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Coexpression cluster:C928: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;5:3.52011198720146:0.00704556022641387:0.0293967985492565!CEBPB#1051;5:4.42841534768045:0.0025225868523706:0.0139876001207716!CHD2#1106;5:5.74667935228714:0.000761042370922:0.00597657750031752!CTBP2#1488;6:41.8113335595521:1.31796279068549e-09:1.1876334417291e-07!E2F6#1876;8:4.45969398373101:1.843503537119e-05:0.000419098097329498!EBF1#1879;5:4.94803713698278:0.00152000342508516:0.00968977828923088!GTF2B#2959;7:24.84520106003:9.99944740019878e-10:9.2829536624832e-08!HEY1#23462;6:2.69340736207047:0.00948764347376227:0.0357447421361516!HMGN3#9324;5:4.54363762408366:0.00224461831902441:0.012891866070204!MAX#4149;5:3.58475306055951:0.00650226248509667:0.0278441015080984!MXI1#4601;5:5.53420646042183:0.00090661270204698:0.00660244920082871!PBX3#5090;5:12.1747292704134:2.1331797509613e-05:0.000470213507831675!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728788320845237!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356679907829407!SIN3A#25942;8:4.80789753494679:1.02597602607548e-05:0.000268013782359423!SMARCC1#6599;7:33.9603905819356:1.13716814408286e-10:1.22564193807915e-08!TAF1#6872;8:2.97159669844026:0.000423374995123481:0.00395960070884761!TBP#6908;8:3.29490727741901:0.000191885322027247:0.00231572811962141!TCF7L2#6934;5:5.98343142396519:0.000630515439732144:0.00518466278326001!TFAP2C#7022;4:4.80410160438232:0.00629930343474712:0.0277873353362711!YY1#7528;6:3.2741138332359:0.00337595890254982:0.0172428487785309!ZNF263#10127;5:4.56768979833926:0.00219130580900913:0.0126336068113224
|tf_chipseq_enrich=CCNT2#905;5:3.52011198720146:0.00704556022641387:0.0293967985492565!CEBPB#1051;5:4.42841534768045:0.0025225868523706:0.0139876001207716!CHD2#1106;5:5.74667935228714:0.000761042370922:0.00597657750031752!CTBP2#1488;6:41.8113335595521:1.31796279068549e-09:1.1876334417291e-07!E2F6#1876;8:4.45969398373101:1.843503537119e-05:0.000419098097329498!EBF1#1879;5:4.94803713698278:0.00152000342508516:0.00968977828923088!GTF2B#2959;7:24.84520106003:9.99944740019878e-10:9.2829536624832e-08!HEY1#23462;6:2.69340736207047:0.00948764347376227:0.0357447421361516!HMGN3#9324;5:4.54363762408366:0.00224461831902441:0.012891866070204!MAX#4149;5:3.58475306055951:0.00650226248509667:0.0278441015080984!MXI1#4601;5:5.53420646042183:0.00090661270204698:0.00660244920082871!PBX3#5090;5:12.1747292704134:2.1331797509613e-05:0.000470213507831675!POLR2A#5430;9:2.14745317655807:0.00102941289260802:0.00728788320845237!REST#5978;4:4.28890165161245:0.00945702594596283:0.0356679907829407!SIN3A#25942;8:4.80789753494679:1.02597602607548e-05:0.000268013782359423!SMARCC1#6599;7:33.9603905819356:1.13716814408286e-10:1.22564193807915e-08!TAF1#6872;8:2.97159669844026:0.000423374995123481:0.00395960070884761!TBP#6908;8:3.29490727741901:0.000191885322027247:0.00231572811962141!TCF7L2#6934;5:5.98343142396519:0.000630515439732144:0.00518466278326001!TFAP2C#7022;4:4.80410160438232:0.00629930343474712:0.0277873353362711!YY1#7528;6:3.2741138332359:0.00337595890254982:0.0172428487785309!ZNF263#10127;5:4.56768979833926:0.00219130580900913:0.0126336068113224
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}}
}}

