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Coexpression cluster:C778: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C778_thalamus_substantia_optic_spinal_globus_hippocampus_corpus
|full_id=C778_thalamus_substantia_optic_spinal_globus_hippocampus_corpus
|id=C778
|id=C778

Revision as of 18:30, 12 September 2012


Full id: C778_thalamus_substantia_optic_spinal_globus_hippocampus_corpus



Phase1 CAGE Peaks

Hg19::chr10:104846929..104846933,+p@chr10:104846929..104846933
+
Hg19::chr14:45603433..45603463,-p@chr14:45603433..45603463
-
Hg19::chr16:15489814..15489859,+p2@MPV17L
Hg19::chr19:36705547..36705597,-p1@ZNF565
Hg19::chr19:53636125..53636178,-p1@ZNF415
Hg19::chr1:92545866..92545917,+p1@BTBD8
Hg19::chr2:230786032..230786119,-p4@TRIP12
Hg19::chr2:3522634..3522680,-p@chr2:3522634..3522680
-
Hg19::chr3:37217852..37217899,+p@chr3:37217852..37217899
+
Hg19::chr8:102195406..102195412,-p1@BC035156


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 organism2.11e-47115
regional part of nervous system2.11e-3294
nervous system2.11e-3294
central nervous system6.62e-3282
neural tube4.99e-3157
neural rod4.99e-3157
future spinal cord4.99e-3157
neural keel4.99e-3157
brain3.04e-2869
future brain3.04e-2869
regional part of brain1.74e-2759
anterior neural tube7.53e-2642
regional part of forebrain1.63e-2541
forebrain1.63e-2541
future forebrain1.63e-2541
neurectoderm5.92e-2590
neural plate1.25e-2386
presumptive neural plate1.25e-2386
anterior region of body4.50e-23129
craniocervical region4.50e-23129
ectoderm2.09e-22173
presumptive ectoderm2.09e-22173
head1.24e-21123
gray matter2.95e-2134
brain grey matter2.95e-2134
ectoderm-derived structure3.60e-21169
telencephalon3.66e-2134
regional part of telencephalon1.36e-2033
cerebral hemisphere8.00e-2032
pre-chordal neural plate1.40e-1761
cerebral cortex1.72e-1525
pallium1.72e-1525
regional part of cerebral cortex3.91e-1522
neocortex8.14e-1420
nucleus of brain3.00e-079
neural nucleus3.00e-079
basal ganglion3.50e-079
nuclear complex of neuraxis3.50e-079
aggregate regional part of brain3.50e-079
collection of basal ganglia3.50e-079
cerebral subcortex3.50e-079
organism subdivision7.63e-07365


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CHD2#110644.137609133646740.01136509692198320.0416608528108877
GABPB1#255353.533841918091090.007669373268468170.0315856963912436
HEY1#2346272.8280777301740.003295391007019310.0170472703641631
IRF1#365953.818581876781950.005465628575453730.0247560405408887
NRF1#489944.884111779084360.00630934732180550.0278257643233835
TAF1#687282.674437028596230.001556617278062390.00988397081125715



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.