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Table 2 Summary of 22 modules consisting of groups of heavily interconnected gene sets

From: Large-scale analysis of expression signatures reveals hidden links among diverse cellular processes

ID

#Sets

Cluster Density

Representitive GeneSet

Biological Theme

Most freqently shared genes between gene sets

Most significantly enriched GO Term

P values

1a

31

13.5

P21_P53_ANY_DN_49 (Sup. Figure 1)

Cell cycle, especially M phase

FOXM1,CCNB1,KIF2C,KIF11,CDC2,CCNB2,UBE2C,CDC20,MKI67,DLG7

Cell Cycle

2.80E-45

1b

29

12.8

DER_IFNB_UP_93 (Figure 3)

Immune response/interferon

MX2,MX1,OAS1,STAT1,OAS2,ISG15,IFITM1,IFIT3,IRF7,IFI27Response to virus

 

1.30E-19

2

15

3.7

IL1_CORNEA_UP_63

Inflammatory response/IL1

IL1B,CCL4,PLAUR,CXCL2,CCL5,TNFAIP3,CD44,IER3,NFKBIA,PLEK

Immune system process

1.00E-15

3

16

3.6

TNFA_NFKB_DEP_UP_18 (Figure 5)

Inflammatory response/TNFa related

GPNMB,CXCL1,SOD2,MMP9,CXCL5,CCL2,CHI3L1,CXCL3,CD9,IL1B

Immune system process

2.70E-20

4

14

3.1

GENOTOXINS_ALL_4HRS_REG_27 (Figure 4)

Cell cycle, DNA damage response

CKS2,ECT2,MAD2L1,BUB1,AURKA,CCNB2,CKS1B,PRC1,TRIP13,RRM2

Cell Cycle

3.10E-22

5

20

2.1

HOHENKIRK_MONOCYTE_DEND_DN_122

Inflammatory response/blood cells

STAT1,RAB2,CXCL3,HSPH1,SFRS3,S100A4,S100A8,TOP2A,ACTR1B,ANXA1

inflammatory response

7.40E-04

6

14

2.0

TGFBETA_ALL_UP_80

Cell adhesion, differentiation

IGFBP3,COL6A3,THBS2,CSPG2,SERPINE1,COL1A2,COL3A1,COL6A1,LOX,TIMP1

Cell adhesion

9.60E-07

7

6

2.0

ESR_FIBROBLAST_DN_18

cell differentiation

GNPNAT1,LCK,NDRG1,SOX7,TAF1C,TP53I11,ZNF507,CEPT1,GABBR1,HGF

--

 

8

35

2.0

HYPOXIA_REG_UP_38 (Figure 6)

Cell cycle arrest

POSTN,MTHFD1,MYC,TFRC,COL6A3,CSPG2,CTPS,SNRPA1,WEE1,ADORA2B

cell cycle arrest

8.30E-02

9

18

1.7

UVC_XPCS_4HR_DN_242

Down-regulated by UV, TNFa

ITGB5,AXL,ARL4C,RGS4,ACTA2,ARHGAP1,ARL6IP5,CAP2,COL1A2,CYFIP2

Signal Transduction

7.50E-04

10

7

1.7

SCHUMACHER_MYC_UP_54 ( Figure 2)

MYC target genes

NME1,HSPE1,HSPD1,LDHA,TFRC,APEX1,CDK4,EBNA1BP2,ENO1,FKBP4

Intracellular organelle lumen

1.80E-02

11

5

1.6

GNATENKO_PLATELET_UP_47

Platelet genes

PF4,PPBP,TMSB4X,GPX1,HIST2H2AA4,ACTB,B2M,CCL5,CD99,CFL1

*

 

12

7

1.6

ADIPOCYTE_PPARG_UP_16

Lipid metabolic process

ADIPOQ,AQP7,DGAT1,FASN,RETN,CIDEC,COX7B,NDUFS1,NR1H3,SCARB1

Lipid metabolic process

7.10E-04

13

27

1.6

CHANG_SERUM_RESPONSE_DN_194

 

SC4MOL,ACTB,HMGCS1,BAK1,ZYX,SCD,BAD,CTNNA1,FDPS,ITGB4

hemopoiesis

3.60E-03

14

4

1.5

CISPLATIN_PROBCELL_UP_17

 

ABI1,CDKN1A,EI24,LPIN1,TOB1,TP53INP1,TXNIP,ABLIM1,CARHSP1,H2AFJ

*

 

15

6

1.3

UVC_LOW_ALL_UP_19

Response to DNA damage, UV

BTG2,CDKN1A,GDF15,BTG1,DDB2,PLXNB2,FDXR,GPRC5A

*

 

16

7

1.3

FLECHNER_KIDNEY_TRANSPLANT_WELL_UP_565

 

RAB1A,ATP2A2,COL1A2,PGK1,RAB2,SPARC,WEE1,AGL,CFLAR,DNAJA1

*

 

17

5

1.2

CMV_HCMV_TIMECOURSE_ALL_UP_470

IL6 induced

MX1,IRF4,TNFSF10,CCNC,DNAJB9,GATM,GNA13,HBEGF,ICAM1,JUNB

Response to stimulus

4.80E-02

18

5

1.2

REN_E2F1_TARGETS_50

E2F1 target genes

PCNA,TOP2A,KIAA0101,POLA2,RFC4

*

 

19

6

1.2

STEMCELL_HEMATOPOIETIC_UP_1452

Stem cell enriched

ATP5D,BTBD14A,EEF1A1,GLUL,NTAN1,NUDCD2,PCGF2,ATP1A1,CD151,DYNC1H

*

 

20

4

1.0

ZHAN_MULTIPLE_MYELOMA_VS_NORMAL_DN_4

Leukemia related

ELA2,BLNK,BZRAP1,CD24,CD7,CEBPD,CST7,DNTT,HGF,KCNE1L

*

 

21

4

1.0

NADLER_OBESITY_DN_38

Obesity down, adipocyte up

PPA1,ACSL1,AGT,ALDH2,CFD,CRAT,FABP4,LDHB,PC,PPARG

*

 
  1. Cluster density is defined by dividing the number of significant overlaps (edges) by the number of gene sets within the sub-network.
  2. * Less than 20 genes.