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Table 4 The GSEA of our dataset compared with the published gene lists derived from monocyte/MDM transcriptomes modulated by HIV

From: Transcriptome analysis of primary monocytes from HIV-positive patients with differential responses to antiretroviral therapy

Gene set name Pathways/biological functions DEGs involved in HIV infection/disease progression Study description Reference Gene set size VIRvs BDL FDR VIRvs CTR FDR BDLvs CTR FDR
Cicala_Cytokine _Chemokine Chemokine and cytokine in vitro gp120-treated vs mock-treated MDM [16] 34 0.288 0.000*** 0.000***
Coberley_HIV_ Induced_Repressed Cell cycle regulators, translation, cell signaling, TNF, MAPK in vitro HIV-infected vs mock-treated MDM [15] 38 0.07* 0.192* 0.226*
Woelk_InteferonStimuated Interferon stimulated genes, host defense genes in vitro HIV-infected vs mock-treated MDM [30] 12 0.004*** 0.000*** 0.007***
Vazquez_HIVinduced _MDM Signal transduction, transcription, cell cycle and apoptosis, adhesion molecules and receptors, chemokines and cytokines, proteases and protease inhibitors, metabolism in vitro HIV-infected vs mock-treated MDM [28] 124 0.059* 0.096* 0.159*
Wen_HIVvsMock_U937 Signaling components, transcription factors, cytokines, apoptotic and anti-apoptotic factors, growth factors, anti-HIV infection genes in vitro HIV-infected vs mock-infected U937 human promonocytes [29] 33 0.094* 0.008*** 0.004***
TILTON_CytokineLevel _Correlation Type I interferon responses, NF-κB, mitogen-activated protein kinase, Jun signaling pathways, general immune activation, immune down-regulation, protein degradation, protein secretion, and apoptosis ex vivo correlations between changes in gene expression values and changes in monocyte cytokine levels in HIV+ patients on and off therapy [21] 1295 0.222* 0.161* 0.156*
Giri_Apoptosis _StableDifferential Apoptosis-related gene signatures, TNF-α signaling, CD40L/CD40 signaling, MAPK signaling, p53 modulation ex vivo HIV+ patients vs healthy controls [19] 36 0.006*** 0.177* 0.003***
Van_HIV_Serostatus _associated _validated Apoptosis, cell cycle, transcriptional regulation, immune response, protein trafficking, lipid metabolism ex vivo HIV+ patients vs healthy controls [22] 24 0.018** 0.003*** 0.000***
Gekonge_Overlap_ ControlStimulatedvsControl_HIVvsControl TLR2-agonist stimulated gene signature TNF (NFκB), p53 and MAPK networks ex vivo and in vitro HIV+ patients vs healthy controls stimulated vs non-stimulated controls [27] 62 0.229* 0.008*** 0.015**
Gekonge_HIVvsControl ERK/MAPK, TNF/IL6 (NFκB) and p53 gene networks, apoptosis-related gene signatures ex vivo HIV+ patients vs healthy controls [27] 281 0.138* 0.066* 0.061*
  1. DEGs: differentially expressed genes; gene set size: number of genes in the published list; FDR: false discovery rate; VIR: the viremic patients; CTR: the healthy control group; MDM: monocyte-derived macrophages; vs: versus. *FDR < 0.25 (default cutoff); **FDR < 0.05(more stringent); ***FDR < 0.01(most stringent).