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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2315_occipital_parietal_temporal_duodenum_medial_brain_putamen
|full_id=C2315_occipital_parietal_temporal_duodenum_medial_brain_putamen
|id=C2315
|id=C2315

Revision as of 15:01, 12 September 2012


Full id: C2315_occipital_parietal_temporal_duodenum_medial_brain_putamen



Phase1 CAGE Peaks

Hg19::chr14:78640068..78640069,+p@chr14:78640068..78640069
+
Hg19::chr16:6069184..6069193,+p29@RBFOX1
Hg19::chr16:6550901..6550907,+p@chr16:6550901..6550907
+
Hg19::chr16:7217007..7217010,+p@chr16:7217007..7217010
+


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
neural tube7.58e-7257
neural rod7.58e-7257
future spinal cord7.58e-7257
neural keel7.58e-7257
central nervous system1.86e-6782
regional part of nervous system1.08e-6494
nervous system1.08e-6494
regional part of brain7.76e-6059
brain5.68e-5869
future brain5.68e-5869
neurectoderm2.12e-5590
regional part of forebrain1.52e-5441
forebrain1.52e-5441
future forebrain1.52e-5441
neural plate1.77e-5486
presumptive neural plate1.77e-5486
anterior neural tube5.54e-5342
gray matter8.31e-5034
brain grey matter8.31e-5034
telencephalon1.04e-4934
regional part of telencephalon5.42e-4833
cerebral hemisphere1.45e-4632
pre-chordal neural plate4.13e-4161
regional part of cerebral cortex1.71e-3922
adult organism5.87e-37115
neocortex8.47e-3620
ectoderm2.73e-35173
presumptive ectoderm2.73e-35173
cerebral cortex4.70e-3425
pallium4.70e-3425
ectoderm-derived structure4.72e-34169
head1.27e-32123
anterior region of body2.39e-30129
craniocervical region2.39e-30129
posterior neural tube4.47e-1915
chordal neural plate4.47e-1915
basal ganglion9.77e-189
nuclear complex of neuraxis9.77e-189
aggregate regional part of brain9.77e-189
collection of basal ganglia9.77e-189
cerebral subcortex9.77e-189
nucleus of brain3.37e-179
neural nucleus3.37e-179
segmental subdivision of nervous system5.34e-1613
tube4.89e-15194
segmental subdivision of hindbrain2.44e-1412
hindbrain2.44e-1412
presumptive hindbrain2.44e-1412
telencephalic nucleus5.68e-147
gyrus1.43e-126
temporal lobe1.43e-127
organ part1.55e-12219
brainstem3.84e-118
limbic system7.23e-115
parietal lobe1.03e-105
occipital lobe1.90e-105
anatomical conduit2.04e-10241
regional part of metencephalon1.03e-099
metencephalon1.03e-099
future metencephalon1.03e-099
corpus striatum4.55e-094
striatum4.55e-094
ventral part of telencephalon4.55e-094
future corpus striatum4.55e-094
epithelium1.27e-08309
anatomical cluster1.69e-08286
cell layer2.17e-08312
caudate-putamen2.80e-073
dorsal striatum2.80e-073
middle temporal gyrus3.22e-073


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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