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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2753_parietal_acute_occipital_temporal_small_duodenum_gastric
|full_id=C2753_parietal_acute_occipital_temporal_small_duodenum_gastric
|id=C2753
|id=C2753

Revision as of 15:32, 12 September 2012


Full id: C2753_parietal_acute_occipital_temporal_small_duodenum_gastric



Phase1 CAGE Peaks

Hg19::chr3:77088920..77088929,+p19@ROBO2
Hg19::chr3:77088946..77088957,+p11@ROBO2
Hg19::chr3:77088958..77088982,+p2@ROBO2
Hg19::chr3:77245493..77245496,+p@chr3:77245493..77245496
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
neuronal stem cell4.20e-088
neurectodermal cell5.16e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system1.48e-3482
ectoderm1.26e-33173
presumptive ectoderm1.26e-33173
regional part of nervous system1.29e-3394
nervous system1.29e-3394
ectoderm-derived structure1.10e-30169
neurectoderm6.43e-2990
neural tube1.09e-2857
neural rod1.09e-2857
future spinal cord1.09e-2857
neural keel1.09e-2857
neural plate9.94e-2686
presumptive neural plate9.94e-2686
brain4.74e-2569
future brain4.74e-2569
regional part of brain7.53e-2559
regional part of forebrain3.58e-2441
forebrain3.58e-2441
future forebrain3.58e-2441
anterior neural tube3.00e-2342
anterior region of body1.09e-22129
craniocervical region1.09e-22129
telencephalon1.81e-2234
gray matter2.37e-2234
brain grey matter2.37e-2234
head3.59e-22123
regional part of telencephalon8.40e-2233
cerebral hemisphere1.18e-2132
adult organism5.28e-20115
pre-chordal neural plate7.12e-2061
cerebral cortex1.51e-1625
pallium1.51e-1625
regional part of cerebral cortex2.41e-1522
neocortex3.44e-1420
organ part1.10e-09219
organism subdivision4.07e-09365
basal ganglion6.94e-089
nuclear complex of neuraxis6.94e-089
aggregate regional part of brain6.94e-089
collection of basal ganglia6.94e-089
cerebral subcortex6.94e-089
embryo2.00e-07612
temporal lobe2.74e-077
nucleus of brain2.89e-079
neural nucleus2.89e-079
organ3.72e-07511
posterior neural tube9.78e-0715
chordal neural plate9.78e-0715
Disease
Ontology termp-valuen
neuroectodermal tumor1.39e-0810


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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