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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4741_Nucleus_Chondrocyte_thyroid_hippocampus_Fibroblast_medial_insula
|full_id=C4741_Nucleus_Chondrocyte_thyroid_hippocampus_Fibroblast_medial_insula
|id=C4741
|id=C4741

Revision as of 17:52, 12 September 2012


Full id: C4741_Nucleus_Chondrocyte_thyroid_hippocampus_Fibroblast_medial_insula



Phase1 CAGE Peaks

Hg19::chr8:19459708..19459747,-p2@CSGALNACT1
Hg19::chr8:19459753..19459765,-p9@CSGALNACT1
Hg19::chr8:19459967..19459992,-p6@CSGALNACT1


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
endothelial cell of vascular tree1.59e-0724
endothelial cell5.18e-0735
Uber Anatomy
Ontology termp-valuen
adult organism1.60e-41115
anatomical conduit4.97e-31241
anatomical cluster7.19e-31286
tube3.17e-30194
neural tube1.73e-2957
neural rod1.73e-2957
future spinal cord1.73e-2957
neural keel1.73e-2957
regional part of brain4.62e-2659
anterior neural tube4.13e-2442
regional part of forebrain9.84e-2441
forebrain9.84e-2441
future forebrain9.84e-2441
central nervous system5.42e-2382
brain5.97e-2369
future brain5.97e-2369
telencephalon3.14e-2034
gray matter5.47e-2034
brain grey matter5.47e-2034
regional part of nervous system9.63e-2094
nervous system9.63e-2094
regional part of telencephalon1.74e-1933
cerebral hemisphere3.14e-1932
neural plate5.77e-1986
presumptive neural plate5.77e-1986
regional part of cerebral cortex2.04e-1722
neurectoderm2.23e-1790
anterior region of body2.54e-16129
craniocervical region2.54e-16129
head4.86e-16123
neocortex5.35e-1620
cerebral cortex1.17e-1425
pallium1.17e-1425
epithelium4.25e-14309
cell layer9.94e-14312
pre-chordal neural plate6.11e-1361
splanchnic layer of lateral plate mesoderm6.12e-1284
multi-tissue structure7.80e-12347
multi-cellular organism1.40e-11659
ectoderm-derived structure5.47e-11169
blood vessel9.29e-1160
epithelial tube open at both ends9.29e-1160
blood vasculature9.29e-1160
vascular cord9.29e-1160
vessel1.35e-1069
organism subdivision2.62e-10365
ectoderm2.63e-10173
presumptive ectoderm2.63e-10173
embryonic structure3.09e-10605
developing anatomical structure3.09e-10605
embryo3.90e-10612
epithelial tube4.63e-10118
germ layer5.60e-10604
embryonic tissue5.60e-10604
presumptive structure5.60e-10604
epiblast (generic)5.60e-10604
anatomical system5.81e-10625
anatomical group8.24e-10626
vasculature5.29e-0979
vascular system5.29e-0979
circulatory system4.18e-08113
cardiovascular system1.36e-07110
systemic artery2.63e-0733
systemic arterial system2.63e-0733
basal ganglion3.31e-079
nuclear complex of neuraxis3.31e-079
aggregate regional part of brain3.31e-079
collection of basal ganglia3.31e-079
cerebral subcortex3.31e-079
nucleus of brain8.18e-079
neural nucleus8.18e-079


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
CTCF#1066435.360256373075030.0064925092527670.0281462444003874
RAD21#5885310.35503389545630.0009004912073565420.00668988484884833
SUZ12#23512350.11578091106297.93834897779404e-060.000223650722657629



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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