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Coexpression cluster:C2237

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Full id: C2237_lung_heart_adipose_breast_left_MCF7_retina



Phase1 CAGE Peaks

Hg19::chr12:71003739..71003750,-p8@PTPRB
Hg19::chr12:71003751..71003810,-p2@PTPRB
Hg19::chr12:71003811..71003822,-p9@PTPRB
Hg19::chr7:45197383..45197437,+p1@RAMP3


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


GO IDGO nameFDR corrected p-value
GO:0015027coreceptor, soluble ligand activity0.0046508889673849
GO:0015026coreceptor activity0.0206544549269588
GO:0019198transmembrane receptor protein phosphatase activity0.0206544549269588
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.0206544549269588
GO:0005887integral to plasma membrane0.0206544549269588
GO:0031226intrinsic to plasma membrane0.0206544549269588
GO:0008277regulation of G-protein coupled receptor protein signaling pathway0.023821772926169
GO:0006898receptor-mediated endocytosis0.023821772926169
GO:0044459plasma membrane part0.0396951492407639



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.22e-54115
tube6.61e-28194
anatomical conduit4.67e-25241
anatomical cluster1.86e-24286
neural tube4.26e-2357
neural rod4.26e-2357
future spinal cord4.26e-2357
neural keel4.26e-2357
neural plate1.41e-2086
presumptive neural plate1.41e-2086
neurectoderm2.17e-2090
central nervous system3.36e-1982
regional part of brain3.40e-1859
brain5.45e-1869
future brain5.45e-1869
anterior neural tube1.46e-1742
regional part of nervous system1.58e-1794
nervous system1.58e-1794
regional part of forebrain7.02e-1741
forebrain7.02e-1741
future forebrain7.02e-1741
splanchnic layer of lateral plate mesoderm4.51e-1684
epithelium4.82e-15309
cell layer1.01e-14312
blood vessel3.14e-1460
epithelial tube open at both ends3.14e-1460
blood vasculature3.14e-1460
vascular cord3.14e-1460
vessel6.01e-1469
circulatory system7.02e-14113
telencephalon8.18e-1434
gray matter9.14e-1434
brain grey matter9.14e-1434
pre-chordal neural plate2.26e-1361
regional part of telencephalon2.78e-1333
multi-cellular organism3.15e-13659
cerebral hemisphere1.06e-1232
cardiovascular system1.92e-12110
vasculature3.24e-1279
vascular system3.24e-1279
epithelial tube3.33e-11118
anatomical system7.15e-11625
regional part of cerebral cortex7.54e-1122
anatomical group1.12e-10626
anterior region of body1.17e-10129
craniocervical region1.17e-10129
multi-tissue structure2.23e-10347
artery2.50e-1042
arterial blood vessel2.50e-1042
arterial system2.50e-1042
head4.40e-10123
neocortex5.82e-1020
cerebral cortex1.37e-0925
pallium1.37e-0925
ectoderm8.33e-09173
presumptive ectoderm8.33e-09173
organism subdivision1.12e-08365
ectoderm-derived structure1.15e-08169
systemic artery2.25e-0833
systemic arterial system2.25e-0833
primary circulatory organ1.13e-0727
organ part2.08e-07219
embryo3.77e-07612
posterior neural tube9.27e-0715
chordal neural plate9.27e-0715


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
CCNT2#90534.752151182721970.01386206996689490.0487093979299015
SPI1#668836.153242631392040.006580387113059030.0280934084004731



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.