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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1470_acute_Renal_clear_Endothelial_diaphragm_skeletal_Lymphatic
|full_id=C1470_acute_Renal_clear_Endothelial_diaphragm_skeletal_Lymphatic
|id=C1470
|id=C1470

Revision as of 14:01, 12 September 2012


Full id: C1470_acute_Renal_clear_Endothelial_diaphragm_skeletal_Lymphatic



Phase1 CAGE Peaks

Hg19::chr1:208060723..208060734,-p@chr1:208060723..208060734
-
Hg19::chr1:208060913..208060939,-p@chr1:208060913..208060939
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Hg19::chr1:208084373..208084384,-p7@CD34
Hg19::chr1:208084387..208084511,-p1@CD34
Hg19::chr1:208084527..208084543,-p5@CD34
Hg19::chr1:208084585..208084627,-p3@CD34


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 organism5.14e-44115
anatomical conduit2.63e-24241
tube6.79e-24194
anatomical cluster2.71e-21286
neural tube5.88e-2157
neural rod5.88e-2157
future spinal cord5.88e-2157
neural keel5.88e-2157
central nervous system4.99e-1882
regional part of brain1.98e-1759
neural plate6.00e-1786
presumptive neural plate6.00e-1786
anterior neural tube1.68e-1642
regional part of nervous system2.97e-1694
nervous system2.97e-1694
regional part of forebrain5.70e-1641
forebrain5.70e-1641
future forebrain5.70e-1641
neurectoderm4.85e-1590
splanchnic layer of lateral plate mesoderm5.63e-1584
brain8.00e-1569
future brain8.00e-1569
gray matter8.20e-1434
brain grey matter8.20e-1434
telencephalon8.33e-1434
vessel1.48e-1369
regional part of telencephalon1.96e-1333
cerebral hemisphere4.43e-1332
cell layer9.45e-13312
epithelium1.64e-12309
circulatory system2.33e-12113
blood vessel2.89e-1160
epithelial tube open at both ends2.89e-1160
blood vasculature2.89e-1160
vascular cord2.89e-1160
cardiovascular system3.87e-11110
vasculature3.96e-1179
vascular system3.96e-1179
cerebral cortex9.76e-1125
pallium9.76e-1125
epithelial tube3.58e-10118
pre-chordal neural plate6.29e-1061
endothelium1.80e-0918
blood vessel endothelium1.80e-0918
cardiovascular system endothelium1.80e-0918
anatomical system2.38e-09625
multi-cellular organism3.05e-09659
anatomical group3.32e-09626
regional part of cerebral cortex3.79e-0922
squamous epithelium1.06e-0825
neocortex1.86e-0820
simple squamous epithelium5.61e-0822
anterior region of body1.48e-07129
craniocervical region1.48e-07129
compound organ6.64e-0769
head7.31e-07123
organ part8.22e-07219


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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