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Coexpression cluster:C3649: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.30e-41!115;UBERON:0002616!6.72e-17!59;UBERON:0005743!8.62e-16!86;UBERON:0001049!1.04e-15!57;UBERON:0005068!1.04e-15!57;UBERON:0006241!1.04e-15!57;UBERON:0007135!1.04e-15!57;UBERON:0000955!1.82e-14!69;UBERON:0006238!1.82e-14!69;UBERON:0003075!2.50e-14!86;UBERON:0007284!2.50e-14!86;UBERON:0001017!9.73e-14!82;UBERON:0000073!1.12e-13!94;UBERON:0001016!1.12e-13!94;UBERON:0002346!3.00e-13!90;UBERON:0003080!6.53e-12!42;UBERON:0002780!3.28e-11!41;UBERON:0001890!3.28e-11!41;UBERON:0006240!3.28e-11!41;UBERON:0000153!6.89e-11!129;UBERON:0007811!6.89e-11!129;UBERON:0000477!1.27e-10!286;UBERON:0000033!2.29e-10!123;UBERON:0000475!6.28e-10!365;UBERON:0004111!7.02e-10!241;UBERON:0003056!2.23e-09!61;UBERON:0000025!1.60e-08!194;UBERON:0002020!2.26e-08!34;UBERON:0003528!2.26e-08!34;UBERON:0001893!4.09e-08!34;UBERON:0002791!7.83e-08!33;UBERON:0004121!1.12e-07!169;UBERON:0000119!1.59e-07!312;UBERON:0000481!1.67e-07!347;UBERON:0001869!2.27e-07!32;UBERON:0000924!2.96e-07!173;UBERON:0006601!2.96e-07!173;UBERON:0000483!4.16e-07!309
|ontology_enrichment_uberon=UBERON:0007023!4.30e-41!115;UBERON:0002616!6.72e-17!59;UBERON:0005743!8.62e-16!86;UBERON:0001049!1.04e-15!57;UBERON:0005068!1.04e-15!57;UBERON:0006241!1.04e-15!57;UBERON:0007135!1.04e-15!57;UBERON:0000955!1.82e-14!69;UBERON:0006238!1.82e-14!69;UBERON:0003075!2.50e-14!86;UBERON:0007284!2.50e-14!86;UBERON:0001017!9.73e-14!82;UBERON:0000073!1.12e-13!94;UBERON:0001016!1.12e-13!94;UBERON:0002346!3.00e-13!90;UBERON:0003080!6.53e-12!42;UBERON:0002780!3.28e-11!41;UBERON:0001890!3.28e-11!41;UBERON:0006240!3.28e-11!41;UBERON:0000153!6.89e-11!129;UBERON:0007811!6.89e-11!129;UBERON:0000477!1.27e-10!286;UBERON:0000033!2.29e-10!123;UBERON:0000475!6.28e-10!365;UBERON:0004111!7.02e-10!241;UBERON:0003056!2.23e-09!61;UBERON:0000025!1.60e-08!194;UBERON:0002020!2.26e-08!34;UBERON:0003528!2.26e-08!34;UBERON:0001893!4.09e-08!34;UBERON:0002791!7.83e-08!33;UBERON:0004121!1.12e-07!169;UBERON:0000119!1.59e-07!312;UBERON:0000481!1.67e-07!347;UBERON:0001869!2.27e-07!32;UBERON:0000924!2.96e-07!173;UBERON:0006601!2.96e-07!173;UBERON:0000483!4.16e-07!309
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00109888958143083!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115134086367702!IRF4#3662;3:21.9145126867441:9.49854535978121e-05:0.00136510056258455!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156569817556798!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269351717021333!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308585249643564!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.0088147420841691
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}}
}}

Revision as of 12:38, 5 September 2012


Full id: C3649_vagina_Adipocyte_adipose_breast_skeletal_heart_Retinal



Phase1 CAGE Peaks

Hg19::chr17:46918991..46919002,+p14@CALCOCO2
Hg19::chr17:46919009..46919024,+p8@CALCOCO2
Hg19::chr17:46919030..46919058,+p2@CALCOCO2


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.30e-41115
regional part of brain6.72e-1759
neural tube1.04e-1557
neural rod1.04e-1557
future spinal cord1.04e-1557
neural keel1.04e-1557
brain1.82e-1469
future brain1.82e-1469
neural plate2.50e-1486
presumptive neural plate2.50e-1486
central nervous system9.73e-1482
regional part of nervous system1.12e-1394
nervous system1.12e-1394
neurectoderm3.00e-1390
anterior neural tube6.53e-1242
regional part of forebrain3.28e-1141
forebrain3.28e-1141
future forebrain3.28e-1141
anterior region of body6.89e-11129
craniocervical region6.89e-11129
anatomical cluster1.27e-10286
head2.29e-10123
organism subdivision6.28e-10365
anatomical conduit7.02e-10241
pre-chordal neural plate2.23e-0961
tube1.60e-08194
gray matter2.26e-0834
brain grey matter2.26e-0834
telencephalon4.09e-0834
regional part of telencephalon7.83e-0833
ectoderm-derived structure1.12e-07169
cell layer1.59e-07312
multi-tissue structure1.67e-07347
cerebral hemisphere2.27e-0732
ectoderm2.96e-07173
presumptive ectoderm2.96e-07173
epithelium4.16e-07309


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
BATF#10538324.35780179230366.91705216281876e-050.00109888958143083
CEBPB#105137.971147625824820.001974187055288560.0115134086367702
IRF4#3662321.91451268674419.49854535978121e-050.00136510056258455
JUND#372736.994663941871030.002921845042734990.0156569817556798
NFKB1#479035.488063424193840.006049381815655430.0269351717021333
NR3C1#2908314.9730233311730.0002978331194675480.00308585249643564
POU2F2#545239.106124057742520.001324165192682130.0088147420841691



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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