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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary
|full_id=C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary
|id=C3993
|id=C3993

Revision as of 17:00, 12 September 2012


Full id: C3993_dura_heart_Lymphatic_lung_acute_Fibroblast_pituitary



Phase1 CAGE Peaks

Hg19::chr1:65990881..65990916,+p5@LEPR
Hg19::chr1:65990922..65990927,+p12@LEPR
Hg19::chr1:65990933..65990946,+p8@LEPR


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
lymphangioblast6.90e-076
endothelial cell of lymphatic vessel6.90e-076
vascular lymphangioblast6.90e-076
Uber Anatomy
Ontology termp-valuen
adult organism1.15e-58115
neural tube2.74e-2357
neural rod2.74e-2357
future spinal cord2.74e-2357
neural keel2.74e-2357
regional part of brain8.44e-1959
neural plate1.93e-1886
presumptive neural plate1.93e-1886
anterior neural tube2.20e-1842
regional part of forebrain1.78e-1741
forebrain1.78e-1741
future forebrain1.78e-1741
neurectoderm8.08e-1790
anatomical cluster4.98e-16286
central nervous system7.47e-1582
anatomical conduit1.07e-14241
brain1.16e-1469
future brain1.16e-1469
gray matter2.87e-1434
brain grey matter2.87e-1434
telencephalon3.99e-1434
anterior region of body5.28e-14129
craniocervical region5.28e-14129
regional part of telencephalon1.43e-1333
regional part of nervous system5.00e-1394
nervous system5.00e-1394
cerebral hemisphere6.05e-1332
head7.99e-13123
pre-chordal neural plate3.54e-1261
regional part of cerebral cortex5.63e-1122
tube1.46e-10194
ectoderm-derived structure7.97e-10169
neocortex1.13e-0920
ectoderm3.69e-09173
presumptive ectoderm3.69e-09173
cerebral cortex5.29e-0925
pallium5.29e-0925
multi-tissue structure4.66e-08347
multi-cellular organism5.58e-08659
brainstem1.31e-078
nucleus of brain3.41e-079
neural nucleus3.41e-079
basal ganglion3.81e-079
nuclear complex of neuraxis3.81e-079
aggregate regional part of brain3.81e-079
collection of basal ganglia3.81e-079
cerebral subcortex3.81e-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
E2F6#187635.017155731697390.00791769806886330.032264874502088
EGR1#195834.988179094810140.008056488137383440.0321002428116965
GATA1#2623313.56030814380040.0004009615963782630.00388244281143607
JUN#3725312.51282919233630.0005103313992726250.00444672960192172



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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