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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 organism2.15e-67114
neural tube6.88e-2856
neural rod6.88e-2856
future spinal cord6.88e-2856
neural keel6.88e-2856
regional part of nervous system5.83e-2653
regional part of brain5.83e-2653
anatomical cluster8.80e-25373
neural plate2.52e-2482
presumptive neural plate2.52e-2482
neurectoderm1.43e-2386
tube6.50e-23192
anatomical conduit7.25e-23240
regional part of forebrain7.73e-2241
forebrain7.73e-2241
anterior neural tube7.73e-2241
future forebrain7.73e-2241
structure with developmental contribution from neural crest1.88e-20132
brain3.05e-2068
future brain3.05e-2068
central nervous system4.14e-1981
nervous system9.59e-1889
telencephalon1.16e-1734
brain grey matter1.51e-1734
gray matter1.51e-1734
pre-chordal neural plate1.04e-1661
ecto-epithelium1.58e-16104
cerebral hemisphere2.73e-1632
regional part of telencephalon2.93e-1632
multi-tissue structure6.29e-15342
regional part of cerebral cortex1.45e-1422
organ system subdivision2.27e-14223
neocortex1.89e-1320
epithelium1.07e-12306
cell layer3.26e-12309
multi-cellular organism4.04e-12656
cerebral cortex6.76e-1225
pallium6.76e-1225
splanchnic layer of lateral plate mesoderm7.80e-1083
embryonic structure1.91e-09564
germ layer1.93e-09560
germ layer / neural crest1.93e-09560
embryonic tissue1.93e-09560
presumptive structure1.93e-09560
germ layer / neural crest derived structure1.93e-09560
epiblast (generic)1.93e-09560
anatomical system1.97e-09624
anatomical group2.55e-09625
ectoderm-derived structure4.70e-09171
ectoderm4.70e-09171
presumptive ectoderm4.70e-09171
vessel6.91e-0968
embryo1.07e-08592
developing anatomical structure1.68e-08581
epithelial tube open at both ends1.70e-0859
blood vessel1.70e-0859
blood vasculature1.70e-0859
vascular cord1.70e-0859
vasculature3.99e-0878
vascular system3.99e-0878
circulatory system7.02e-08112
organ1.91e-07503
neural nucleus2.54e-079
nucleus of brain2.54e-079
posterior neural tube2.89e-0715
chordal neural plate2.89e-0715
basal ganglion5.48e-079
nuclear complex of neuraxis5.48e-079
aggregate regional part of brain5.48e-079
collection of basal ganglia5.48e-079
cerebral subcortex5.48e-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
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.