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Coexpression cluster:C2889: Difference between revisions

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|full_id=C2889_B_papillotubular_clear_small_Prostate_splenic_Intestinal
|full_id=C2889_B_papillotubular_clear_small_Prostate_splenic_Intestinal
|id=C2889
|id=C2889
|ontology_enrichment_celltype=CL:0002076!1.53e-12!43;CL:0000037!1.63e-12!172;CL:0000566!1.63e-12!172;CL:0002032!3.89e-12!165;CL:0000837!3.89e-12!165;CL:0000945!4.10e-12!24;CL:0000826!4.10e-12!24;CL:0000988!4.06e-10!182;CL:0002031!1.46e-07!124;CL:0000738!2.04e-07!140;CL:0002251!2.78e-07!21;CL:0000223!4.41e-07!59;CL:0000542!5.67e-07!53;CL:0000051!5.67e-07!53
|ontology_enrichment_celltype=CL:0002076!1.09e-13!42;CL:0000945!8.28e-11!24;CL:0000826!8.28e-11!24;CL:0002251!1.42e-08!20;CL:0000223!1.59e-07!58
|ontology_enrichment_disease=DOID:1749!3.21e-08!14;DOID:305!1.72e-07!106;DOID:2531!9.30e-07!51;DOID:0060083!9.30e-07!51
|ontology_enrichment_disease=DOID:1749!6.33e-09!14;DOID:305!7.79e-09!106;DOID:299!1.48e-07!25
|ontology_enrichment_uberon=UBERON:0004119!7.76e-09!169;UBERON:0000925!7.76e-09!169;UBERON:0006595!7.76e-09!169;UBERON:0001004!5.20e-08!72;UBERON:0001007!8.32e-08!155;UBERON:0001555!8.32e-08!155;UBERON:0007026!8.32e-08!155;UBERON:0004921!4.09e-07!129;UBERON:0004185!4.09e-07!129
|ontology_enrichment_uberon=UBERON:0004119!9.38e-12!160;UBERON:0000925!9.38e-12!160;UBERON:0006595!9.38e-12!160;UBERON:0001007!2.88e-10!145;UBERON:0001555!2.88e-10!145;UBERON:0007026!2.88e-10!145;UBERON:0004921!4.19e-09!118;UBERON:0000161!1.59e-07!36;UBERON:0001004!2.58e-07!74;UBERON:0005409!5.26e-07!25;UBERON:0005911!8.33e-07!82
|tf_chipseq_enrich=ATF3#467;4:22.4631745260087:3.92475754624726e-06:0.000127574775403834!BCLAF1#9774;4:21.6526476101218:4.54636978835329e-06:0.000141906250545675!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819878224743831!CTCFL#140690;4:19.7464743589744:6.5732084880439e-06:0.000193543648515031!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200062354529691!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161262000489708!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435365108674961!ESR1#2099;4:30.7686032961545:1.11467714392546e-06:4.61784078676838e-05!ETS1#2113;4:9.72876092220234:0.000111595531741814:0.00154821011418481!GATA3#2625;3:20.4273872679045:0.000192441557625832:0.00232109987722419!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186614173372105!IRF4#3662;4:21.9145126867441:4.33289161192893e-06:0.000136755172879494!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387205348066562!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00486561998820694!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00889948839584745!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00769366531914265!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444946611708821!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188797437215025!SIX5#147912;4:17.086715355459:1.17257016123224e-05:0.000297743873252938!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00685745668783697!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249899221913569!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323331774761399!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0245026977895133!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00120295793132312!WRNIP1#56897;4:109.819964349376:6.85077246696163e-09:5.3634769541005e-07!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107094582033722!ZEB1#6935;4:16.8884320175439:1.22862303393937e-05:0.000305296600146548!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000621978309152899
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}}
}}

Revision as of 14:32, 19 October 2012


Full id: C2889_B_papillotubular_clear_small_Prostate_splenic_Intestinal



Phase1 CAGE Peaks

Hg19::chr7:20256965..20257034,-p1@MACC1
Hg19::chr7:20257037..20257051,-p2@MACC1
Hg19::chr7:20257073..20257093,-p3@MACC1
Hg19::chr7:20257095..20257125,-p4@MACC1


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
endo-epithelial cell1.09e-1342
lymphocyte of B lineage8.28e-1124
pro-B cell8.28e-1124
epithelial cell of alimentary canal1.42e-0820
endodermal cell1.59e-0758
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.38e-12160
endoderm9.38e-12160
presumptive endoderm9.38e-12160
digestive system2.88e-10145
digestive tract2.88e-10145
primitive gut2.88e-10145
subdivision of digestive tract4.19e-09118
orifice1.59e-0736
respiratory system2.58e-0774
gastrointestinal system5.26e-0725
endo-epithelium8.33e-0782
Disease
Ontology termp-valuen
squamous cell carcinoma6.33e-0914
carcinoma7.79e-09106
adenocarcinoma1.48e-0725


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
ATF3#467422.46317452600873.92475754624726e-060.000127574775403834
BCLAF1#9774421.65264761012184.54636978835329e-060.000141906250545675
CTCF#1066445.360256373075030.001211145381643620.00819878224743831
CTCFL#140690419.74647435897446.5732084880439e-060.000193543648515031
EBF1#187948.9064668465690.00015887907472010.00200062354529691
ELF1#199744.258097958807540.003041525565781240.0161262000489708
EP300#203346.77394172622320.0004748459821442640.00435365108674961
ESR1#2099430.76860329615451.11467714392546e-064.61784078676838e-05
ETS1#211349.728760922202340.0001115955317418140.00154821011418481
GATA3#2625320.42738726790450.0001924415576258320.00232109987722419
HEY1#2346244.040111043105710.00375304636917980.0186614173372105
IRF4#3662421.91451268674414.33289161192893e-060.000136755172879494
JUND#372735.245997956403270.01043432751748420.0387205348066562
MAX#414946.452555509007120.0005767613195645490.00486561998820694
MYC#460945.22228187160940.001344309395272740.00889948839584745
NFKB1#479045.488063424193840.001102199566301980.00769366531914265
PAX5#507946.669565531177830.0005052774169483260.00444946611708821
POU2F2#545249.106124057742520.000145395665174930.00188797437215025
SIX5#147912417.0867153554591.17257016123224e-050.000297743873252938
SP1#666745.69838137814090.0009482606065333980.00685745668783697
SPI1#668848.204323508522730.000220661881527680.00249899221913569
TAF1#687243.343046285745290.008005664898701650.0323331774761399
TBP#690843.706770687096390.005296377814784350.0245026977895133
TCF12#6938410.63446490218647.8163066689251e-050.00120295793132312
WRNIP1#568974109.8199643493766.85077246696163e-095.3634769541005e-07
YY1#752844.911170749853860.00171871838055440.0107094582033722
ZEB1#6935416.88843201754391.22862303393937e-050.000305296600146548
ZNF143#7702413.50087655222793.00867915035614e-050.000621978309152899



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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