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Coexpression cluster:C1687: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!6.14e-08!14
|ontology_enrichment_disease=DOID:2394!6.14e-08!14
|ontology_enrichment_uberon=UBERON:0000914!1.11e-21!83;UBERON:0002329!1.11e-21!83;UBERON:0003077!1.11e-21!83;UBERON:0003059!1.11e-21!83;UBERON:0007282!1.11e-21!83;UBERON:0009618!1.11e-21!83;UBERON:0007285!1.11e-21!83;UBERON:0004290!8.23e-20!70;UBERON:0005256!1.06e-19!143;UBERON:0000486!1.59e-19!82;UBERON:0000490!1.11e-18!138;UBERON:0002049!3.31e-18!79;UBERON:0007798!3.31e-18!79;UBERON:0002100!4.07e-18!216;UBERON:0001134!3.44e-17!61;UBERON:0002036!3.44e-17!61;UBERON:0003082!3.44e-17!61;UBERON:0000055!1.27e-16!69;UBERON:0002385!2.19e-16!63;UBERON:0001015!2.19e-16!63;UBERON:0000383!2.19e-16!63;UBERON:0001981!9.91e-16!60;UBERON:0007500!9.91e-16!60;UBERON:0004537!9.91e-16!60;UBERON:0006965!9.91e-16!60;UBERON:0004872!1.09e-15!84;UBERON:0000475!2.83e-15!365;UBERON:0003914!1.23e-14!118;UBERON:0001637!3.59e-14!42;UBERON:0003509!3.59e-14!42;UBERON:0004572!3.59e-14!42;UBERON:0003104!4.42e-13!238;UBERON:0009142!4.42e-13!238;UBERON:0004535!2.80e-12!110;UBERON:0004573!4.85e-12!33;UBERON:0004571!4.85e-12!33;UBERON:0000119!1.82e-11!312;UBERON:0003102!1.95e-11!95;UBERON:0002199!2.26e-11!45;UBERON:0002416!2.26e-11!45;UBERON:0001009!2.73e-11!113;UBERON:0000483!5.96e-11!309;UBERON:0002097!9.36e-11!40;UBERON:0000468!5.50e-10!659;UBERON:0000467!3.81e-09!625;UBERON:0000480!5.94e-09!626;UBERON:0000481!1.05e-08!347;UBERON:0000947!2.48e-08!21;UBERON:0010191!2.48e-08!21;UBERON:0000926!1.06e-07!448;UBERON:0004120!1.06e-07!448;UBERON:0006603!1.06e-07!448
|ontology_enrichment_uberon=UBERON:0000914!1.11e-21!83;UBERON:0002329!1.11e-21!83;UBERON:0003077!1.11e-21!83;UBERON:0003059!1.11e-21!83;UBERON:0007282!1.11e-21!83;UBERON:0009618!1.11e-21!83;UBERON:0007285!1.11e-21!83;UBERON:0004290!8.23e-20!70;UBERON:0005256!1.06e-19!143;UBERON:0000486!1.59e-19!82;UBERON:0000490!1.11e-18!138;UBERON:0002049!3.31e-18!79;UBERON:0007798!3.31e-18!79;UBERON:0002100!4.07e-18!216;UBERON:0001134!3.44e-17!61;UBERON:0002036!3.44e-17!61;UBERON:0003082!3.44e-17!61;UBERON:0000055!1.27e-16!69;UBERON:0002385!2.19e-16!63;UBERON:0001015!2.19e-16!63;UBERON:0000383!2.19e-16!63;UBERON:0001981!9.91e-16!60;UBERON:0007500!9.91e-16!60;UBERON:0004537!9.91e-16!60;UBERON:0006965!9.91e-16!60;UBERON:0004872!1.09e-15!84;UBERON:0000475!2.83e-15!365;UBERON:0003914!1.23e-14!118;UBERON:0001637!3.59e-14!42;UBERON:0003509!3.59e-14!42;UBERON:0004572!3.59e-14!42;UBERON:0003104!4.42e-13!238;UBERON:0009142!4.42e-13!238;UBERON:0004535!2.80e-12!110;UBERON:0004573!4.85e-12!33;UBERON:0004571!4.85e-12!33;UBERON:0000119!1.82e-11!312;UBERON:0003102!1.95e-11!95;UBERON:0002199!2.26e-11!45;UBERON:0002416!2.26e-11!45;UBERON:0001009!2.73e-11!113;UBERON:0000483!5.96e-11!309;UBERON:0002097!9.36e-11!40;UBERON:0000468!5.50e-10!659;UBERON:0000467!3.81e-09!625;UBERON:0000480!5.94e-09!626;UBERON:0000481!1.05e-08!347;UBERON:0000947!2.48e-08!21;UBERON:0010191!2.48e-08!21;UBERON:0000926!1.06e-07!448;UBERON:0004120!1.06e-07!448;UBERON:0006603!1.06e-07!448
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}}
}}

Revision as of 17:32, 8 August 2012


Full id: C1687_liposarcoma_basal_Preadipocyte_Fibroblast_mesenchymal_Smooth_leiomyoma



Phase1 CAGE Peaks

Hg19::chr12:78333942..78333956,+p4@NAV3
Hg19::chr12:78334017..78334054,+p2@NAV3
Hg19::chr12:78334061..78334110,+p1@NAV3
Hg19::chr12:78334115..78334165,+p3@NAV3
Hg19::chr12:78334166..78334180,+p6@NAV3


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>


Uber Anatomy
Ontology termp-valuen
somite1.11e-2183
paraxial mesoderm1.11e-2183
presomitic mesoderm1.11e-2183
presumptive segmental plate1.11e-2183
trunk paraxial mesoderm1.11e-2183
presumptive paraxial mesoderm1.11e-2183
dermomyotome8.23e-2070
trunk mesenchyme1.06e-19143
multilaminar epithelium1.59e-1982
unilaminar epithelium1.11e-18138
vasculature3.31e-1879
vascular system3.31e-1879
trunk4.07e-18216
skeletal muscle tissue3.44e-1761
striated muscle tissue3.44e-1761
myotome3.44e-1761
vessel1.27e-1669
muscle tissue2.19e-1663
musculature2.19e-1663
musculature of body2.19e-1663
blood vessel9.91e-1660
epithelial tube open at both ends9.91e-1660
blood vasculature9.91e-1660
vascular cord9.91e-1660
splanchnic layer of lateral plate mesoderm1.09e-1584
organism subdivision2.83e-15365
epithelial tube1.23e-14118
artery3.59e-1442
arterial blood vessel3.59e-1442
arterial system3.59e-1442
mesenchyme4.42e-13238
entire embryonic mesenchyme4.42e-13238
cardiovascular system2.80e-12110
systemic artery4.85e-1233
systemic arterial system4.85e-1233
cell layer1.82e-11312
surface structure1.95e-1195
integument2.26e-1145
integumental system2.26e-1145
circulatory system2.73e-11113
epithelium5.96e-11309
skin of body9.36e-1140
multi-cellular organism5.50e-10659
anatomical system3.81e-09625
anatomical group5.94e-09626
multi-tissue structure1.05e-08347
aorta2.48e-0821
aortic system2.48e-0821
mesoderm1.06e-07448
mesoderm-derived structure1.06e-07448
presumptive mesoderm1.06e-07448
Disease
Ontology termp-valuen
ovarian cancer6.14e-0814


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


No analysis results for this cluster

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.