Table 2 Signaling pathway impact analysis of RAG-1−/− brain

From: CD4+ but not CD8+ T cells revert the impaired emotional behavior of immunocompromised RAG-1-deficient mice

Name

ID

pSize

NDE

pNDE

tA

pPERT

pG

pGFdr

pGFWER

Status

KEGGLINK

Parkinson’s disease

5012

117

62

4.21E−19

4.097

0.2

3.78E−18

4.73E−16

4.73E−-16

Activated

http://www.genome.jp/dbget-bin/show_pathway? mmu05012+66725+22202+22195+57320+68943+13063+104130+17991+17992+17993+225887+226646+227197+230075+407785+54405+595136+66046+66108+66218+66495+67130+67184+67264+67273+68198+68349+69875+72900+66925+66945+66152+66576+66594+66694+67003+67530+110323+12858+12859+12865+12866+12868+12869+20463+66142+75483+11949+11950+11957+228033+28080+67126+67942+71679+11739+11740+22334+22335+140499+67128+214084

Huntington’s disease

5016

172

77

9.54E−18

−0.372

0.797

3.07E−16

1.92E−14

3.84E−14

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu05016+104130+17991+17992+17993+225887+226646+227197+230075+407785+54405+595136+66046+66108+66218+66495+67130+67184+67264+67273+68198+68349+69875+72900+66925+66945+66152+66576+66594+66694+67003+67530+110323+12858+12859+12865+12866+12868+12869+20463+66142+75483+11949+11950+11957+228033+28080+67126+67942+71679+15194+15182+433759+12914+328572+20020+20022+231329+66420+67710+69241+69920+14810+14812+108071+18798+16438+11739+11740+22334+22335+13063+72504+21780+12757+381917+68922+12913

Alzheimer’s disease

5010

164

70

5.83E−15

−1.6765

0.558

1.12E−13

4.66E−12

1.40E−11

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu05010+66340+11487+13063+104130+17991+17992+17993+225887+226646+227197+230075+407785+54405+595136+66046+66108+66218+66495+67130+67184+67264+67273+68198+68349+69875+72900+66925+66945+66152+66576+66594+66694+67003+67530+11949+11950+11957+228033+28080+67126+67942+71679+110323+12858+12859+12865+12866+12868+12869+20463+66142+75483+20192+16438+16439+18798+14810+14811+14812+12288+12289+15108+14102+18125+78943+11816+19059+16971+14433+234664

ECM–receptor interaction

4512

84

28

0.000175059

−13.7865

5.00E−06

1.91E−08

5.98E−07

2.39E−06

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu04512+16772+16774+16775+16776+16779+226519+23928+12814+12825+12826+12827+12830+12833+12835+12842+12843+245026+81877+22371+20750+14268+21825+15529+20971+15530+16400+19699+11603

RNA transport

3013

161

56

2.67E−08

0.7715

0.271

1.43E−07

3.57E−06

1.79E−05

Activated

http://www.genome.jp/dbget-bin/show_pathway?mmu03013+433702+68092+56698+53975+69731+237221+20901+66069+60365+192170+56215+56009+237082+71805+114671+408191+72124+69912+54563+77595+107939+227720+20610+22218+13627+97112+66235+68969+53356+54709+56347+68135+78655+70047+102614+117109+208366+227522+54364+66161+67053+69961+386612+66231+26905+67204+218693+13681+13682+218268+230861+217869+108067+13667+209354+69482

Small-cell lung cancer

5222

86

22

0.026137813

−20.07421825

5.00E−06

2.20E−06

4.59E−05

0.000275271

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu05222+16400+56469+218772+17187+19211+30955+13063+12826+12827+12830+14268+16772+16774+16775+16776+16779+226519+23928+11797+19225+12567+12571

Olfactory transduction

4740

989

40

1

−23.1386

5.00E−06

6.60E−05

0.001179114

0.008253795

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu04740+100038860+18345+18369+235256+257884+257939+258027+258228+258247+258266+258278+258286+258407+258421+258446+258482+258483+258502+258533+258541+258570+258620+258648+258656+258677+258683+258712+258743+258922+258972+259006+259103+259105+404335+404336+56015+56860+57272+333329+19092

Focal adhesion

4510

199

41

0.095748092

−20.21166302

0.001

0.000981781

0.01486948

0.122722602

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu04510+16400+192176+286940+67268+67938+19211+30955+21894+70549+12814+12825+12826+12827+12830+12833+12835+12842+12843+14268+16772+16774+16775+16776+16779+19699+20750+21825+22371+226519+23928+245026+81877+12389+12390+11797+12445+16001+18596+107746+109905+57257

Calcium signaling pathway

4020

179

47

0.000966948

−5.8395

0.109

0.001070603

0.01486948

0.133825321

Inhibited

http://www.genome.jp/dbget-bin/show_pathway?mmu04020+320404+432530+18125+22334+22335+110891+20541+19059+12494+13869+18596+14810+14811+18438+228139+18803+18802+16438+16439+102093+18679+18682+68961+20190+20191+20192+18798+12288+12289+12286+12287+12290+108071+11550+12669+21338+21390+243764+26361+21924+11739+11740+11515+12291+239556+58226+11941

  1. Abbreviations: ECM, extracellular matrix; pG, global P-values, obtained by combining the pPERT and pNDE using Fisher’s method; pGFdr, global P-values after fdf correction; pGFWER, global P-value adjusted by the Bonferroni’s method; pNDE, P-value by the number of differentially expressed genes (classical test for the enrichment of genes in a certain pathway); pPERT, P-value by perturbation (calculated based on the amount of perturbation measured in each pathway).
  2. Microarray data of RAG-1−/− and wild-type brains were analyzed by a moderate t-statistics and fold change, and subsequently analyzed for the pathway enrichment with a bootstrap technique using the Bioconductor package, SPIA. Significantly modulated pathways were selected by a global pathway significance P-value with considering false discovery rate (P<0.05), which combines the enrichment and perturbation P-values.
  3. The analysis was perfomed by SPIA (Bioconductor package).
Back to article page