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Table 2 Interactions by protein function. Sixteen "over-connected" genes in VL-blood expression profile

From: Vitiligo blood transcriptomics provides new insights into disease mechanisms and identifies potential novel therapeutic targets

Protein Function Gene IDs in active data set Gene Title Object name Fold change A n R N E Ratio z-score p-value
TFs IRF9 interferon regulatory factor 9 IRF9 −1.7 7 102 60 26494 0.231 30.3 14.1 3.32E-09
STAT1 signal transducer and activator of transcription 1, 91kDa STAT1 −2.6 22 102 575 26494 2.214 9.9 13.5 4.04E-16
Receptors FCGR2B Fc fragment of IgG, low affinity IIb, receptor (CD32) Fc gamma RII beta −1.4 2 102 35 26494 0.135 14.8 5.1 0.0080
Kinases PRKCD protein kinase C, delta PKC-delta −1.7 8 102 386 26494 1.486 5.4 5.4 0.0001
Proteases PSMB9 proteasome (prosome, macropain) subunit, beta type, 9 PSMB9 −1.7 3 102 38 26494 0.146 20.5 7.5 0.0004
PSMB8 proteasome (prosome, macropain) subunit, beta type, 8 PSMB8(LMP7) −1.6 2 102 30 26494 0.115 17.3 5.6 0.0059
Phosphatases PTPN6 protein tyrosine phosphatase, non-receptor type 6 SHP-1 −1.9 5 102 200 26494 0.770 6.5 4.8 0.0010
Enzymes MX1; MX2 myxovirus (influenza virus) resistance 2 (mouse) MxA −3.5 ; -2.2 3 102 57 26494 0.219 13.7 6.0 0.0013
Others IFIT1 interferon-induced protein with tetratricopeptide repeats 1 IFIT1 −4.0 4 102 15 26494 0.058 69.3 16.4 2.74E-07
TOMM34 translocase of outer mitochondrial membrane 34 TOM34 −1.6 2 102 21 26494 0.081 24.7 6.8 0.0029
IFIT3 interferon-induced protein with tetratricopeptide repeats 3 RIG-G −3.5 6 102 66 26494 0.254 23.6 11.4 2.11E-07
SERPING1 serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 C1 inhibitor −4.0 2 102 23 26494 0.089 22.6 6.4 0.0035
NCF4 neutrophil cytosolic factor 4, 40kDa p40-phox −1.8 2 102 23 26494 0.089 22.6 6.4 0.0035
TAP1 transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) TAP1 (PSF1) −1.6 4 102 51 26494 0.196 20.4 8.6 4.5E-0
ISG15 ISG15 ubiquitin-like modifier ISG15 −4.2 8 102 256 26494 0.986 8.1 7.1 6.83E-06
  1. Explanation of each column
  2. Protein Function: overall associated functions with proteins; Gene IDs in active data sets: gene symbol associated with the VL skin transcriptional profile; Gene Title: Full name of gene; Object Name: network object in metabase; Fold change: expression by microarray VL vs control. A: number of network objects in the activated signatures which interact with the chosen object; n: number of network objects in the signature; R: number of network objects in the background list which interact with the chosen object; N: total number of protein-based objects in the background list; E (Expected): mean of hypergeometric distribution; Ratio: connectivity ratio (actual/expected); z-score: (actual-expected)/(standard deviation); p-value: probability to have the value of Actual or higher (lower for negative z-score) by chance under null hypothesis of no over- or under-connectivity; TFs: Transcription factors
  3. “Over-connected” genes (encoded protein) by “function” is based on the connectivity of genes in the active dataset with genes from the Human Proteome in the MetaCore database (metabase). We found sixteen (MX1 and MX2 are both in the dataset and map to a group in metabase) significantly over-connected genes in VL-blood transcriptional profile where the number of observed interactions exceeded the number of expected interactions. There were no under-connected genes observed