1 Single cell expression data

CROP-seq data are from this paper: On the design of CRISPR-based single cell molecular screens, GEO accession: GSE108699.

Perturbations:
Knock-outs of 29 tumor-suppressor genes (TP53, …), 1 non-targeting control.

Cells:
MCF10A cells (normal human breast epithelial cells) with exposure to a DNA damaging agent, doxorubicin.
Only cells with a single type of gRNA readout were kept, resulted in 4507 cells.

Genes:
Only genes detected in > 10% of cells were kept, resulted in 8046 genes.

Normalization:
Seurat “LogNormalize”: log(count per 10K + 1).
Library size was regressed out, so were the non-targeting control (NTC) condition per cell. The residuals were used as input.

2 Permutation

Cell labels in the expression data were permuted randomly so that they are no longer correlated with the KO conditions. Then GSFA was performed still using all conditions other than NTC as guides.

2.1 Factor ~ KO Beta PIP

2.2 Factor ~ KO Posterior Association

2.3 LFSR

Permutation 1, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 2, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 3, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 4, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 371 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 5, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 6, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 7, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 8, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 9, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA
Permutation 10, # of genes that passed LFSR cutoff of 0.05:
KO APC ARID1A ARID1B ATM BAP1 BID BRCA1 BRCA2 CASP8 CDH1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO CDKN1B CDKN2A CHEK1 CTCF GATA3 MLH1 MLL2 MLL3 NCOR1 NF1
Num_genes 0 0 0 0 0 0 0 0 0 0
KO PTEN PTPN22 PTPRD RAD51 RB1 RUNX1 SETD2 STK11 TP53
Num_genes 0 0 0 0 0 0 0 0 0 NA