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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2274_amygdala_argyrophil_liposarcoma_parietal_medial_brain_insula
|full_id=C2274_amygdala_argyrophil_liposarcoma_parietal_medial_brain_insula
|id=C2274
|id=C2274

Revision as of 14:58, 12 September 2012


Full id: C2274_amygdala_argyrophil_liposarcoma_parietal_medial_brain_insula



Phase1 CAGE Peaks

Hg19::chr13:96742352..96742378,+p@chr13:96742352..96742378
+
Hg19::chr13:96742396..96742407,+p@chr13:96742396..96742407
+
Hg19::chr13:97154628..97154630,+p@chr13:97154628..97154630
+
Hg19::chr13:97320979..97320984,+p@chr13:97320979..97320984
+


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
central nervous system8.29e-4182
neural tube2.06e-3857
neural rod2.06e-3857
future spinal cord2.06e-3857
neural keel2.06e-3857
regional part of nervous system1.55e-3794
nervous system1.55e-3794
regional part of forebrain6.19e-3541
forebrain6.19e-3541
future forebrain6.19e-3541
anterior neural tube1.09e-3342
adult organism1.91e-33115
gray matter6.24e-3334
brain grey matter6.24e-3334
telencephalon6.76e-3334
brain8.98e-3369
future brain8.98e-3369
regional part of brain2.45e-3259
regional part of telencephalon6.99e-3233
cerebral hemisphere1.58e-3132
neural plate4.89e-3086
presumptive neural plate4.89e-3086
neurectoderm7.47e-3090
cerebral cortex3.17e-2525
pallium3.17e-2525
regional part of cerebral cortex4.49e-2422
pre-chordal neural plate6.01e-2461
neocortex4.33e-2220
ectoderm4.04e-21173
presumptive ectoderm4.04e-21173
ectoderm-derived structure7.23e-21169
head1.06e-18123
anterior region of body1.25e-18129
craniocervical region1.25e-18129
tube2.59e-14194
epithelium1.31e-10309
anatomical conduit1.85e-10241
cell layer3.34e-10312
anatomical cluster1.92e-09286
basal ganglion2.20e-099
nuclear complex of neuraxis2.20e-099
aggregate regional part of brain2.20e-099
collection of basal ganglia2.20e-099
cerebral subcortex2.20e-099
temporal lobe2.31e-097
nucleus of brain4.35e-099
neural nucleus4.35e-099
organism subdivision5.93e-08365
multi-tissue structure6.35e-08347
gyrus1.48e-076
telencephalic nucleus2.53e-077


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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