ELIMINATOR: essentiality analysis using multisystem networks and integer programming

BMC Bioinformatics

Table 3 BRCA essentiality results

geneID	# pathways	# connections	p.hyper	p.adj	# cancer essential	# total essential	Achilles score
RACGAP1	3	4	3.25E-07	4.91E-05	118	118	− 1.45764
MIB1	1	3	2.33E-06	1.76e-04	110	110	− 0.34808
EZR	3	4	1.02E-05	5.13e-04	103	103	0.094074
PCNA	2	3	1.94E-05	7.34e-04	126	128	− 1.88689
TUBG1	1	2	1.40e-04	4.21e-03	88	88	− 1.31599
CASP3	7	10	5.20e-04	9.81e-03	79	79	0.073582
PKCDELTA	13	18	5.20e-04	9.81e-03	79	79	NA
SDC2	2	25	5.20e-04	9.81e-03	79	79	− 0.06373
BIRC3	4	12	1.68e-03	2.31e-02	89	90	0.149018
GNAI1	1	1	1.68e-03	2.31e-02	70	70	− 0.10703

geneID gene identifier in HGNC nomenclature; #pathways: number of NCI-PID pathways where the gene appears; #connections: number of connected genes in those pathways (parents/children); p.hyper p-value from a hypergeometric test; p.adj adjusted p-value after multiple-testing comparison, #cancer essential: number of cancer samples predicted as essential; #total essential: number of total samples predicted as essential; Achilles score average Achilles score across all the BRCA cell lines from the CCLE. Essential genes (Achilles score < − 0.5) are denoted in bold
Number of cancer samples = 153, Total number healthy samples = 11

ISSN: 1471-2105