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Coexpression cluster:C2800: Difference between revisions

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|tf_chipseq_enrich=BCLAF1#9774;3:16.2394857075914:0.00038025670676648:0.00376718176797423!CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370379385623466!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240598335148832!EP300#2033;3:5.0804562946674:0.0114429840539824:0.041912527586935!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365993453844263!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387109065965164!NANOG#79923;3:21.9335838607595:0.000155753581638277:0.00196529519303129!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435174565543661!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227725548700598!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172735591080187!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195892196011959!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123880434878703!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140383483421481!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162872167123718!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158671294065947!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499639035567292!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483270036776274!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613515190168546!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279876934391191
|tf_chipseq_enrich=BCLAF1#9774;3:16.2394857075914:0.00038025670676648:0.00376718176797423!CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370379385623466!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240598335148832!EP300#2033;3:5.0804562946674:0.0114429840539824:0.041912527586935!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365993453844263!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0387109065965164!NANOG#79923;3:21.9335838607595:0.000155753581638277:0.00196529519303129!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435174565543661!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227725548700598!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172735591080187!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195892196011959!RFX5#5993;3:9.03593312039632:0.00214456119132407:0.0123880434878703!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140383483421481!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162872167123718!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158671294065947!TRIM28#10155;3:13.9428937839469:0.000597285818425842:0.00499639035567292!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483270036776274!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613515190168546!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279876934391191
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2800_pineal_teratocarcinoma_hepatoblastoma_optic_testicular_spinal_H9



Phase1 CAGE Peaks

Hg19::chr5:115808548..115808552,-p@chr5:115808548..115808552
-
Hg19::chr5:115910459..115910474,-p2@SEMA6A
Hg19::chr5:115910475..115910491,-p3@SEMA6A
Hg19::chr5:115910498..115910536,-p1@SEMA6A


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>

Cell Type
Ontology termp-valuen
melanocyte1.99e-0710
melanoblast1.99e-0710
Uber Anatomy
Ontology termp-valuen
adult organism3.54e-34114
central nervous system1.65e-3381
nervous system1.28e-3289
neural tube1.77e-3056
neural rod1.77e-3056
future spinal cord1.77e-3056
neural keel1.77e-3056
regional part of nervous system2.01e-2853
regional part of brain2.01e-2853
brain2.40e-2668
future brain2.40e-2668
neurectoderm2.93e-2586
organ system subdivision3.89e-25223
neural plate3.32e-2482
presumptive neural plate3.32e-2482
anatomical cluster3.82e-23373
regional part of forebrain1.06e-2241
forebrain1.06e-2241
anterior neural tube1.06e-2241
future forebrain1.06e-2241
ectoderm-derived structure2.07e-22171
ectoderm2.07e-22171
presumptive ectoderm2.07e-22171
ecto-epithelium2.60e-20104
brain grey matter1.28e-1934
gray matter1.28e-1934
telencephalon1.82e-1934
regional part of telencephalon2.47e-1832
cerebral hemisphere3.95e-1832
pre-chordal neural plate8.52e-1761
anatomical conduit2.84e-16240
structure with developmental contribution from neural crest5.79e-16132
tube4.05e-15192
cerebral cortex2.23e-1425
pallium2.23e-1425
multi-tissue structure9.62e-14342
regional part of cerebral cortex2.28e-1322
neocortex2.90e-1220
cell layer4.41e-12309
epithelium5.18e-12306
multi-cellular organism7.94e-11656
embryo3.22e-10592
posterior neural tube7.11e-0915
chordal neural plate7.11e-0915
organ part9.83e-09218
developing anatomical structure2.00e-08581
anatomical group7.71e-08625
organ1.01e-07503
anatomical system1.09e-07624
segmental subdivision of nervous system1.20e-0713
segmental subdivision of hindbrain5.92e-0712
hindbrain5.92e-0712
presumptive hindbrain5.92e-0712


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
BCLAF1#9774316.23948570759140.000380256706766480.00376718176797423
CTBP2#1488347.03775025449611.60047699357395e-050.000370379385623466
EBF1#187936.679850134926750.005184294118278910.0240598335148832
EP300#203335.08045629466740.01144298405398240.041912527586935
IRF4#3662316.43588451505810.0003669431395554610.00365993453844263
JUND#372735.245997956403270.01043432751748420.0387109065965164
NANOG#79923321.93358386075950.0001557535816382770.00196529519303129
PAX5#507935.002174148383370.01196533174786410.0435174565543661
POU2F2#545236.829593043306890.004860473775203740.0227725548700598
RAD21#588537.766275421592250.0033411193858720.0172735591080187
REST#597837.237521537096020.004104697304192610.0195892196011959
RFX5#599339.035933120396320.002144561191324070.0123880434878703
TAF7#687938.574802053692940.00250055433515240.0140383483421481
TCF12#693837.975848676639820.003090920396013070.0162872167123718
TCF7L2#693438.077632422353010.002978381685834620.0158671294065947
TRIM28#10155313.94289378394690.0005972858184258420.00499639035567292
USF1#739134.771124457905970.01370465887188020.0483270036776274
ZEB1#6935312.66632401315790.000793336075912850.00613515190168546
ZNF263#1012736.166381227758010.006539814347975980.0279876934391191



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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