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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1015_occipital_neuroectodermal_temporal_parietal_duodenum_brain_small
|full_id=C1015_occipital_neuroectodermal_temporal_parietal_duodenum_brain_small
|id=C1015
|id=C1015

Revision as of 13:25, 12 September 2012


Full id: C1015_occipital_neuroectodermal_temporal_parietal_duodenum_brain_small



Phase1 CAGE Peaks

Hg19::chr12:45269119..45269133,-p@chr12:45269119..45269133
-
Hg19::chr12:45269871..45269882,-p5@NELL2
Hg19::chr12:45269952..45269963,-p6@NELL2
Hg19::chr12:45269964..45269979,-p2@NELL2
Hg19::chr12:45269990..45270001,-p4@NELL2
Hg19::chr12:45270077..45270143,-p1@NELL2
Hg19::chr12:45270151..45270162,-p3@NELL2
Hg19::chr17:44091602..44091622,+p@chr17:44091602..44091622
+


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
mature alpha-beta T cell6.49e-1018
alpha-beta T cell6.49e-1018
immature T cell6.49e-1018
mature T cell6.49e-1018
immature alpha-beta T cell6.49e-1018
CD8-positive, alpha-beta T cell2.20e-0811
Uber Anatomy
Ontology termp-valuen
adult organism4.52e-39115
regional part of nervous system4.76e-3594
nervous system4.76e-3594
central nervous system8.33e-3282
neural tube7.92e-3157
neural rod7.92e-3157
future spinal cord7.92e-3157
neural keel7.92e-3157
neurectoderm4.07e-2990
neural plate5.63e-2786
presumptive neural plate5.63e-2786
regional part of brain7.14e-2759
regional part of forebrain1.62e-2541
forebrain1.62e-2541
future forebrain1.62e-2541
anterior neural tube2.11e-2542
brain2.44e-2569
future brain2.44e-2569
pre-chordal neural plate3.50e-2361
telencephalon6.98e-2234
gray matter1.14e-2134
brain grey matter1.14e-2134
cerebral hemisphere2.71e-2132
regional part of telencephalon3.66e-2133
ectoderm4.86e-21173
presumptive ectoderm4.86e-21173
ectoderm-derived structure2.45e-19169
anterior region of body7.65e-18129
craniocervical region7.65e-18129
regional part of cerebral cortex1.16e-1722
cerebral cortex1.84e-1725
pallium1.84e-1725
head1.09e-16123
neocortex2.99e-1620
temporal lobe5.95e-077
blood8.17e-0715
haemolymphatic fluid8.17e-0715
organism substance8.17e-0715
posterior neural tube8.79e-0715
chordal neural plate8.79e-0715


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTBP2#1488215.6792500848320.006675872541887170.0284046872159274



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.