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Table 3 GSEA tests for enrichment of MSigDB C2 gene sets

From: Gene set enrichment analysis of microarray data from Pimephales promelas (Rafinesque), a non-mammalian model organism

  

Gene Set Name

Size

ES

NES

NOM p-value

FDR q-value

Acute exposure

Down-regulated

None

     
 

Up-regulated

XU_CBP_UP

19

0.633

1.987

0.000

0.051

  

CALRES_MOUSE_DN

28

0.575

1.920

0.000

0.108

  

BYSTRYKH_HSC_CIS_GLOCUS

82

0.516

1.889

0.000

0.097

  

BYSTRYKH_HSC_BRAIN_CIS_GLOCUS

43

0.600

1.855

0.000

0.102

  

PENG_GLUTAMINE_DN

209

0.519

1.828

0.000

0.130

  

UVC_LOW_ALL_DN

38

0.473

1.817

0.000

0.121

  

CMV_ALL_UP

64

0.530

1.764

0.000

0.214

  

SANSOM_APC_LOSS5_UP

55

0.544

1.734

0.037

0.274

  

BLEO_MOUSE_LYMPH_HIGH_24HRS_DN

31

0.669

1.730

0.000

0.255

  

SHEPARD_CRASH_AND_BURN_MUT_VS_WT_UP

124

0.452

1.710

0.000

0.289

  

PENG_RAPAMYCIN_DN

163

0.516

1.706

0.023

0.275

  

PRMT5_KD_DN

19

0.572

1.694

0.038

0.298

  

HSA00970_AMINOACYL_TRNA_BIOSYNTHESIS

29

0.702

1.690

0.029

0.286

  

MRNA_SPLICING

44

0.633

1.689

0.000

0.266

  

WANG_MLL_CBP_VS_GMP_DN

30

0.579

1.688

0.000

0.254

  

JAIN_NEMO_DIFF

59

0.458

1.688

0.000

0.240

  

HSA00563_GLYCOSYLPHOSPHATIDYLINOSITOL_ANCHOR_BIOSYNTHESIS

16

0.616

1.684

0.000

0.239

  

BLEO_MOUSE_LYMPH_LOW_24HRS_DN

22

0.697

1.681

0.000

0.238

  

OLDONLY_FIBRO_UP

28

0.485

1.674

0.000

0.243

  

CMV_24HRS_UP

54

0.524

1.673

0.000

0.232

  

KUROKAWA_5FU_IFN_SENSITIVE_VS_RESISTANT_DN

22

0.624

1.669

0.000

0.232

  

CHANG_SERUM_RESPONSE_UP

109

0.480

1.668

0.000

0.224

  

ROS_MOUSE_AORTA_UP

21

0.731

1.656

0.036

0.237

  

UVB_NHEK2_DN

64

0.456

1.649

0.000

0.242

  

SCHUMACHER_MYC_UP

44

0.504

1.649

0.023

0.234

  

STEMCELL_COMMON_UP

149

0.458

1.643

0.023

0.242

  

MYC_ONCOGENIC_SIGNATURE

137

0.406

1.641

0.000

0.239

  

ZHAN_MMPC_SIM_BC_AND_MM

36

0.472

1.635

0.000

0.242

  

AMINOACYL_TRNA_BIOSYNTHESIS

21

0.732

1.633

0.048

0.238

Chronic exposure

Down-regulated

TNFR1PATHWAY

24

-0.724

-1.968

0.000

0.026

  

CASPASEPATHWAY

16

-0.684

-1.865

0.000

0.049

  

DEATHPATHWAY

25

-0.719

-1.836

0.000

0.063

  

HIVNEFPATHWAY

44

-0.593

-1.765

0.000

0.104

  

MITOCHONDRIAPATHWAY

17

-0.785

-1.728

0.000

0.151

  

TSA_PANC50_UP

25

-0.584

-1.684

0.000

0.216

 

Up-regulated

None

     
  1. Results for MSigDB C2 gene sets (drawn from 1892 sets representing all systems, pathways and functions in that database), listing sets with NES scores that are both statistically significant and below the FDR threshold. Size refers to the number of genes in the set; ES and NES are the enrichment scores and normalized enrichment scores (respectively) for the set; NOM p-value is the nominal p-value for the NES, FDR q-vlaue is the false discovery rate ratio (values lower than 0.25 are considered to be passing as per Subramanian et al. [4]). One of these sets (in bold) is a liver associated set highlighted in Table 4.
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BMC Genomics

ISSN: 1471-2164

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