Review
Copyright ©The Author(s) 2016.
World J Clin Infect Dis. May 25, 2016; 6(2): 6-21
Published online May 25, 2016. doi: 10.5495/wjcid.v6.i2.6
Table 5 Features of gene expression studies comparing cells treated with latency reversing agents of different functional classes and untreated cells
Study characteristicsJiang et al[95]Mohammadi et al[42]Sung and Rice[97]Banerjee et al[98]
Cells usedPrimary cells from HIV-infected individuals on cARTIn vitro primary CD4+ T cell latency modelPrimary resting CD4+ T cellsJ-Lat 10.6 T cell line
LRA (functional class)Valproic acid (HDACi)Disulfiram (alcohol dehydrogenase inhibitor)Prostratin (PKC agonist)JQ1 (bromodomain inhibitor)
Concentration1 mmol/L (+20 U/mL IL-2)0.5 μmol/L250 ng/mL0.1 μmol/L, 1 μmol/L
Time of treatment6 h8 and 24 h48 h24 h
Experiment replicates4Not reported3Not reported
Gene expression profiling platformMicroarrays (Agilent)RNA-Seq (polyA RNA library; Illumina HiSeq2000)Microarrays (Affymetrix Human Genome U133 Plus 2.0)Microarrays (Affymetrix ST 1.0)
Methods to identify DEGsRosetta Resolver system (P < 0.01)Generalized linear modeling (DESeq, FDR < 0.05)t-test with FDR correctionANOVA (P < 1E-5)
Databases used for functional analysesNot usedReactome pathways Ver.40; MsigDbGO consortium, KEGG pathwaysGO consortium
Total number of DEGs199 (fold change > 3)1892514 (fold change > 1.5)Not reported