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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal
|full_id=C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal
|id=C3272
|id=C3272

Revision as of 16:09, 12 September 2012


Full id: C3272_endometrial_lung_lymphangiectasia_rhabdomyosarcoma_pineal_meningioma_spinal



Phase1 CAGE Peaks

Hg19::chr12:26277994..26278001,-p6@BHLHE41
Hg19::chr12:26278008..26278024,-p4@BHLHE41
Hg19::chr12:26278030..26278039,-p7@BHLHE41


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 organism3.06e-35115
neural plate4.53e-2686
presumptive neural plate4.53e-2686
neurectoderm2.22e-2590
neural tube2.83e-2357
neural rod2.83e-2357
future spinal cord2.83e-2357
neural keel2.83e-2357
regional part of brain4.63e-2059
regional part of nervous system8.18e-2094
nervous system8.18e-2094
central nervous system1.25e-1882
brain1.60e-1869
future brain1.60e-1869
pre-chordal neural plate1.01e-1661
anterior region of body1.55e-15129
craniocervical region1.55e-15129
head1.60e-15123
anterior neural tube2.97e-1542
regional part of forebrain3.98e-1541
forebrain3.98e-1541
future forebrain3.98e-1541
organism subdivision5.35e-15365
ectoderm-derived structure1.08e-14169
ectoderm1.29e-14173
presumptive ectoderm1.29e-14173
telencephalon2.69e-1134
gray matter3.07e-1134
brain grey matter3.07e-1134
regional part of telencephalon9.07e-1133
cerebral hemisphere3.30e-1032
anatomical conduit3.47e-10241
multi-tissue structure4.15e-10347
organ1.16e-09511
posterior neural tube1.60e-0915
chordal neural plate1.60e-0915
tube1.69e-09194
anatomical cluster2.99e-09286
cell layer3.06e-09312
multi-cellular organism4.91e-09659
epithelium7.78e-09309
segmental subdivision of nervous system1.89e-0813
regional part of cerebral cortex2.14e-0822
embryo5.05e-08612
segmental subdivision of hindbrain8.80e-0812
hindbrain8.80e-0812
presumptive hindbrain8.80e-0812
neocortex1.60e-0720
cerebral cortex4.26e-0725
pallium4.26e-0725
anatomical group7.84e-07626
embryonic structure9.73e-07605
developing anatomical structure9.73e-07605


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
JUND#372736.994663941871030.002921845042734990.0156305165403985
MAX#414936.452555509007120.003721913834265510.0185978163215566
SUZ12#23512350.11578091106297.93834897779404e-060.000221558853258106
TRIM28#10155318.59052504526250.0001555969297255280.00196593125376293
USF1#739136.361499277207960.00388404057290560.018967797315706



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.