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Coexpression cluster:C2679: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2679_optic_pons_pituitary_ductus_seminal_paracentral_parietal
|full_id=C2679_optic_pons_pituitary_ductus_seminal_paracentral_parietal
|id=C2679
|id=C2679

Revision as of 15:26, 12 September 2012


Full id: C2679_optic_pons_pituitary_ductus_seminal_paracentral_parietal



Phase1 CAGE Peaks

Hg19::chr2:191272875..191272890,+p7@MFSD6
Hg19::chr2:191272893..191272923,+p2@MFSD6
Hg19::chr2:191272963..191272983,+p6@MFSD6
Hg19::chr2:191273052..191273121,+p1@MFSD6


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism6.52e-46115
neural tube1.23e-2157
neural rod1.23e-2157
future spinal cord1.23e-2157
neural keel1.23e-2157
anterior neural tube2.30e-1842
regional part of forebrain4.62e-1841
forebrain4.62e-1841
future forebrain4.62e-1841
regional part of brain7.26e-1759
brain1.23e-1569
future brain1.23e-1569
central nervous system2.09e-1482
telencephalon4.57e-1434
gray matter5.08e-1434
brain grey matter5.08e-1434
regional part of telencephalon1.94e-1333
cerebral hemisphere7.40e-1332
regional part of nervous system2.02e-1294
nervous system2.02e-1294
anterior region of body7.99e-12129
craniocervical region7.99e-12129
regional part of cerebral cortex8.44e-1222
neural plate9.30e-1286
presumptive neural plate9.30e-1286
organ1.31e-11511
neocortex8.39e-1120
head1.02e-10123
ectoderm-derived structure3.15e-10169
neurectoderm5.26e-1090
cerebral cortex1.53e-0925
pallium1.53e-0925
hematopoietic system1.64e-09102
blood island1.64e-09102
pre-chordal neural plate3.82e-0961
ectoderm4.15e-09173
presumptive ectoderm4.15e-09173
bone marrow9.05e-0880
hemolymphoid system3.41e-07112


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
CCNT2#90546.336201576962630.0006203100587215640.00512820092003653
CTBP2#1488462.71700033932816.45042639894877e-083.96280048635183e-06
E2F6#187645.017155731697390.00157802193473060.00997983727996421
ELF1#199744.258097958807540.003041525565781240.0161106602710669
GABPB1#255335.300762877136630.01012678824234270.0378726504777638
PAX5#507946.669565531177830.0005052774169483260.00444421998893938
TCF12#6938410.63446490218647.8163066689251e-050.00120154143684997
ZEB1#6935416.88843201754391.22862303393937e-050.000304716601856077
ZNF263#1012748.221841637010680.0002187871180958320.00249344258258518



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.