MultiDCoX: Multi-factor analysis of differential co-expression

BMC Bioinformatics

Table 3 Examples of genesets whose co-expression is influenced by more than one factor. (1) geneset in the 1st row, containing CXCL13 and MMP1, is differentially co-expressed by ER and Grade covariates

Co-expression	Genes	ER coefficient	ER pvalue	p53 coefficient	p53 pvalue	Grade coefficient	Grade pvalue
ER+ & Grade+	HORMAD1,SCGB1D2, ABCB1,IGHM,CXCL13, FAM20B,IGK,CCL18, LOC100291464,FCRL5, IGHA1,LOC100293440, IGL,IGLV1–44,IGH, IGKV4–1, IGHD, LOC100130100,FABP7, NKG7,MMP1,PIGR, LOC652493	0.592	3.64E-05	−0.343	0.000 658	1.525	5.05E-24
ER+ & P53- & Grade+	CLEC3A, MUC5B, RAD51C,CYP2A6,CHGB, CARTPT,GRIA2,INSM1, NTS,PCSK1	0.662	3.16E-05	−0.818	4.14E-17	1.124	1.77E-40
ER- & p53+	FMO5, VGLL1, FABP7, GABRP, PKP1,TFCP2L1, NRTN,KRT15, PTX3, KRT16, MIA,CTAG1A, ELF5,HORMAD1,C8orf4 6,FAM150B	−0.906	7.80E-14	0.844	8.84E-23	0.127	0.305

The co-expression of the set occurs in ER-positive tumors and higher grade tumors (referred to as Grade+) only. Joint occurrence of ER+ and Grade3 will result in higher co-expression. (2) Geneset in the 2nd row is differentially co-expressed by all covariates. The co-expression of the set occurs in ER-positive tumors, p53-negative tumors and higher grade tumors (referred to as Grade+). Joint occurrence of ER+, p53- and Grade3 will result in higher co-expression. (3) Gene set in the 3rd row is differentially co-expressed by ER and p53 covariates. The co-expression of the set occurs in ER-negative tumors, p53-positive tumors. Joint occurrence of ER- and p53+ will result in higher co-expression

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