Revision as of 14:34, 26 November 2012


Full id: C928_Retinal_Cardiac_mesothelioma_Renal_Meningeal_Smooth_Astrocyte



Phase1 CAGE Peaks

Hg19::chr1:12677510..12677525,-p3@DHRS3
Hg19::chr1:12677714..12677729,-p4@DHRS3
Hg19::chr1:12677781..12677800,-p2@DHRS3
Hg19::chr1:12678119..12678130,-p14@DHRS3
Hg19::chr1:12678194..12678203,-p13@DHRS3
Hg19::chr1:12678204..12678238,-p1@DHRS3
Hg19::chr1:12678241..12678252,-p11@DHRS3
Hg19::chr1:12678258..12678280,-p8@DHRS3
Hg19::chr1:12679956..12679993,-p@chr1:12679956..12679993
-


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><br>

Uber Anatomy
Ontology termp-valuen
epithelial tube1.27e-19117
mesenchyme2.57e-19160
entire embryonic mesenchyme2.57e-19160
trunk8.73e-19199
anatomical conduit1.61e-18240
trunk mesenchyme3.11e-18122
organism subdivision1.50e-17264
epithelium1.83e-17306
cell layer2.10e-17309
anatomical cluster2.74e-17373
multi-tissue structure5.43e-16342
tube6.05e-15192
unilaminar epithelium1.08e-14148
muscle tissue1.31e-1364
musculature1.31e-1364
musculature of body1.31e-1364
skeletal muscle tissue2.49e-1362
striated muscle tissue2.49e-1362
myotome2.49e-1362
artery2.08e-1142
arterial blood vessel2.08e-1142
arterial system2.08e-1142
epithelial tube open at both ends4.49e-1159
blood vessel4.49e-1159
blood vasculature4.49e-1159
vascular cord4.49e-1159
vasculature4.57e-1178
vascular system4.57e-1178
epithelial vesicle5.14e-1178
multi-cellular organism2.07e-10656
vessel2.38e-1068
splanchnic layer of lateral plate mesoderm6.14e-1083
systemic artery1.41e-0933
systemic arterial system1.41e-0933
somite2.80e-0971
presomitic mesoderm2.80e-0971
presumptive segmental plate2.80e-0971
dermomyotome2.80e-0971
trunk paraxial mesoderm2.80e-0971
paraxial mesoderm3.36e-0972
presumptive paraxial mesoderm3.36e-0972
dense mesenchyme tissue5.16e-0973
circulatory system6.95e-09112
cardiovascular system1.35e-08109
compound organ1.48e-0868
intermediate mesoderm1.95e-0828
multilaminar epithelium3.52e-0883
anatomical system3.97e-08624
anatomical group6.67e-08625
subdivision of trunk2.00e-07112
pigment epithelium of eye3.11e-0711
abdominal segment of trunk6.86e-0760
abdomen6.86e-0760


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#90553.520111987201460.007045560226413870.0293967985492565
CEBPB#105154.428415347680450.00252258685237060.0139876001207716
CHD2#110655.746679352287140.0007610423709220.00597657750031752
CTBP2#1488641.81133355955211.31796279068549e-091.1876334417291e-07
E2F6#187684.459693983731011.843503537119e-050.000419098097329498
EBF1#187954.948037136982780.001520003425085160.00968977828923088
GTF2B#2959724.845201060039.99944740019878e-109.2829536624832e-08
HEY1#2346262.693407362070470.009487643473762270.0357447421361516
HMGN3#932454.543637624083660.002244618319024410.012891866070204
MAX#414953.584753060559510.006502262485096670.0278441015080984
MXI1#460155.534206460421830.000906612702046980.00660244920082871
PBX3#5090512.17472927041342.1331797509613e-050.000470213507831675
POLR2A#543092.147453176558070.001029412892608020.00728788320845237
REST#597844.288901651612450.009457025945962830.0356679907829407
SIN3A#2594284.807897534946791.02597602607548e-050.000268013782359423
SMARCC1#6599733.96039058193561.13716814408286e-101.22564193807915e-08
TAF1#687282.971596698440260.0004233749951234810.00395960070884761
TBP#690883.294907277419010.0001918853220272470.00231572811962141
TCF7L2#693455.983431423965190.0006305154397321440.00518466278326001
TFAP2C#702244.804101604382320.006299303434747120.0277873353362711
YY1#752863.27411383323590.003375958902549820.0172428487785309
ZNF263#1012754.567689798339260.002191305809009130.0126336068113224



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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