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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3397_epidermoid_testis_transitionalcell_large_argyrophil_testicular_papillotubular
|full_id=C3397_epidermoid_testis_transitionalcell_large_argyrophil_testicular_papillotubular
|id=C3397
|id=C3397

Revision as of 16:18, 12 September 2012


Full id: C3397_epidermoid_testis_transitionalcell_large_argyrophil_testicular_papillotubular



Phase1 CAGE Peaks

Hg19::chr14:104394760..104394768,+p4@TDRD9
Hg19::chr14:104394770..104394820,+p1@TDRD9
Hg19::chr14:104394868..104394874,+p5@TDRD9


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 organism1.33e-27115
neural tube3.78e-1757
neural rod3.78e-1757
future spinal cord3.78e-1757
neural keel3.78e-1757
neural plate3.13e-1586
presumptive neural plate3.13e-1586
regional part of brain7.79e-1559
neurectoderm1.59e-1390
anterior neural tube4.57e-1242
regional part of forebrain9.97e-1241
forebrain9.97e-1241
future forebrain9.97e-1241
brain3.39e-1169
future brain3.39e-1169
central nervous system9.99e-1182
anterior region of body1.25e-10129
craniocervical region1.25e-10129
head1.94e-10123
pre-chordal neural plate3.60e-1061
telencephalon7.95e-1034
gray matter9.57e-1034
brain grey matter9.57e-1034
regional part of telencephalon2.46e-0933
cerebral hemisphere4.32e-0932
organ1.06e-08511
regional part of nervous system1.25e-0894
nervous system1.25e-0894
regional part of cerebral cortex6.12e-0822
hematopoietic system9.79e-08102
blood island9.79e-08102
neocortex2.80e-0720
hemolymphoid system4.71e-07112
bone marrow5.64e-0780
anatomical system5.89e-07625
multi-cellular organism6.75e-07659
ectoderm-derived structure7.08e-07169
skeletal element7.29e-07101
skeletal system7.29e-07101
anatomical group7.73e-07626


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#186934.907389214879320.008460985347239390.0324289643172349
E2F6#187635.017155731697390.00791769806886330.0321194977127214



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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