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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2873_cerebellum_pineal_mesothelioma_Endothelial_Lymphatic_merkel_chronic
|full_id=C2873_cerebellum_pineal_mesothelioma_Endothelial_Lymphatic_merkel_chronic
|id=C2873
|id=C2873

Revision as of 15:40, 12 September 2012


Full id: C2873_cerebellum_pineal_mesothelioma_Endothelial_Lymphatic_merkel_chronic



Phase1 CAGE Peaks

Hg19::chr7:103629614..103629646,-p5@RELN
Hg19::chr7:103630045..103630056,-p3@RELN
Hg19::chr7:103630073..103630088,-p2@RELN
Hg19::chr7:103630096..103630116,-p1@RELN


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 organism7.17e-37115
neural plate1.33e-2886
presumptive neural plate1.33e-2886
neurectoderm2.09e-2790
neural tube5.14e-2657
neural rod5.14e-2657
future spinal cord5.14e-2657
neural keel5.14e-2657
regional part of brain4.06e-2459
central nervous system5.54e-2482
anatomical cluster6.86e-24286
regional part of nervous system1.31e-2394
nervous system1.31e-2394
anatomical conduit2.94e-23241
brain1.58e-2269
future brain1.58e-2269
tube6.19e-22194
pre-chordal neural plate9.99e-2161
anterior neural tube2.59e-1842
regional part of forebrain6.51e-1841
forebrain6.51e-1841
future forebrain6.51e-1841
epithelium7.68e-18309
cell layer9.43e-18312
anterior region of body2.25e-17129
craniocervical region2.25e-17129
head4.34e-17123
ectoderm-derived structure3.62e-16169
ectoderm7.81e-16173
presumptive ectoderm7.81e-16173
telencephalon7.92e-1634
gray matter1.05e-1534
brain grey matter1.05e-1534
regional part of telencephalon2.97e-1533
cerebral hemisphere4.93e-1532
organism subdivision2.15e-14365
regional part of cerebral cortex1.06e-1322
multi-tissue structure9.66e-13347
neocortex1.22e-1220
cerebral cortex1.06e-1125
pallium1.06e-1125
multi-cellular organism1.48e-11659
organ part3.53e-10219
anatomical system3.03e-09625
anatomical group4.19e-09626
posterior neural tube6.24e-0915
chordal neural plate6.24e-0915
organ8.86e-08511
segmental subdivision of nervous system1.83e-0713
pigment epithelium of eye3.18e-0711
segmental subdivision of hindbrain3.55e-0712
hindbrain3.55e-0712
presumptive hindbrain3.55e-0712


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
CTCFL#140690314.80985576923080.0004996291767563340.00441088517254901
E2F6#187645.017155731697390.00157802193473060.0099925442818971
ZBTB7A#5134135.513931980906920.009038352821081090.0342609077482901



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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