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

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*