xcore: an R package for inference of gene expression regulators

BMC Bioinformatics

Table 2 Recovering measles infection transcriptional regulators

Top signatures	293SLAM				COBL-a				COBL-a rinderpest(-C)
	ISMARA	Lisa	xcore		ISMARA	Lisa	xcore		ISMARA	Lisa	xcore
	ISMARA	Lisa	ReMap2020	ChIP-Atlas	ISMARA	Lisa	ReMap2020	ChIP-Atlas	ISMARA	Lisa	ReMap2020	ChIP-Atlas
1–10	STAT2, IRF3, IRF9	TP53, STAT1	IRF9	TP53			RELA	TP53	STAT2		RELA, IRF9	TP53
11–50	RELA, JUN	STAT3, IRF9, RELA, STAT5B, STAT2	RELA, STAT1	NFKB1, RELA, STAT2	FOS	TP53, STAT3	TP53, FOS	STAT1, RELA, JUN	IRF3	TP53, STAT3	STAT5A	NFKB1, JUN
51–100	NFKB1, FOS, STAT1			FOS	STAT2, IRF3	JUN, RELA	JUN, STAT5A		FOS, RELA	JUN, RELA	FOS, TP53

Table summarizing measles infection pathway-related transcriptional regulators recovered by ISMARA, Lisa and xcore among their top-scoring signatures based on rinderpest infection datasets. The list of measles infection pathway-related transcriptional regulators used to assess the recovery was constructed using KEGG pathway Measles (map05162) by including only regulators available in the references of all tools

ISSN: 1471-2105