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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 20:05, 8 August 2012


Full id: C4508_cervical_acute_gastric_medial_gall_bile_large



Phase1 CAGE Peaks

Hg19::chr5:58571396..58571416,-p2@uc003jsd.1
Hg19::chr5:58571425..58571440,-p3@uc003jsd.1
Hg19::chr5:58571461..58571474,-p4@uc003jsd.1


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
endothelial cell of vascular tree2.83e-0924
endothelial cell4.20e-0835
Uber Anatomy
Ontology termp-valuen
adult organism4.73e-35115
neural tube7.27e-1857
neural rod7.27e-1857
future spinal cord7.27e-1857
neural keel7.27e-1857
regional part of forebrain1.49e-1741
forebrain1.49e-1741
future forebrain1.49e-1741
anterior neural tube7.52e-1742
neocortex4.34e-1620
regional part of brain8.42e-1659
regional part of cerebral cortex1.38e-1522
telencephalon1.63e-1534
anatomical cluster1.83e-15286
gray matter3.56e-1534
brain grey matter3.56e-1534
neural plate3.63e-1586
presumptive neural plate3.63e-1586
cerebral hemisphere4.90e-1532
regional part of telencephalon1.11e-1433
neurectoderm9.80e-1490
brain1.10e-1369
future brain1.10e-1369
central nervous system7.06e-1382
cerebral cortex7.51e-1325
pallium7.51e-1325
organ part5.62e-12219
pre-chordal neural plate2.03e-1161
anatomical conduit2.57e-11241
larynx1.82e-109
regional part of nervous system7.82e-1094
nervous system7.82e-1094
tube3.94e-09194
multi-tissue structure2.05e-08347
organ3.37e-08511
large intestine8.43e-0811
anatomical system5.36e-07625
anatomical group6.57e-07626
gyrus7.64e-076
anterior region of body9.03e-07129
craniocervical region9.03e-07129


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)

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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.