Table 4

Pathways

CFinder

module ID

Protein IDs

Pathways


High

Int-2

-

na

Int-3

-

na

Int-4

-

na

Int-7

POLR3G POLR3A POLR3 H POLR1A

ZNRD1 POLR1D

POLR2C POLR2E POLR2 H POLR2L

POLR1B POLR3GL POLR1C

hsa03020 RNA polymerase

Lit-2

-

na

Lit-5

POLR2A POLR2C POLR2 D POLR2E

POLR2G POLR2 H POLR2L

hsa03020 RNA polymerase

Lit-9

LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 LSM7

LSM1 LSM2 LSM3 LSM4 LSM5 LSM6 LSM7

hsa03018 RNA degradation

hsa03040 Spliceosome

Lit-11

SKIV2L2 EXOSC2 EXOSC4 EXOSC5

EXOSC6 EXOSC7 EXOSC8 EXOSC9

hsa03018 RNA degradation

Ortho-8

POLR3G POLR3A POLR3 H POLR1A

ZNRD1 POLR1 D POLR2E POLR2F

POLR2 H POLR2L POLR1B POLR3GL POLR1C

hsa03020 RNA polymerase

Ortho-12

PSMA1 PSMA2 PSMA4

PSMA6 PSMA7 PSMB1

PSMB2 PSMB3 PSMB5

hsa03050 Proteasome


Medium

Int-18

PSMA1 PSMB2 PSMC2 PSMC3

PSMD11 PSMD12 PSMD13 PSMD6

hsa03050 Proteasome

Ortho-18

PSMA1 PSMB2 PSMC2 PSMC3

PSMD11 PSMD12 PSMD13 PSMD6

hsa03050 Proteasome


Low

Int-13

TAF1 TAF2 TAF4 TAF5

TAF6 TAF7 TAF9 TAF10

TAF12 TAF13 TBP

hsa03022 Basal transcription factors

Lit-4

MYC RUVBL1

hsa04310 Wnt signaling pathway

Lit-14

TAF1 TAF2 TAF4

TAF5 TAF6 TAF7

TAF9 TAF10 TAF12

hsa03022 Basal transcription factors

Ortho-7

EXOSC2 EXOSC3 EXOSC4 EXOSC5

hsa03018 RNA degradation


MCODE

module ID

Protein IDs

Pathways


High

Int-5

-

na

Lit-4

-

na

Ortho-4

DDX6 LSM1 LSM2

hsa03018 RNA degradation

Ortho-5

RPL3 RPL12 RPL27A RPS2

hsa03010 Ribosome


Low

Lit-11

-.

na

Lit-13

TAF1 TAF2 TAF4 TAF5

TAF6 TAF7 TAF9 TAF10

TAF12 HDAC1 HDAC2

hsa03022 Basal transcription factors

hsa04110 Cell cycle

Ortho-2

TAF9B TAF5 TAF6 TAF12

hsa03022 Basal transcription factors

Ortho-10

PPP1CA PPP1CB

hsa04720 Long-term potentiation

hsa03018 RNA degradation

hsa04810 Regulation of actin cytoskeleton

hsa04910 Insulin signaling pathway

hsa04510 Focal adhesion


Pathways results for CFinder and MCODE High, Medium and Low confidence modules (KEGG source [55], na: not annotated). See also: Figure 9-12.

Marras et al. BMC Systems Biology 2010 4:102   doi:10.1186/1752-0509-4-102

Open Data