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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1123_medial_middle_parietal_occipital_paracentral_frontal_cerebral
|full_id=C1123_medial_middle_parietal_occipital_paracentral_frontal_cerebral
|id=C1123
|id=C1123

Revision as of 13:35, 12 September 2012


Full id: C1123_medial_middle_parietal_occipital_paracentral_frontal_cerebral



Phase1 CAGE Peaks

Hg19::chr10:79383809..79383833,+p@chr10:79383809..79383833
+
Hg19::chr12:90987338..90987355,+p@chr12:90987338..90987355
+
Hg19::chr2:175757825..175757858,-p@chr2:175757825..175757858
-
Hg19::chr2:86707317..86707337,+p@chr2:86707317..86707337
+
Hg19::chr4:146071958..146071961,-p15@OTUD4
Hg19::chr8:27606125..27606134,-p6@CCDC25
Hg19::chr8:27606152..27606165,-p3@CCDC25


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
adult organism2.39e-49115
neural tube3.51e-4557
neural rod3.51e-4557
future spinal cord3.51e-4557
neural keel3.51e-4557
regional part of brain1.30e-3659
central nervous system7.52e-3682
brain1.42e-3569
future brain1.42e-3569
neural plate1.01e-3486
presumptive neural plate1.01e-3486
regional part of forebrain1.02e-3441
forebrain1.02e-3441
future forebrain1.02e-3441
neurectoderm7.61e-3490
anterior neural tube1.29e-3342
regional part of nervous system3.44e-3294
nervous system3.44e-3294
telencephalon5.21e-3134
gray matter7.69e-3134
brain grey matter7.69e-3134
regional part of telencephalon1.43e-2933
cerebral hemisphere1.34e-2832
regional part of cerebral cortex9.31e-2322
pre-chordal neural plate4.75e-2261
neocortex4.17e-2020
cerebral cortex2.49e-1925
pallium2.49e-1925
anterior region of body7.31e-18129
craniocervical region7.31e-18129
ectoderm-derived structure5.10e-17169
ectoderm5.69e-17173
presumptive ectoderm5.69e-17173
head7.00e-17123
basal ganglion8.95e-149
nuclear complex of neuraxis8.95e-149
aggregate regional part of brain8.95e-149
collection of basal ganglia8.95e-149
cerebral subcortex8.95e-149
nucleus of brain1.31e-139
neural nucleus1.31e-139
posterior neural tube2.30e-1215
chordal neural plate2.30e-1215
tube5.53e-12194
telencephalic nucleus3.60e-117
gyrus9.39e-116
anatomical conduit7.05e-09241
segmental subdivision of hindbrain7.59e-0912
hindbrain7.59e-0912
presumptive hindbrain7.59e-0912
brainstem7.92e-098
limbic system2.06e-085
segmental subdivision of nervous system5.39e-0813
temporal lobe2.53e-077
corpus striatum4.22e-074
striatum4.22e-074
ventral part of telencephalon4.22e-074
future corpus striatum4.22e-074
organism subdivision8.17e-07365
epithelium8.24e-07309


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.