Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation

Table 2 Features of gene expression studies comparing latently infected vs uninfected cells

Study characteristics	Krishnan and Zeichner[18]	Iglesias-Ussel et al[19]	Mohammadi et al[42]	Evans et al[76]
Cells used	Cell lines ACH-2, A3.01, J1.1	Primary CD4+ T cells	Primary CD4+ T cells co-cultured with feeder H80 human brain tumor cell line	Primary resting CD4+ T cells co-cultured with dendritic cells
Virus used	CXCR4 tropic HIV-1 LAV strain	CXCR4 tropic GFP reporter virus (GFP inserted in place of Nef)	CXCR4 tropic GFP reporter virus with mutations in Gag, Vif, Vpr, Vpu, Env and Nef	CCR5 tropic GFP reporter virus (GFP inserted into the Nef open reading frame)
Proportion of uninfected cells	≤ 1.1%	0%	8%-18%	99.7%
Proportion of GFP+ or p24+ cells	8.20%	8.15%	Approximately 16%	0% (removed by sorting)
Proportion of latently infected cells	98.9%	100%	Approximately 82%-92%	Approximately 0.3%
Time of culture	N/A (chronically infected)	20-22 d	13 wk	5 d
Experiment replicates	8	4	Not reported	4
Gene expression profiling platform	Microarrays (Hs. UniGem2)	Microarrays (Agilent-012391 Whole Human Genome Oligo Microarray G4112A)	RNA-Seq (polyA RNA library; Illumina HiSeq2000)	Microarrays (Illumina Human-Ref8)
Method to identify DEGs	Parametric one-sample random variance t-test (BRB-Array Tools, P < 0.001)	Linear modeling and using an empirical Bayes method with FDR correction (limma)	Generalized linear modeling (DESeq, FDR < 0.05)	Linear modeling and using an empirical Bayes method (limma, FDR < 0.05)
Databases used for functional analyses	NIH mAdb	GO consortium;	Reactome pathways Ver.40;	IPA
		MsigDb;	MsigDb
		KEGG pathways
Total number of DEGs	32	875	227	Not reported

CXCR4: Chemokine (C-X-C motif) receptor 4; LAV: Lymphadenopathy-associated virus; CCR5: Chemokine (C-C motif) receptor 5 (gene/pseudogene); GFP: Green fluorescent protein; polyA: Polyadenylated; DEGs: Differentially expressed genes; BRB: Biometric Research Branch; FDR: False discovery rate; NIH: National Institutes of Health; mAdb: Mad Bee; GO: Gene ontology; MsigDb: Molecular Signature database; KEGG: Kyoto Encyclopedia of Genes and Genomes; IPA: Ingenuity Pathway Analysis; N/A: Not applicable.