0358296 13/123
R-HSA-68882 Mitotic Anaphase 2.456476 0.0021076 0.0358296 13/123
R-HSA-69620 Cell Cycle Checkpoints 2.421046 0.0011190 0.0281957 15/144
R-HSA-194315 Signaling by Rho GTPases 2.387020 0.0002884 0.0166676 19/185
R-HSA-68886 M Phase 2.224118 0.0005098 0.0194565 20/209
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol 2.220577 0.0026787 0.0438195 15/157
R-HSA-5663205 Infectious disease 2.045954 0.0003609 0.0194565 25/284
Factor 20 : 25 significant Reactome pathways
GeneSet description enrichmentRatio pValue FDR GeneRatio
R-HSA-2871809 FCERI mediated Ca+2 mobilization 11.639553 0.0002517 0.0189361 4/11
R-HSA-442729 CREB phosphorylation through the activation of CaMKII 11.639553 0.0002517 0.0189361 4/11
R-HSA-442982 Ras activation upon Ca2+ influx through NMDA receptor 11.639553 0.0002517 0.0189361 4/11
R-HSA-8876725 Protein methylation 10.669591 0.0003685 0.0213016 4/12
R-HSA-451326 Activation of kainate receptors upon glutamate binding 10.002741 0.0000904 0.0111986 5/16
R-HSA-500792 GPCR ligand binding 9.484081 0.0000010 0.0004162 8/27
R-HSA-8982491 Glycogen metabolism 9.145363 0.0007100 0.0304598 4/14
R-HSA-5626467 RHO GTPases activate IQGAPs 8.891326 0.0001687 0.0182799 5/18
R-HSA-2672351 Stimuli-sensing channels 8.617746 0.0000097 0.0028088 7/26
R-HSA-5578775 Ion homeostasis 8.350114 0.0000533 0.0077003 6/23
R-HSA-442742 CREB phosphorylation through the activation of Ras 8.002193 0.0012298 0.0444267 4/16
R-HSA-4086398 Ca2+ pathway 6.668494 0.0007201 0.0304598 5/24
R-HSA-418346 Platelet homeostasis 6.401754 0.0002621 0.0189361 6/30
R-HSA-418594 G alpha (i) signalling events 5.909312 0.0000005 0.0004162 12/65
R-HSA-5576891 Cardiac conduction 5.334795 0.0007378 0.0304598 6/36
R-HSA-114608 Platelet degranulation 5.092305 0.0003553 0.0213016 7/44
R-HSA-76005 Response to elevated platelet cytosolic Ca2+ 5.092305 0.0003553 0.0213016 7/44
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission 4.481228 0.0007932 0.0312581 7/50
R-HSA-194138 Signaling by VEGF 4.073844 0.0014166 0.0491286 7/55
R-HSA-983712 Ion channel transport 4.064606 0.0006545 0.0304598 8/63
R-HSA-388396 GPCR downstream signalling 3.765738 0.0000142 0.0030881 14/119
R-HSA-373760 L1CAM interactions 3.765738 0.0010969 0.0413468 8/68
R-HSA-372790 Signaling by GPCR 3.643275 0.0000209 0.0036285 14/123
R-HSA-76002 Platelet activation, signaling and aggregation 3.556530 0.0004160 0.0225434 10/90
R-HSA-109582 Hemostasis 2.609411 0.0004966 0.0253246 15/184
Summary:
Factor 1 2 3 4 5 6 7 8 9 10
Signif_GO_terms 0 43 0 0 17 30 45 89 31 29
Factor 11 12 13 14 15 16 17 18 19 20
Signif_GO_terms 20 47 45 2 67 62 39 0 50 25