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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum
|full_id=C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum
|id=C2982
|id=C2982

Revision as of 15:48, 12 September 2012


Full id: C2982_thyroid_oral_throat_spleen_ductus_uterus_cerebellum



Phase1 CAGE Peaks

Hg19::chr10:116164244..116164268,-p1@AFAP1L2
Hg19::chr10:116164270..116164290,-p2@AFAP1L2
Hg19::chr10:116164538..116164562,-p3@AFAP1L2


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.07e-12254
endo-epithelial cell3.49e-1143
endodermal cell1.84e-0859
Uber Anatomy
Ontology termp-valuen
adult organism7.94e-29115
ectoderm-derived structure4.50e-21169
ectoderm1.38e-19173
presumptive ectoderm1.38e-19173
anterior region of body6.30e-19129
craniocervical region6.30e-19129
head2.16e-18123
organ part8.37e-18219
neural tube3.91e-1757
neural rod3.91e-1757
future spinal cord3.91e-1757
neural keel3.91e-1757
central nervous system6.48e-1782
organ2.85e-16511
neural plate8.00e-1686
presumptive neural plate8.00e-1686
brain1.29e-1569
future brain1.29e-1569
regional part of brain5.56e-1559
neurectoderm5.34e-1490
anatomical system9.45e-14625
anatomical group1.59e-13626
organism subdivision3.60e-13365
multi-tissue structure4.80e-13347
regional part of nervous system4.87e-1394
nervous system4.87e-1394
multi-cellular organism7.71e-13659
embryo3.59e-12612
endoderm-derived structure6.55e-12169
endoderm6.55e-12169
presumptive endoderm6.55e-12169
anterior neural tube1.57e-1142
cell layer2.72e-11312
regional part of forebrain4.28e-1141
forebrain4.28e-1141
future forebrain4.28e-1141
anatomical conduit5.64e-11241
epithelium6.93e-11309
embryonic structure6.95e-11605
developing anatomical structure6.95e-11605
germ layer1.66e-10604
embryonic tissue1.66e-10604
presumptive structure1.66e-10604
epiblast (generic)1.66e-10604
pre-chordal neural plate4.71e-1061
gray matter6.88e-1034
brain grey matter6.88e-1034
telencephalon8.31e-1034
anatomical cluster1.35e-09286
regional part of telencephalon1.71e-0933
cerebral hemisphere3.84e-0932
digestive system1.29e-08155
digestive tract1.29e-08155
primitive gut1.29e-08155
extraembryonic membrane1.21e-0714
membranous layer1.21e-0714
reproductive structure2.05e-0759
reproductive system2.05e-0759
cerebral cortex2.18e-0725
pallium2.18e-0725
regional part of cerebral cortex3.37e-0722
anatomical space3.43e-07104
posterior neural tube4.36e-0715
chordal neural plate4.36e-0715
trunk region element4.49e-07107
renal system4.55e-0745
immaterial anatomical entity6.67e-07126
Disease
Ontology termp-valuen
squamous cell carcinoma5.38e-0714


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

No analysis results for this cluster

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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