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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4361_heart_Neural_mature_skin_spinal_hippocampus_caudate
|full_id=C4361_heart_Neural_mature_skin_spinal_hippocampus_caudate
|id=C4361
|id=C4361

Revision as of 17:25, 12 September 2012


Full id: C4361_heart_Neural_mature_skin_spinal_hippocampus_caudate



Phase1 CAGE Peaks

Hg19::chr4:114214481..114214493,+p17@ANK2
Hg19::chr4:114214538..114214547,+p16@ANK2
Hg19::chr4:114214566..114214602,+p3@ANK2


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
non-terminally differentiated cell2.15e-08180
fat cell6.04e-0715
Uber Anatomy
Ontology termp-valuen
adult organism1.33e-52115
neural tube1.05e-3757
neural rod1.05e-3757
future spinal cord1.05e-3757
neural keel1.05e-3757
central nervous system3.03e-3482
regional part of brain7.02e-3259
anterior neural tube8.92e-2942
regional part of nervous system2.15e-2894
nervous system2.15e-2894
regional part of forebrain3.79e-2841
forebrain3.79e-2841
future forebrain3.79e-2841
brain1.28e-2669
future brain1.28e-2669
neural plate1.62e-2686
presumptive neural plate1.62e-2686
gray matter5.55e-2534
brain grey matter5.55e-2534
telencephalon1.47e-2434
neurectoderm4.42e-2490
regional part of telencephalon5.49e-2433
cerebral hemisphere5.42e-2332
cerebral cortex1.01e-1725
pallium1.01e-1725
anterior region of body1.28e-16129
craniocervical region1.28e-16129
regional part of cerebral cortex2.33e-1622
pre-chordal neural plate2.76e-1661
ectoderm-derived structure3.79e-16169
head1.20e-15123
organism subdivision1.62e-15365
ectoderm4.94e-15173
presumptive ectoderm4.94e-15173
neocortex1.10e-1420
multi-cellular organism4.15e-13659
tube1.12e-12194
multi-tissue structure2.71e-12347
anatomical cluster5.19e-12286
anatomical conduit9.51e-12241
epithelium2.62e-10309
organ2.74e-10511
posterior neural tube6.51e-1015
chordal neural plate6.51e-1015
anatomical system7.21e-10625
cell layer7.62e-10312
anatomical group9.70e-10626
organ part5.56e-09219
nucleus of brain9.10e-099
neural nucleus9.10e-099
basal ganglion1.19e-089
nuclear complex of neuraxis1.19e-089
aggregate regional part of brain1.19e-089
collection of basal ganglia1.19e-089
cerebral subcortex1.19e-089
primary circulatory organ7.14e-0827
segmental subdivision of nervous system7.79e-0813
brainstem7.92e-088
embryo1.18e-07612
segmental subdivision of hindbrain1.89e-0712
hindbrain1.89e-0712
presumptive hindbrain1.89e-0712
tissue2.08e-07787
telencephalic nucleus4.72e-077
temporal lobe5.08e-077
heart6.90e-0724
primitive heart tube6.90e-0724
primary heart field6.90e-0724
anterior lateral plate mesoderm6.90e-0724
heart tube6.90e-0724
heart primordium6.90e-0724
cardiac mesoderm6.90e-0724
cardiogenic plate6.90e-0724
heart rudiment6.90e-0724


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.