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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C977_hippocampus_medulla_locus_heart_thalamus_parietal_occipital
|full_id=C977_hippocampus_medulla_locus_heart_thalamus_parietal_occipital
|id=C977
|id=C977

Revision as of 18:47, 12 September 2012


Full id: C977_hippocampus_medulla_locus_heart_thalamus_parietal_occipital



Phase1 CAGE Peaks

Hg19::chr10:30593748..30593775,-p@chr10:30593748..30593775
-
Hg19::chr14:102551297..102551343,-p2@HSP90AA1
Hg19::chr1:10436736..10436761,+p@chr1:10436736..10436761
+
Hg19::chr2:115488494..115488498,+p@chr2:115488494..115488498
+
Hg19::chr4:114180981..114181005,+p@chr4:114180981..114181005
+
Hg19::chr4:83551544..83551586,-p@chr4:83551544..83551586
-
Hg19::chr8:26486642..26486674,+p@chr8:26486642..26486674
+
Hg19::chr8:26486701..26486754,+p@chr8:26486701..26486754
+


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
neural tube2.68e-2857
neural rod2.68e-2857
future spinal cord2.68e-2857
neural keel2.68e-2857
central nervous system3.89e-2782
regional part of nervous system8.15e-2694
nervous system8.15e-2694
anterior neural tube9.19e-2542
regional part of forebrain2.91e-2441
forebrain2.91e-2441
future forebrain2.91e-2441
brain1.25e-2269
future brain1.25e-2269
regional part of brain2.48e-2159
gray matter3.62e-2034
brain grey matter3.62e-2034
telencephalon5.47e-2034
regional part of telencephalon1.91e-1933
cerebral hemisphere8.41e-1932
adult organism1.59e-18115
neurectoderm3.97e-1890
neural plate1.10e-1686
presumptive neural plate1.10e-1686
regional part of cerebral cortex7.90e-1522
cerebral cortex1.11e-1425
pallium1.11e-1425
neocortex1.77e-1320
pre-chordal neural plate2.59e-1361
ectoderm7.66e-13173
presumptive ectoderm7.66e-13173
ectoderm-derived structure9.74e-12169
head4.18e-09123
anterior region of body4.60e-09129
craniocervical region4.60e-09129
basal ganglion5.31e-079
nuclear complex of neuraxis5.31e-079
aggregate regional part of brain5.31e-079
collection of basal ganglia5.31e-079
cerebral subcortex5.31e-079
nucleus of brain5.56e-079
neural nucleus5.56e-079
Disease
Ontology termp-valuen
cancer2.43e-13235
disease of cellular proliferation4.44e-13239
cell type cancer2.05e-08143


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.