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Coexpression cluster:C3265: Difference between revisions

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|id=C3265
|id=C3265
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:114!2.02e-10!2
|ontology_enrichment_uberon=UBERON:0007023!4.47e-44!115;UBERON:0001049!2.77e-21!57;UBERON:0005068!2.77e-21!57;UBERON:0006241!2.77e-21!57;UBERON:0007135!2.77e-21!57;UBERON:0001017!2.77e-21!82;UBERON:0005743!1.27e-20!86;UBERON:0000073!1.83e-20!94;UBERON:0001016!1.83e-20!94;UBERON:0002616!5.67e-20!59;UBERON:0003080!1.30e-17!42;UBERON:0003075!1.90e-17!86;UBERON:0007284!1.90e-17!86;UBERON:0000955!5.05e-17!69;UBERON:0006238!5.05e-17!69;UBERON:0002346!5.08e-17!90;UBERON:0002780!1.29e-16!41;UBERON:0001890!1.29e-16!41;UBERON:0006240!1.29e-16!41;UBERON:0002020!6.10e-15!34;UBERON:0003528!6.10e-15!34;UBERON:0001893!1.48e-14!34;UBERON:0001869!4.14e-14!32;UBERON:0002791!6.12e-14!33;UBERON:0002619!4.00e-13!22;UBERON:0003056!3.23e-11!61;UBERON:0000956!4.92e-11!25;UBERON:0000203!4.92e-11!25;UBERON:0001950!7.48e-11!20;UBERON:0004121!1.74e-09!169;UBERON:0000924!1.88e-09!173;UBERON:0006601!1.88e-09!173;UBERON:0000153!1.35e-08!129;UBERON:0007811!1.35e-08!129;UBERON:0000033!9.39e-08!123;UBERON:0000468!2.49e-07!659
|ontology_enrichment_uberon=UBERON:0007023!5.33e-40!114;UBERON:0001049!7.94e-21!56;UBERON:0005068!7.94e-21!56;UBERON:0006241!7.94e-21!56;UBERON:0007135!7.94e-21!56;UBERON:0000073!1.32e-19!53;UBERON:0002616!1.32e-19!53;UBERON:0003075!1.09e-18!82;UBERON:0007284!1.09e-18!82;UBERON:0002346!1.33e-17!86;UBERON:0003978!4.25e-15!3;UBERON:0009751!4.25e-15!3;UBERON:0000946!4.25e-15!3;UBERON:0002523!4.25e-15!3;UBERON:0005983!4.25e-15!3;UBERON:0002165!4.25e-15!3;UBERON:0002062!4.25e-15!3;UBERON:0007280!4.25e-15!3;UBERON:0010314!5.15e-15!132;UBERON:0001017!1.04e-14!81;UBERON:0000955!3.15e-14!68;UBERON:0006238!3.15e-14!68;UBERON:0010371!9.72e-14!104;UBERON:0001016!7.62e-13!89;UBERON:0002780!1.25e-12!41;UBERON:0001890!1.25e-12!41;UBERON:0003080!1.25e-12!41;UBERON:0006240!1.25e-12!41;UBERON:0004797!8.35e-11!7;UBERON:0003528!9.56e-11!34;UBERON:0002020!9.56e-11!34;UBERON:0002133!1.06e-10!2;UBERON:0002081!1.46e-10!2;UBERON:0010227!1.46e-10!2;UBERON:0000025!1.67e-10!192;UBERON:0003076!4.52e-10!15;UBERON:0003057!4.52e-10!15;UBERON:0007100!5.56e-10!27;UBERON:0002791!2.61e-09!32;UBERON:0001869!2.61e-09!32;UBERON:0004733!5.44e-09!12;UBERON:0002028!5.44e-09!12;UBERON:0007277!5.44e-09!12;UBERON:0004111!7.89e-09!240;UBERON:0001893!1.09e-08!34;UBERON:0002619!1.46e-08!22;UBERON:0004732!2.82e-08!13;UBERON:0002680!4.78e-08!9;UBERON:0001895!4.78e-08!9;UBERON:0010092!4.78e-08!9;UBERON:0003056!9.00e-08!61;UBERON:0000956!1.83e-07!25;UBERON:0000203!1.83e-07!25;UBERON:0004151!2.67e-07!3;UBERON:0004121!2.78e-07!171;UBERON:0000924!2.78e-07!171;UBERON:0006601!2.78e-07!171;UBERON:0003103!3.66e-07!68;UBERON:0000200!3.67e-07!6;UBERON:0001950!4.76e-07!20;UBERON:0002298!5.05e-07!6
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}}
}}

Revision as of 14:56, 19 October 2012


Full id: C3265_heart_umbilical_left_smooth_globus_Cardiac_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr12:2079855..2079865,+p12@CACNA1C
Hg19::chr1:237207955..237207959,+p@chr1:237207955..237207959
+
Hg19::chr6:129287144..129287148,+p@chr6:129287144..129287148
+


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
adult organism5.33e-40114
neural tube7.94e-2156
neural rod7.94e-2156
future spinal cord7.94e-2156
neural keel7.94e-2156
regional part of nervous system1.32e-1953
regional part of brain1.32e-1953
neural plate1.09e-1882
presumptive neural plate1.09e-1882
neurectoderm1.33e-1786
valve4.25e-153
cardiac mesenchyme4.25e-153
cardial valve4.25e-153
tunica intima4.25e-153
heart layer4.25e-153
endocardium4.25e-153
endocardial cushion4.25e-153
presumptive endocardium4.25e-153
structure with developmental contribution from neural crest5.15e-15132
central nervous system1.04e-1481
brain3.15e-1468
future brain3.15e-1468
ecto-epithelium9.72e-14104
nervous system7.62e-1389
regional part of forebrain1.25e-1241
forebrain1.25e-1241
anterior neural tube1.25e-1241
future forebrain1.25e-1241
blood vessel layer8.35e-117
brain grey matter9.56e-1134
gray matter9.56e-1134
atrioventricular valve1.06e-102
cardiac atrium1.46e-102
future cardiac atrium1.46e-102
tube1.67e-10192
posterior neural tube4.52e-1015
chordal neural plate4.52e-1015
primary circulatory organ5.56e-1027
regional part of telencephalon2.61e-0932
cerebral hemisphere2.61e-0932
segmental subdivision of hindbrain5.44e-0912
hindbrain5.44e-0912
presumptive hindbrain5.44e-0912
anatomical conduit7.89e-09240
telencephalon1.09e-0834
regional part of cerebral cortex1.46e-0822
segmental subdivision of nervous system2.82e-0813
regional part of metencephalon4.78e-089
metencephalon4.78e-089
future metencephalon4.78e-089
pre-chordal neural plate9.00e-0861
cerebral cortex1.83e-0725
pallium1.83e-0725
cardiac chamber2.67e-073
ectoderm-derived structure2.78e-07171
ectoderm2.78e-07171
presumptive ectoderm2.78e-07171
compound organ3.66e-0768
gyrus3.67e-076
neocortex4.76e-0720
brainstem5.05e-076
Disease
Ontology termp-valuen
heart disease2.02e-102


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.

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