KEGG Pathway analysis of the differentially expressed genes.

<p>KEGG Pathway analysis of the differentially expressed genes.</p

From the co-expression network constructed using the top 25 up-regulated and 25 down-regulated differentially expressed genes identified in PBMC infected with HIV-2 as input genes, three functional modules were clustered.

<p>The color of the node signifies the following: Pink circle denotes input genes, Blue circle denotes co-expressed genes.</p

Gene Ontology (GO) analysis of differentially expressed genes in HIV-2 ROD infected cells.

<p>The top GO (biological process) terms that occur in the differently expressed genes in PBMCs infected cells with HIV-2 ROD are shown. The bar plot shows Fold Enrichment value of the significant enrichment terms. Pathway analysis for differentially expressed (A) up regulated genes and (B) down regulated genes.</p

Real-time PCR detection of host genes in PBMCs infected with HIV-1 (MN) or HIV-2 (ROD) fifteen days post infection.

<p>The RT-PCR results from RNA isolated from PBMCs infected with HIV-1(MN) and HIV-2 (ROD) <i>(</i>A) genes differentially up regulated in HIV-1 and HIV-2 infected cells and (B) genes differentially down regulated in HIV-1 and HIV-2 infected cells. The RT-PCR data are derived from independent experiments using PBMCs isolated from five different donors. Each experimental sample subjected to real- time PCR amplification was normalized relative to the endogenous GAPDH control and the relative amount of target gene quantitated. Final results are expressed as n-fold difference in expression of gene-of-interest relative to GAPDH gene for infected and uninfected cells as n-fold = 2^ − (ΔCt infected −ΔCt uninfected). Each sample was run in triplicate to ensure accurate fold change estimation and the results expressed as mean ±SEM.</p

Scatter plot of genes expressed in HIV-1 or HIV-2 infected cells, Day 7 post infection.

<p>The values of X and Y axes in the Scatter-Plot are the normalized signal values of the averaged normalized signal values of the compared groups. The green lines are Fold Change Lines (The default fold change value is 1.5). The genes above the top green line and below the bottom green line indicated more than 1.5 fold change of genes between two samples or groups.</p

PHGDH and PSAT1 protein expression in PBMC cells infected with HIV-1 and HIV-2 determined by Western blot.

<p>(A) PHGDH and (B) PSAT1 protein expression in PBMC cells infected with HIV-1 and HIV-2 determined by Western blot. Lane 1 is denoted as no virus infection control, Lane 2 is denoted as HIV-1 (MN) infected PBMC and Lane 3 is denoted as HIV-2 (ROD) infected PBMC respectively. The data is a representative of three independent experiments. (C) Quantitation of PHGDH and PSAT1 protein expression from Western blot data. The results are derived from independent experiments using PBMCs isolated from three different donors. Each experimental sample subjected to Western Blot analysis was normalized relative to the endogenous β-Actin control and the relative amount of target gene quantitated. The results are expressed as mean ± SEM.</p

Real-time PCR detection of host genes in Jurkat cells infected with HIV-1 or HIV-2 seven days post infection.

<p>The RT-PCR results from RNA isolated from Jurkat cells infected with HIV-1(MN) and HIV-2 (ROD) to validate microarray data <i>(</i>A) genes differentially up regulated in HIV-1 and HIV-2 infected cells and (B) genes differentially down regulated in HIV-1 and HIV-2 infected cells. The data depicts results from 3 independent experiments. Each experimental sample subjected to real-time PCR amplification was normalized relative to the endogenous GAPDH control and the relative amount of target gene quantitated. Final results are expressed as n-fold difference in expression of gene-of-interest relative to GAPDH gene for infected and uninfected cells as n-fold = 2^ − (ΔCt infected −ΔCt uninfected). Each sample was run in triplicate to ensure accurate fold change estimation and the results expressed as mean ± SEM.</p

Quantification of HIV-1 (P-24) and HIV-2 (P-26) antigens.

<p>Quantification of HIV-1 (P-24) and HIV-2 (P-26) antigens.</p

HSPA6 interactive gene network.

<p>The interactive network generated automatically using the STRING database (STRING software 9.1) for heat shock protein 6 (HSPA6) gene that was differentially upregulated in HIV-2 infected cells is shown here. The input differentially expressed gene HSPA6 is depicted as Red circles. Predicted Functional Partners proteins depicted as Green circles are given below: DNAJB1---DnaJ (Hsp40) homolog, subfamily member 1; UBC---Ubiquitin C; MAPK8---mitogen-activated protein kinase 8; DNAJA1---DnaJ (Hsp40) homolog, subfamily member A; DNAJB2---DnaJ (Hsp40) homolog, subfamily member B; TLR2---Toll-like receptor 2; DNAJC5---DnaJ (Hsp40) homolog, subfamily member C; DNAJC5G ---DnaJ (Hsp40) homolog, subfamily member C; DNAJC5B ---DnaJ (Hsp40) homolog, subfamily member C; DNAJC3---DnaJ (Hsp40) homolog, subfamily member C. Multiple Edges color represents: Green---Neighborhood; Red---Gene Fusion; Blue---Co-occurrence; Black---Coexpression; Purple---Experiments; Light Blue---Database; Light Green---Textmining.</p

ApoC1, FADS1 and FADS2 interactive gene network.

<p>The differentially expressed genes ApoC1, FADS1 and FADS2 interactive network generated automatically using the STRING database (STRING software 9.1) is shown here. The input differentially expressed genes ApoC1, FADS1 and FADS2 are depicted as Purple circles. The Predicted Functional Partner proteins depicted as Green circles are given below: ELOVL2---elongation of very long fatty acids-like 2; ELOVL5---elongation of very long fatty acids-like 5; ACSL1---acyl-CoA synthetase long-chain family member 1; PPARA---peroxisome proliferator-activated receptor alpha; PLA2G1B ---phospholipase A2, group IB (pancreas); PLA2G12B ---phospholipase A2, group XIIB; SCL27A2---solute carrier family 27 (fatty acid transporter); ACSL3---acyl-CoA synthetase long-chain family member 3; PLA2G4A ---phospholipase A2, group IVA (cytosolic, calcium dependent); PLA2G2C ---phospholipase A2, group IIC. Multiple Edges color represents: Green---Neighborhood; Red---Gene Fusion; Blue---Co-occurrence; Black---Coexpression; Purple---Experiments; Light Blue---Database; Light Green---Textmining.</p