Additional file 8. Ingenuity functional prediction ...

Proliferation of tumor cell lines        z‐score = 2.7 (increased) Genes in  dataset

Prediction

Ct

p‐value 

MMP9 SIK1 AREG ENC1 PBK MNDA IL12RB2 TYMS PFKFB3 CD38 CCNE1 DTL NAMPT E2F8 PER1 NFKBIA MKI67 PRC1 CHEK1 ADAM9 ODC1 DUSP10 KIF11 VAV3 PTGER4 ZNF267 MXD1 NR4A3 PTP4A1 NCAPG DNAJA3 FGF9 NR4A2 SGK1 TOP2A TAF1D TTK MMP8 LTF S100A8 CD83 TNFAIP3 SAT1 DUSP5 SOD2 NRAS MYC VIPR1 HRH2 FABP5 BUB1B BCL6 CD55 PLK4 ADCY3 ID3

Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Increased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Decreased Affected Affected Affected Affected Affected Affected

4.960 4.219 3.486 3.190 2.770 2.525 2.364 1.889 1.756 1.688 1.648 1.610 1.610 1.510 1.475 1.429 1.220 1.150 1.110 1.090 1.069 1.060 0.994 0.950 0.861 0.791 0.670 0.551 0.529 0.334 ‐0.428 ‐1.980 Upregulated* NA 0.230 0.130 0.090 3.622 3.48 3.11 2.20 2.14 1.403 1.078 0.696 0.542 ‐0.946 NA 0.07 0.060 1.75 1.07 0.93 0.72 ‐0.56 NA

1.20E‐10 1.05E‐26 8.61E‐15 6.76E‐20 1.84E‐07 2.47E‐12 4.83E‐17 2.47E‐13 2.50E‐11 7.78E‐15 3.17E‐16 6.68E‐09 3.62E‐16 9.92E‐11 1.15E‐11 2.38E‐20 9.68E‐09 1.10E‐12 5.31E‐13 3.46E‐08 1.48E‐14 2.45E‐12 4.33E‐09 1.42E‐11 1.34E‐13 1.27E‐10 1.40E‐08 1.96E‐03 2.85E‐05 1.62E‐02 2.10E‐03 1.72E‐14     NS NS NS 1.01E‐14 1.16E‐11 5.04E‐12 6.94E‐17 1.53E‐20 7.31E‐15 6.33E‐09 9.68E‐07 3.90E‐06 4.04E‐10 NS NS 1.48E‐07 1.21E‐11 1.48E‐09 4.60E‐06 1.49E‐06  

Apoptosis  z‐score=‐1.9 (decreased) Genes in  dataset MMP9 AREG CSTA PBK TNFAIP3 TYMS CD38 NAMPT NFKBIA MCM10 SRGN CHEK1 HERPUD1 VAV3 SOD2 MXD1 NR4A3 NRAS RNASEL DNAJA3 MYC UBASH3A FGF9 NR4A2 SGK1 ID3 OLR1 S100A8 PMAIP1 CCNE1 PER1 SAT1 MAP3K8 GADD45B BCL6 CD55 HSPB1 CCR8 TOP2A TNFRSF10D TTK LTF ENC1 ODC1 ADORA2A AKTIP

Prediction

Ct

p‐value

Decreased 4.96 1.20E‐10 Decreased 3.49 8.61E‐15 Decreased 2.81 2.21E‐06 Decreased 2.77 1.84E‐07 Decreased 2.14 1.53E‐20 Decreased 1.89 2.47E‐13 Decreased 1.69 7.78E‐15 Decreased 1.61 3.62E‐16 Decreased 1.43 2.38E‐20 Decreased 1.34 4.16E‐08 Decreased 1.162 2.14E‐12 Decreased 1.11 5.31E‐13 Decreased 0.99 2.05E‐09 Decreased 0.95 1.42E‐11 Decreased 0.70 9.68E‐07 Decreased 0.67 1.40E‐08 Decreased 0.55 1.96E‐03 Decreased 0.54 3.90E‐06 Decreased ‐0.32 2.55E‐02 Decreased ‐0.43 2.10E‐03 Decreased ‐0.95 4.04E‐10 Decreased ‐1.33 2.53E‐13 Decreased ‐1.98 1.72E‐14 Decreased Upregulated* Decreased NA Decreased NA Increased 3.480 5.80E‐13 Increased 3.112 5.04E‐12 Increased 2.640 3.10E‐13 Increased 1.648 3.17E‐16 Increased 1.475 1.15E‐11 Increased 1.403 7.31E‐15 Increased 1.300 3.89E‐10 Increased 1.208 1.11E‐13 Increased 1.070 1.21E‐11 Increased 0.926 1.48E‐09 Increased ‐1.439 1.92E‐09 Increased ‐2.500 2.47E‐15 Increased 0.230 NS Increased 0.150 NS Increased 0.090 NS Affected 3.484 1.16E‐11 Affected 3.190 6.76E‐20 Affected 1.069 1.48E‐14 Affected ‐1.248 7.13E‐09 Affected ‐0.007 NS

   

Interphase of tumors cell lines  (G1/S/G2)                        z‐score=1.8 (increased) Genes in  dataset CCNE1 E2F8 NFKBIA MCM10 CHEK1 RBBP8 MXD1 MYC ID3 MMP9 TYMS DTL ZBTB10

Prediction

Ct

p‐value

Increased Increased Increased Increased Increased Increased Increased Decreased Decreased Affected Affected Affected Affected

1.65 1.51 1.43 1.34 1.11 0.80 0.67 ‐0.95 NA 4.96 1.89 1.61 1.17

3.17E‐16 9.92E‐11 2.38E‐20 4.16E‐08 5.31E‐13 1.01E‐08 1.40E‐08 4.04E‐10 1.20E‐10 2.47E‐13 6.68E‐09 3.48E‐13

  Cytostasis (arrest)  z‐score=2.2 (increased) Genes in  dataset PER1 NFKBIA GADD45B BCL6 MXD1 TOP2A NRAS

Prediction

Ct

p‐value

Increased Increased Increased Increased Increased Increased Affected

1.48 1.43 1.21 1.07 0.67 0.23 0.54

1.15E‐11 2.38E‐20 1.11E‐13 1.21E‐11 1.40E‐08 NS 3.90E‐06

  Mitosis  z‐score=‐1.187 (decreased) Genes in  dataset

Prediction

Ct

p‐value

CHEK1 KIF11 RBBP8 FGF9 BUB1B CCNE1 SKA3 PTP4A1 TOP2A TTK

Decreased Decreased Decreased Decreased Increased Increased Affected Affected Affected Affected

1.11 0.99 0.80 ‐1.98 1.75 1.65 2.77 0.53 0.23 0.09

5.31E‐13 4.33E‐09 1.01E‐08 1.72E‐14 1.48E‐07 3.17E‐16 6.37E‐04 2.85E‐05 NS NS

Additional file 8. Ingenuity functional prediction analysis of the

 

signature of TCM cells in HIV infection. Ingenuity functional prediction analysis was made with IPA software. ΔΔCt and p-values represent RT-PCR validation values. * Upregulation was inferred in the absence of a ΔΔCt value, based on amplification in patients' cells (ΔCt=6.5), but no amplification in cells from controls. NS: Not significant. NA: no amplification.