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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4398_choriocarcinoma_pancreatic_gastric_synovial_small_astrocytoma_Fibroblast
|full_id=C4398_choriocarcinoma_pancreatic_gastric_synovial_small_astrocytoma_Fibroblast
|id=C4398
|id=C4398

Revision as of 17:27, 12 September 2012


Full id: C4398_choriocarcinoma_pancreatic_gastric_synovial_small_astrocytoma_Fibroblast



Phase1 CAGE Peaks

Hg19::chr4:183378727..183378731,+p@chr4:183378727..183378731
+
Hg19::chr4:183424089..183424094,+p@chr4:183424089..183424094
+
Hg19::chr4:183481247..183481253,+p@chr4:183481247..183481253
+


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
neural cell2.22e-0725
Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.22e-2694
nervous system3.22e-2694
central nervous system1.43e-2582
brain1.81e-2169
future brain1.81e-2169
neural tube3.14e-2157
neural rod3.14e-2157
future spinal cord3.14e-2157
neural keel3.14e-2157
neural plate4.18e-2086
presumptive neural plate4.18e-2086
regional part of brain2.08e-1959
neurectoderm1.47e-1890
ectoderm-derived structure6.22e-17169
ectoderm4.35e-16173
presumptive ectoderm4.35e-16173
anterior neural tube4.81e-1642
regional part of forebrain6.92e-1641
forebrain6.92e-1641
future forebrain6.92e-1641
gray matter2.75e-1334
brain grey matter2.75e-1334
pre-chordal neural plate2.85e-1361
anterior region of body5.10e-13129
craniocervical region5.10e-13129
cerebral hemisphere8.99e-1332
telencephalon1.12e-1234
head1.24e-12123
regional part of telencephalon2.32e-1233
adult organism3.06e-12115
regional part of cerebral cortex2.73e-1022
cerebral cortex5.30e-1025
pallium5.30e-1025
neocortex4.77e-0920
organ part7.92e-08219
organism subdivision2.07e-07365


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.