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Coexpression cluster:C3359: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324182569770465!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321107668769033!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319612384935117!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000674893058692587!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293652343214155
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324182569770465!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321107668769033!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319612384935117!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000674893058692587!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293652343214155
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}}
}}

Revision as of 16:05, 26 November 2012


Full id: C3359_Dendritic_Neural_signet_corpus_caudate_optic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr13:24734844..24734873,+p4@SPATA13
Hg19::chr13:24734880..24734918,+p2@SPATA13
Hg19::chr13:24734939..24734950,+p8@SPATA13


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 organism1.82e-27114
central nervous system1.16e-2581
neural tube3.86e-2556
neural rod3.86e-2556
future spinal cord3.86e-2556
neural keel3.86e-2556
regional part of nervous system2.32e-2353
regional part of brain2.32e-2353
nervous system1.15e-2189
organ system subdivision3.42e-21223
brain5.33e-2068
future brain5.33e-2068
neural plate8.05e-1982
presumptive neural plate8.05e-1982
regional part of forebrain3.31e-1841
forebrain3.31e-1841
anterior neural tube3.31e-1841
future forebrain3.31e-1841
neurectoderm4.22e-1886
brain grey matter4.04e-1734
gray matter4.04e-1734
telencephalon5.31e-1734
regional part of telencephalon5.45e-1632
cerebral hemisphere9.33e-1632
anatomical cluster1.48e-15373
structure with developmental contribution from neural crest2.72e-15132
pre-chordal neural plate1.09e-1261
anatomical conduit2.24e-12240
ectoderm-derived structure3.37e-12171
ectoderm3.37e-12171
presumptive ectoderm3.37e-12171
tube6.49e-12192
ecto-epithelium9.23e-12104
cerebral cortex1.02e-1125
pallium1.02e-1125
regional part of cerebral cortex3.46e-1022
neocortex3.63e-0920
multi-tissue structure4.25e-09342
posterior neural tube3.91e-0815
chordal neural plate3.91e-0815
epithelium1.94e-07306
cell layer2.46e-07309
organ part2.60e-07218
neural nucleus4.79e-079
nucleus of brain4.79e-079
segmental subdivision of nervous system5.02e-0713


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
E2F1#186934.907389214879320.008460985347239390.0324182569770465
E2F6#187635.017155731697390.00791769806886330.0321107668769033
EGR1#195834.988179094810140.008056488137383440.0319612384935117
ESR1#2099330.76860329615453.43136389821584e-050.000674893058692587
MYC#460935.22228187160940.007020843755740150.0293652343214155



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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