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Coexpression cluster:C2555: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512455008881676!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817652311011495!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193053802385494!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106535217431222!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997259063544288!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101486273198822!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160975973528924!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390440579253117!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186188680292024!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.0024819343394308!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485659723083141!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088814732371514!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.33868902406402e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768185655689104!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443415424122144!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000794317904121132!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444122775194969!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129466957890663!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796778707582424!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241684190985302!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438083927324156!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322446446724065!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244409863290148!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106909606281549!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249045316913467
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00512455008881676!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00817652311011495!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193053802385494!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106535217431222!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997259063544288!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101486273198822!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160975973528924!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390440579253117!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186188680292024!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.0024819343394308!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00485659723083141!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088814732371514!NANOG#79923;4:29.2447784810127:1.36586687657858e-06:5.33868902406402e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768185655689104!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443415424122144!NRF1#4899;4:12.2102794477109:4.49717228915276e-05:0.000794317904121132!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444122775194969!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129466957890663!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00796778707582424!SMARCB1#6598;4:18.2527157811574:9.00423392720929e-06:0.000241684190985302!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000438083927324156!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322446446724065!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244409863290148!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106909606281549!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249045316913467
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}}
}}

Revision as of 15:34, 26 November 2012


Full id: C2555_Mast_brain_Hepatic_thymus_optic_cervical_corpus



Phase1 CAGE Peaks

Hg19::chr1:204463845..204463857,-p3@PIK3C2B
Hg19::chr1:204463865..204463876,-p4@PIK3C2B
Hg19::chr1:204463880..204463915,-p2@PIK3C2B
Hg19::chr1:204463918..204463963,-p1@PIK3C2B


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
endothelial cell2.61e-0736
endothelial cell of vascular tree2.80e-0724
epithelial cell4.10e-07253
Uber Anatomy
Ontology termp-valuen
adult organism1.24e-30114
neural tube1.82e-1756
neural rod1.82e-1756
future spinal cord1.82e-1756
neural keel1.82e-1756
organ system subdivision1.28e-16223
regional part of nervous system4.74e-1653
regional part of brain4.74e-1653
regional part of forebrain4.81e-1441
forebrain4.81e-1441
anterior neural tube4.81e-1441
future forebrain4.81e-1441
central nervous system7.75e-1481
nervous system6.65e-1389
brain1.92e-1268
future brain1.92e-1268
brain grey matter2.56e-1234
gray matter2.56e-1234
telencephalon2.66e-1234
neurectoderm3.97e-1286
neural plate4.43e-1282
presumptive neural plate4.43e-1282
regional part of telencephalon2.85e-1132
cerebral hemisphere4.32e-1132
organ part7.98e-11218
anatomical cluster2.27e-10373
regional part of cerebral cortex3.39e-1022
neocortex1.43e-0920
subdivision of digestive tract3.25e-09118
pre-chordal neural plate8.70e-0961
cerebral cortex2.44e-0825
pallium2.44e-0825
anatomical conduit2.55e-08240
foregut1.55e-0787
tube2.06e-07192
Disease
Ontology termp-valuen
carcinoma8.91e-07106


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90546.336201576962630.0006203100587215640.00512455008881676
CTCF#1066445.360256373075030.001211145381643620.00817652311011495
CTCFL#140690419.74647435897446.5732084880439e-060.000193053802385494
E2F1#186944.907389214879320.001724022357361790.0106535217431222
E2F6#187645.017155731697390.00157802193473060.00997259063544288
EGR1#195844.988179094810140.001615011500076050.0101486273198822
ELF1#199744.258097958807540.003041525565781240.0160975973528924
GABPB1#255347.067683836182170.0004006876864423170.00390440579253117
HEY1#2346244.040111043105710.00375304636917980.0186188680292024
HMGN3#932448.178547723350590.0002234570284440470.0024819343394308
MAX#414946.452555509007120.0005767613195645490.00485659723083141
MYC#460945.22228187160940.001344309395272740.0088814732371514
NANOG#79923429.24477848101271.36586687657858e-065.33868902406402e-05
NFKB1#479045.488063424193840.001102199566301980.00768185655689104
NR3C1#2908414.9730233311731.98868032687801e-050.000443415424122144
NRF1#4899412.21027944771094.49717228915276e-050.000794317904121132
PAX5#507946.669565531177830.0005052774169483260.00444122775194969
RAD21#5885410.35503389545638.6948481184721e-050.00129466957890663
SIN3A#2594245.408884726815140.001168172384885160.00796778707582424
SMARCB1#6598418.25271578115749.00423392720929e-060.000241684190985302
SMC3#9126415.04493284493281.95092670935632e-050.000438083927324156
TAF1#687243.343046285745290.008005664898701650.0322446446724065
TBP#690843.706770687096390.005296377814784350.0244409863290148
YY1#752844.911170749853860.00171871838055440.0106909606281549
ZNF263#1012748.221841637010680.0002187871180958320.00249045316913467



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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