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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus
|full_id=C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus
|id=C1435
|id=C1435

Revision as of 13:59, 12 September 2012


Full id: C1435_Renal_lung_retina_Mesenchymal_placenta_Hepatic_uterus



Phase1 CAGE Peaks

Hg19::chr17:40913145..40913205,+p2@RAMP2
Hg19::chr17:40913210..40913221,+p3@RAMP2
Hg19::chr17:40913222..40913233,+p4@RAMP2
Hg19::chr17:40913236..40913252,+p1@RAMP2
Hg19::chr17:40913264..40913273,+p6@RAMP2
Hg19::chr17:72966776..72966789,+p@chr17:72966776..72966789
+


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 organism3.32e-31115
anatomical conduit3.00e-24241
tube1.16e-23194
cell layer2.80e-21312
epithelium4.81e-21309
anatomical cluster6.72e-21286
regional part of nervous system5.06e-1794
nervous system5.06e-1794
neurectoderm2.60e-1590
central nervous system3.47e-1582
multi-cellular organism2.22e-14659
neural tube2.62e-1457
neural rod2.62e-1457
future spinal cord2.62e-1457
neural keel2.62e-1457
neural plate4.15e-1486
presumptive neural plate4.15e-1486
brain5.83e-1269
future brain5.83e-1269
regional part of brain6.53e-1259
epithelial tube6.97e-12118
anterior neural tube1.90e-1142
organism subdivision3.87e-11365
regional part of forebrain6.65e-1141
forebrain6.65e-1141
future forebrain6.65e-1141
anatomical system7.99e-11625
anatomical group1.02e-10626
multi-tissue structure1.85e-10347
pre-chordal neural plate6.13e-1061
embryo8.01e-10612
telencephalon1.17e-0934
splanchnic layer of lateral plate mesoderm1.86e-0984
gray matter2.32e-0934
brain grey matter2.32e-0934
regional part of telencephalon2.67e-0933
ectoderm4.66e-09173
presumptive ectoderm4.66e-09173
cerebral hemisphere5.50e-0932
organ part8.65e-09219
vessel9.21e-0969
endothelium1.04e-0818
blood vessel endothelium1.04e-0818
cardiovascular system endothelium1.04e-0818
embryonic structure2.52e-08605
developing anatomical structure2.52e-08605
ectoderm-derived structure3.22e-08169
vasculature4.58e-0879
vascular system4.58e-0879
germ layer5.03e-08604
embryonic tissue5.03e-08604
presumptive structure5.03e-08604
epiblast (generic)5.03e-08604
compound organ7.49e-0869
regional part of cerebral cortex8.30e-0822
neocortex2.67e-0720
cerebral cortex3.71e-0725
pallium3.71e-0725
blood vessel3.82e-0760
epithelial tube open at both ends3.82e-0760
blood vasculature3.82e-0760
vascular cord3.82e-0760
anterior region of body4.57e-07129
craniocervical region4.57e-07129


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#1066443.573504248716680.01316635007238510.0466065765730013
REST#597858.041690596773356.54774545315482e-050.00106186333444416
USF1#739155.30124939767330.0005003327549858890.00441224796064944



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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