A transcriptome-based model of central memory CD4 T cell death in HIV infection

BMC Genomics

Table 1 Enriched categories of functions according to TCM gene expression signature in HIV infection

General category	DAVID		GSEA	IPA
General category	EASE < 0.05	Number of genes	FDR < 0.05, p < 0.001	p < 0.01	Number of genes	Prediction sense
Cell cycle	Cell cycle	15	DNA replication	Proliferation of tumor cell lines	31	Positive
	Cell division	10	Cell cycle	Proliferation of cells	53	Positive
	mitosis	9	Mitotic M/G1	Cytostasis	6	Positive
			G1/S transition	Cytostasis od tumor cell lines	5	Positive
			Cell cycle check points	Interphase of tumor cell lines	11	Positive
			Cyclin E associated event during G1/S transition	Cell survival	28	Positive
			Assembly of pre-replicative complex	Interphase	13	Positive
			G0 and early G1	Mitosis	10	Negative
			G2/M check points
DNA damage or repair	p53 signaling pathway	5	p53 dependent G1 DNA damage response
	ATM signal pathway	3
	Cell cycle checkpoints	5
Apoptosis	Apoptosis	13		Apoptosis of tumor cell lines	32	Negative
				Cell death of cancer cells	6	Negative
				Apoptosis of cervical cancer cell lines	10	Negative
Immune responses			Toll endogenous pathway	Synthesis of reactive oxygen species	7	Positive
			IL1 signaling
			IFN-alpha/beta signaling
			Chemokine receptors bind chemokines
			NOD like receptors signaling
			NFKB activation by IKKS complex
			Myd88 cascade
			TLR4 signaling
			IL12 pathway
			FOXO Pathway

Enriched categories of functions according to differential expression of 210 genes in T_CM cells from HIV⁺ patients and controls. DAVID and IPA tools show in a column the number of genes supporting each prediction. EASE Score is the P-Value of a modified Fisher Exact test of the significance of gene enrichment in a gen-set. FDR: False discovery rate. In IPA, the sign indicates if the function would be up-regulated (positive) or down-regulated (negative)

ISSN: 1471-2164