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Coexpression cluster:C2714: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2714_salivary_dura_skin_trachea_rectum_skeletal_spinal
|full_id=C2714_salivary_dura_skin_trachea_rectum_skeletal_spinal
|id=C2714
|id=C2714

Revision as of 15:29, 12 September 2012


Full id: C2714_salivary_dura_skin_trachea_rectum_skeletal_spinal



Phase1 CAGE Peaks

Hg19::chr3:112930306..112930338,+p2@BOC
Hg19::chr3:112930339..112930363,+p4@BOC
Hg19::chr3:112930373..112930384,+p5@BOC
Hg19::chr3:112930387..112930431,+p1@BOC


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell8.84e-10180
neurectodermal cell3.86e-0959
ectodermal cell2.78e-0871
Uber Anatomy
Ontology termp-valuen
adult organism2.83e-28115
ectoderm1.07e-27173
presumptive ectoderm1.07e-27173
ectoderm-derived structure3.66e-27169
central nervous system1.75e-2682
regional part of nervous system8.68e-2694
nervous system8.68e-2694
organism subdivision4.38e-24365
neural tube1.48e-2357
neural rod1.48e-2357
future spinal cord1.48e-2357
neural keel1.48e-2357
head2.69e-23123
anterior region of body2.86e-23129
craniocervical region2.86e-23129
neurectoderm3.93e-2390
neural plate8.52e-2386
presumptive neural plate8.52e-2386
brain3.65e-2269
future brain3.65e-2269
regional part of brain7.21e-2259
multi-tissue structure4.44e-16347
anterior neural tube6.80e-1642
regional part of forebrain2.52e-1541
forebrain2.52e-1541
future forebrain2.52e-1541
pre-chordal neural plate4.76e-1561
multi-cellular organism1.87e-14659
gray matter5.17e-1334
brain grey matter5.17e-1334
telencephalon2.64e-1234
regional part of telencephalon2.92e-1233
organ4.50e-12511
organ part1.54e-11219
cerebral hemisphere1.64e-1132
embryo1.38e-10612
cell layer5.50e-10312
cerebral cortex9.44e-1025
pallium9.44e-1025
epithelium1.30e-09309
anatomical cluster1.68e-09286
anatomical system3.04e-09625
posterior neural tube4.77e-0915
chordal neural plate4.77e-0915
anatomical group5.06e-09626
embryonic structure8.22e-09605
developing anatomical structure8.22e-09605
germ layer1.73e-08604
embryonic tissue1.73e-08604
presumptive structure1.73e-08604
epiblast (generic)1.73e-08604
anatomical conduit2.68e-08241
regional part of cerebral cortex2.95e-0822
surface structure2.43e-0795
neocortex3.21e-0720
segmental subdivision of hindbrain4.46e-0712
hindbrain4.46e-0712
presumptive hindbrain4.46e-0712
segmental subdivision of nervous system6.05e-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#186944.907389214879320.001724022357361790.0106648801149386
ZNF263#1012748.221841637010680.0002187871180958320.00249425912310999



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.