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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2240_anaplastic_cerebellum_occipital_insula_medial_frontal_postcentral
|full_id=C2240_anaplastic_cerebellum_occipital_insula_medial_frontal_postcentral
|id=C2240
|id=C2240

Revision as of 14:56, 12 September 2012


Full id: C2240_anaplastic_cerebellum_occipital_insula_medial_frontal_postcentral



Phase1 CAGE Peaks

Hg19::chr12:72665340..72665355,+p@chr12:72665340..72665355
+
Hg19::chr12:72665366..72665378,+p@chr12:72665366..72665378
+
Hg19::chr12:72665423..72665456,+p@chr12:72665423..72665456
+
Hg19::chr3:56809721..56809764,-p8@ARHGEF3


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 tube9.34e-4157
neural rod9.34e-4157
future spinal cord9.34e-4157
neural keel9.34e-4157
regional part of nervous system7.17e-3994
nervous system7.17e-3994
central nervous system1.17e-3582
regional part of brain2.91e-3559
neurectoderm7.60e-3590
neural plate4.62e-3386
presumptive neural plate4.62e-3386
regional part of forebrain1.60e-3241
forebrain1.60e-3241
future forebrain1.60e-3241
adult organism2.17e-32115
brain2.66e-3269
future brain2.66e-3269
anterior neural tube2.33e-3142
telencephalon4.39e-2734
pre-chordal neural plate4.69e-2761
gray matter1.09e-2634
brain grey matter1.09e-2634
regional part of telencephalon4.71e-2633
cerebral hemisphere6.69e-2632
regional part of cerebral cortex9.75e-2022
cerebral cortex1.50e-1925
pallium1.50e-1925
ectoderm8.66e-19173
presumptive ectoderm8.66e-19173
head5.53e-18123
anterior region of body7.09e-18129
craniocervical region7.09e-18129
neocortex7.75e-1820
ectoderm-derived structure2.05e-17169
organism subdivision1.54e-10365
posterior neural tube2.39e-1015
chordal neural plate2.39e-1015
tube3.59e-09194
basal ganglion4.40e-099
nuclear complex of neuraxis4.40e-099
aggregate regional part of brain4.40e-099
collection of basal ganglia4.40e-099
cerebral subcortex4.40e-099
segmental subdivision of hindbrain1.18e-0812
hindbrain1.18e-0812
presumptive hindbrain1.18e-0812
nucleus of brain1.42e-089
neural nucleus1.42e-089
gyrus8.46e-086
segmental subdivision of nervous system1.02e-0713
organ part1.69e-07219
anatomical conduit2.64e-07241
telencephalic nucleus3.22e-077
temporal lobe4.13e-077
multi-tissue structure4.79e-07347
diencephalon8.30e-077
future diencephalon8.30e-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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