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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1846_pancreas_anaplastic_duodenum_temporal_spinal_gall_locus
|full_id=C1846_pancreas_anaplastic_duodenum_temporal_spinal_gall_locus
|id=C1846
|id=C1846

Revision as of 14:28, 12 September 2012


Full id: C1846_pancreas_anaplastic_duodenum_temporal_spinal_gall_locus



Phase1 CAGE Peaks

Hg19::chr1:208216610..208216649,-p@chr1:208216610..208216649
-
Hg19::chr4:72052474..72052490,+p@chr4:72052474..72052490
+
Hg19::chr4:72052624..72052640,+p7@SLC4A4
Hg19::chr4:72133815..72133816,+p@chr4:72133815..72133816
+
Hg19::chr4:72338539..72338551,+p@chr4:72338539..72338551
+


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 cell2.24e-07180
Uber Anatomy
Ontology termp-valuen
adult organism1.39e-36115
neural tube1.17e-2957
neural rod1.17e-2957
future spinal cord1.17e-2957
neural keel1.17e-2957
regional part of brain8.31e-2759
central nervous system2.31e-2682
neural plate5.30e-2686
presumptive neural plate5.30e-2686
regional part of nervous system1.65e-2494
nervous system1.65e-2494
neurectoderm4.20e-2390
brain6.45e-2369
future brain6.45e-2369
anterior neural tube1.28e-2242
regional part of forebrain2.72e-2241
forebrain2.72e-2241
future forebrain2.72e-2241
pre-chordal neural plate5.37e-1961
gray matter7.12e-1934
brain grey matter7.12e-1934
telencephalon1.45e-1834
regional part of telencephalon4.60e-1833
cerebral hemisphere1.35e-1732
organism subdivision3.09e-16365
multi-tissue structure3.44e-16347
regional part of cerebral cortex1.17e-1422
anterior region of body3.51e-14129
craniocervical region3.51e-14129
head7.96e-14123
tube8.25e-14194
cerebral cortex2.25e-1325
pallium2.25e-1325
neocortex2.27e-1320
epithelium3.29e-12309
cell layer3.82e-12312
anatomical cluster2.51e-11286
ectoderm-derived structure3.44e-11169
anatomical conduit8.76e-11241
ectoderm4.41e-10173
presumptive ectoderm4.41e-10173
posterior neural tube3.67e-0815
chordal neural plate3.67e-0815
multi-cellular organism2.96e-07659
organ3.31e-07511
basal ganglion4.67e-079
nuclear complex of neuraxis4.67e-079
aggregate regional part of brain4.67e-079
collection of basal ganglia4.67e-079
cerebral subcortex4.67e-079
nucleus of brain4.77e-079
neural nucleus4.77e-079


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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