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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3117_occipital_parietal_medial_pineal_thalamus_temporal_spinal
|full_id=C3117_occipital_parietal_medial_pineal_thalamus_temporal_spinal
|id=C3117
|id=C3117

Revision as of 15:59, 12 September 2012


Full id: C3117_occipital_parietal_medial_pineal_thalamus_temporal_spinal



Phase1 CAGE Peaks

Hg19::chr11:131240593..131240604,+p12@NTM
Hg19::chr3:123751366..123751377,+p@chr3:123751366..123751377
+
Hg19::chr5:138205824..138205832,-p@chr5:138205824..138205832
-


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>

Uber Anatomy
Ontology termp-valuen
neural tube7.02e-5657
neural rod7.02e-5657
future spinal cord7.02e-5657
neural keel7.02e-5657
central nervous system4.66e-5582
adult organism3.45e-53115
regional part of nervous system1.52e-5194
nervous system1.52e-5194
regional part of brain5.84e-4859
neural plate1.42e-4786
presumptive neural plate1.42e-4786
brain2.42e-4769
future brain2.42e-4769
neurectoderm4.09e-4690
regional part of forebrain2.10e-4541
forebrain2.10e-4541
future forebrain2.10e-4541
anterior neural tube5.14e-4442
gray matter2.43e-4134
brain grey matter2.43e-4134
telencephalon4.96e-4134
regional part of telencephalon1.20e-3933
cerebral hemisphere2.06e-3832
pre-chordal neural plate4.48e-3461
ectoderm-derived structure2.36e-31169
regional part of cerebral cortex4.51e-3122
ectoderm4.77e-31173
presumptive ectoderm4.77e-31173
cerebral cortex4.58e-2925
pallium4.58e-2925
neocortex2.61e-2820
anterior region of body2.76e-27129
craniocervical region2.76e-27129
head2.45e-26123
tube2.23e-15194
nucleus of brain1.14e-139
neural nucleus1.14e-139
basal ganglion1.40e-139
nuclear complex of neuraxis1.40e-139
aggregate regional part of brain1.40e-139
collection of basal ganglia1.40e-139
cerebral subcortex1.40e-139
posterior neural tube1.15e-1215
chordal neural plate1.15e-1215
anatomical conduit5.86e-11241
telencephalic nucleus7.26e-117
gyrus3.07e-106
segmental subdivision of nervous system3.63e-1013
epithelium7.28e-10309
temporal lobe8.25e-107
cell layer1.43e-09312
brainstem2.27e-098
anatomical cluster2.46e-09286
segmental subdivision of hindbrain5.32e-0912
hindbrain5.32e-0912
presumptive hindbrain5.32e-0912
organism subdivision5.75e-09365
occipital lobe6.54e-095
parietal lobe7.63e-095
organ part2.72e-08219
limbic system2.76e-085
embryo2.12e-07612
organ3.24e-07511
multi-cellular organism6.98e-07659


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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