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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
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BMC Genomics

ISSN: 1471-2164

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