Table 3

Genes corresponding to protein interactions in the four statistically significant functional modules A, B, C and D (in Figure 3)

Gene name

Chromosomal band

Description

GO term


Module A

DNAJC14

[12q13.2]

Nuclear protein Hcc-1 (Proliferation associated cytokine-inducible protein CIP29)

Heat shock protein binding, unfolded protein binding

HNRPLL

[2p22.1]

Heterogeneous nuclear ribonucleoprotein L-like (Stromal RNA-regulating factor)

Nucleotide binding, RNA binding, mRNA processing

BAT1

[6p21.33]

Spliceosome RNA helicase BAT1 (HLA-B associated transcript-1)

Nucleotide binding, nucleic acid binding, ATP-dependent RNA helicase activity, nuclear mRNA splicing, mRNA export from nucleus, ATP biosynthetic process, ion transport

ITPR3

[6p21.31]

Inositol 1,4,5-trisphosphate receptor type 3

Ion channel activity, calcium channel activity, calcium ion transport, protein binding, signal transduction

RPS18

[6p21.32]

40S ribosomal protein S18 (Ke-3)

RNA binding, structural constituent of ribosome, rRNA binding, translation

TUBB

[6p21.33]

Tubulin beta-2 chain

Nucleotide binding, GTPase activity, cell motility, natural killer cell mediated cytotoxicity

LMO7

[13q22.2]

LIM domain only protein 7 (LOMP) (F-box only protein 20)

Protein ubiquination, actomyosin structure and biogenesis, protein binding, ion binding

WDR1

[4p16.1]

WD repeat domain 1 (WDR1), transcript variant 1

Actin binding, protein binding, sensory perception of sound

RPS15A

[16p12.3]

40S ribosomal protein S15a

Protein binding, structural constituent of ribosome, translation

ELF5

[11p13]

ETS-related transcription factor Elf-5 (E74-like factor 5)

Transcription factor activity, sequence-specific DNA binding, regulation of transcription, cell proliferation

Module B

RDBP

[6p21.3]

RD RNA-binding protein, MHC complex gene RD

RNA binding, nucleotide binding, transcription, regulation of transcription

GTF2H

[2q14.3]

Basic transcription factor 2 89 kDa subunit, DNA excision repair protein ERCC-3

DNA binding, ATP-dependent DNA helicase activity, transcription-coupled nucleotide-excision repair, regulation of transcription

RRN3

[16p13.11]

RNA polymerase I-specific transcription initiation factor

RNA polymerase I transcription factor activity, regulation of transcription

ERCC4

[16p13.12]

DNA excision repair protein, DNA repair endonuclease

DNA binding, magnesium ion binding, nucleotide excision repair

TAF1A

[1q41]

TATA box binding protein (TBP)-associated factor, RNA polymerase I

DNA binding, RNA polymerase I transcription factor activity, regulation of transcription

TYW3

[1p31.1]

tRNA-yW synthesizing protein 3 homolog

None

GUF1

[4p13]

GTP-binding protein GUF1 homolog, GTPase of unknown function

Nucleotide binding, translation initiation factor activity, GTPase activity, small GTPase mediated activity

Module C

MOG

[6p22.1]

Myelin-oligodendrocyte glycoprotein precursor

Synaptic transmission, central nervous system development

APLP2

[11q24.3]

Amyloid-like protein 2 precursor (APPH)

DNA binding, protein binding, G-protein coupled receptor protein signaling pathway

NTRI

[11q25]

Neurotrimin precursor (hNT)

Protein binding, cell adhesion, neuron recognition

Module D

DDX52

[17q12]

Probable ATP-dependent RNA helicase DDX52 (DEAD box protein 52)

Nucleotide binding, ATP binding, ATP-dependent helicase activity

RPL23A

[17q11.2]

60S ribosomal protein L23a

Nucleotide binding, rRNA binding, translation

NPM1

[5q35.1]

Nucleophosmin (NPM) (Nucleolar phosphoprotein B23)

Transcription coactivator activity, RNA binding, intracellular protein transport, anti-apoptosis, response to stress

RPL26L1

[5q35.1]

60S ribosomal protein L26-like 1

Structural constituent of ribosome, translation

PRDX1

[1p34.1]

Natural killer cell-enhancing factor A, Peroxiredoxin-1

Oxidoreductase activity, peroxiredoxin, cell proliferation

RPS7

[2p25.3]

40S ribosomal protein S7

RNA binding, protein binding, translation

NGB

[14q24.3]

Neuroglobin

Oxygen transporter activity, metal ion binding

FLOT1

[6p21.33]

Flotillin 1, integral membrane component of caveolae

Protein binding

SESN1

[6q21]

Sestrin-1 (p53-regulated protein PA26)

Response to DNA damage stimulus, cell cycle arrest, negative regulation of cell proliferation

SESN2

[1p35.3]

Sestrin-2, hypoxia induced gene 95 (Hi95)

Cell cycle arrest


Genes corresponding to protein interactions in the four statistically significant functional modules A, B, C and D (in Figure 3). Gene names, chromosomal bands, short descriptions and gene ontology terms (molecular function and biological process) are provided.

Bergholdt et al. Genome Biology 2007 8:R253   doi:10.1186/gb-2007-8-11-r253

Open Data