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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3727_parietal_small_occipital_Dendritic_temporal_duodenum_CD19
|full_id=C3727_parietal_small_occipital_Dendritic_temporal_duodenum_CD19
|id=C3727
|id=C3727

Revision as of 16:41, 12 September 2012


Full id: C3727_parietal_small_occipital_Dendritic_temporal_duodenum_CD19



Phase1 CAGE Peaks

Hg19::chr18:52989646..52989657,-p@chr18:52989646..52989657
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Hg19::chr18:52993630..52993631,-p@chr18:52993630..52993631
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Hg19::chr18:53254566..53254567,-p8@TCF4


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><br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system8.85e-2994
nervous system8.85e-2994
central nervous system1.86e-2882
neural tube3.03e-2457
neural rod3.03e-2457
future spinal cord3.03e-2457
neural keel3.03e-2457
brain1.06e-2369
future brain1.06e-2369
regional part of brain9.16e-2259
adult organism1.57e-21115
regional part of forebrain1.80e-1941
forebrain1.80e-1941
future forebrain1.80e-1941
anterior neural tube3.24e-1942
gray matter4.08e-1734
brain grey matter4.08e-1734
telencephalon9.33e-1734
regional part of telencephalon1.89e-1633
neurectoderm3.20e-1690
cerebral hemisphere7.11e-1632
neural plate6.05e-1586
presumptive neural plate6.05e-1586
cerebral cortex2.75e-1325
pallium2.75e-1325
ectoderm3.95e-12173
presumptive ectoderm3.95e-12173
regional part of cerebral cortex6.82e-1222
pre-chordal neural plate2.21e-1161
ectoderm-derived structure3.96e-11169
neocortex1.00e-1020
head2.42e-10123
anterior region of body3.72e-10129
craniocervical region3.72e-10129


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.