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Coexpression cluster:C747: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;3:6.12632032527511:0.0111162339916476:0.0408820466882767!BCLAF1#9774;3:5.90526753003323:0.0122864557732326:0.0445303010306995!CHD2#1106;7:6.58255998534709:1.82852745688608e-05:0.000416055727820751!E2F1#1869;10:4.46126292261757:1.10540139252827e-06:4.58123079501033e-05!E2F4#1874;10:11.5164184684404:9.56616236582045e-11:1.03854514690636e-08!E2F6#1876;9:4.1049455986615:1.83835844928222e-05:0.000418201520550175!EBF1#1879;7:5.66775162963482:4.91015352587259e-05:0.000852129485025934!ELF1#1997;8:3.09679851549639:0.000758011352761729:0.00595770226302545!ETS1#2113;7:6.19102967776512:2.74425924207753e-05:0.000583722384894777!FOSL2#2355;4:6.15643658347698:0.00286737656398896:0.015536494991774!HDAC2#3066;6:7.31761103815978:5.69712326977083e-05:0.000950482199954626!HEY1#23462;10:3.67282822100519:7.3527784911531e-06:0.000211140179498911!HNF4A#3172;6:12.6176129252475:2.49318000901648e-06:8.78492668561648e-05!HNF4G#3174;3:7.84184250721276:0.00562367765123593:0.0254211941749234!IRF1#3659;5:3.47143806980177:0.00894716207586585:0.0339324809369364!IRF3#3661;3:12.8132596940426:0.00139865858349401:0.00909951434632351!MAX#4149;9:5.27936359827855:2.09889244785612e-06:7.65652212230686e-05!MXI1#4601;8:7.2447793663704:1.28440155682788e-06:5.13166083372406e-05!MYC#4609;9:4.27277607677133:1.30375226575527e-05:0.000318732637835241!NFYA#4800;6:10.0503167453621:9.29686132166058e-06:0.000247566267101711!NFYB#4801;7:10.6653229795232:7.15961572771292e-07:3.20369797337879e-05!NRF1#4899;4:4.44010161734942:0.00927703375725097:0.0350460872666402!PBX3#5090;5:9.96114213033824:7.24136591048148e-05:0.00113863446902255!POLR2A#5430;10:1.95223016050734:0.0030407318184143:0.0161342778226577!POU2F2#5452;8:6.6226356783582:2.56270583551105e-06:9.01166446986324e-05!SIN3A#25942;10:4.9171679334683:4.26535327044908e-07:2.04907649591735e-05!SP1#6667;10:5.18034670740082:2.55812246304286e-07:1.32919279561061e-05!TAF1#6872;10:3.03913298704117:4.59104772732301e-05:0.00080707697962277!TAF7#6879;6:6.23621967541304:0.000140196002821237:0.00182886964010082!TBP#6908;10:3.36979153372399:1.6942293653553e-05:0.000390001368058942!THAP1#55145;3:8.55522125532309:0.004407746242643:0.0208828075592176!USF1#7391;9:5.20486304498833:2.37429471822852e-06:8.41143032825877e-05!USF2#7392;6:7.08665311912887:6.8302134157013e-05:0.00109040149636568!ZNF143#7702;6:7.3641144830334:5.49636173278436e-05:0.000930514707424649
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}}
}}

Revision as of 14:26, 26 November 2012


Full id: C747_Mesenchymal_alveolar_Trabecular_Alveolar_carcinoid_Renal_chronic



Phase1 CAGE Peaks


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



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



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>


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



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
ATF3#46736.126320325275110.01111623399164760.0408820466882767
BCLAF1#977435.905267530033230.01228645577323260.0445303010306995
CHD2#110676.582559985347091.82852745688608e-050.000416055727820751
E2F1#1869104.461262922617571.10540139252827e-064.58123079501033e-05
E2F4#18741011.51641846844049.56616236582045e-111.03854514690636e-08
E2F6#187694.10494559866151.83835844928222e-050.000418201520550175
EBF1#187975.667751629634824.91015352587259e-050.000852129485025934
ELF1#199783.096798515496390.0007580113527617290.00595770226302545
ETS1#211376.191029677765122.74425924207753e-050.000583722384894777
FOSL2#235546.156436583476980.002867376563988960.015536494991774
HDAC2#306667.317611038159785.69712326977083e-050.000950482199954626
HEY1#23462103.672828221005197.3527784911531e-060.000211140179498911
HNF4A#3172612.61761292524752.49318000901648e-068.78492668561648e-05
HNF4G#317437.841842507212760.005623677651235930.0254211941749234
IRF1#365953.471438069801770.008947162075865850.0339324809369364
IRF3#3661312.81325969404260.001398658583494010.00909951434632351
MAX#414995.279363598278552.09889244785612e-067.65652212230686e-05
MXI1#460187.24477936637041.28440155682788e-065.13166083372406e-05
MYC#460994.272776076771331.30375226575527e-050.000318732637835241
NFYA#4800610.05031674536219.29686132166058e-060.000247566267101711
NFYB#4801710.66532297952327.15961572771292e-073.20369797337879e-05
NRF1#489944.440101617349420.009277033757250970.0350460872666402
PBX3#509059.961142130338247.24136591048148e-050.00113863446902255
POLR2A#5430101.952230160507340.00304073181841430.0161342778226577
POU2F2#545286.62263567835822.56270583551105e-069.01166446986324e-05
SIN3A#25942104.91716793346834.26535327044908e-072.04907649591735e-05
SP1#6667105.180346707400822.55812246304286e-071.32919279561061e-05
TAF1#6872103.039132987041174.59104772732301e-050.00080707697962277
TAF7#687966.236219675413040.0001401960028212370.00182886964010082
TBP#6908103.369791533723991.6942293653553e-050.000390001368058942
THAP1#5514538.555221255323090.0044077462426430.0208828075592176
USF1#739195.204863044988332.37429471822852e-068.41143032825877e-05
USF2#739267.086653119128876.8302134157013e-050.00109040149636568
ZNF143#770267.36411448303345.49636173278436e-050.000930514707424649



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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