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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus
|full_id=C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus
|gostat_on_coexpression_clusters=GO:0043034!costamere!0.0154520836096565!1756$GO:0043043!peptide biosynthetic process!0.0154520836096565!1756$GO:0016998!cell wall catabolic process!0.0194157566529812!55074$GO:0010382!cell wall metabolic process!0.0194157566529812!55074$GO:0007047!cell wall organization and biogenesis!0.0194157566529812!55074$GO:0016010!dystrophin-associated glycoprotein complex!0.0194157566529812!1756$GO:0045229!external encapsulating structure organization and biogenesis!0.0194157566529812!55074$GO:0006518!peptide metabolic process!0.0216182731161402!1756$GO:0005605!basal lamina!0.0246949599187639!1756$GO:0008307!structural constituent of muscle!0.0246949599187639!1756$GO:0004089!carbonate dehydratase activity!0.0246949599187639!770$GO:0030016!myofibril!0.0272601251068618!1756$GO:0044449!contractile fiber part!0.0282061916009638!1756$GO:0043292!contractile fiber!0.0282061916009638!1756$GO:0005604!basement membrane!0.0304302166801092!1756$GO:0005200!structural constituent of cytoskeleton!0.0326402487061384!1756$GO:0016836!hydro-lyase activity!0.0326402487061384!770$GO:0016835!carbon-oxygen lyase activity!0.0345834233518151!770$GO:0006979!response to oxidative stress!0.0389048363651696!55074$GO:0044420!extracellular matrix part!0.040334478647165!1756$GO:0006730!one-carbon compound metabolic process!0.0440785620807245!770$GO:0003012!muscle system process!0.0440785620807245!1756$GO:0006936!muscle contraction!0.0440785620807245!1756$GO:0007517!muscle development!0.0440785620807245!1756
|gostat_on_coexpression_clusters=GO:0043034!costamere!0.0154520836096565!1756$GO:0043043!peptide biosynthetic process!0.0154520836096565!1756$GO:0016998!cell wall catabolic process!0.0194157566529812!55074$GO:0010382!cell wall metabolic process!0.0194157566529812!55074$GO:0007047!cell wall organization and biogenesis!0.0194157566529812!55074$GO:0016010!dystrophin-associated glycoprotein complex!0.0194157566529812!1756$GO:0045229!external encapsulating structure organization and biogenesis!0.0194157566529812!55074$GO:0006518!peptide metabolic process!0.0216182731161402!1756$GO:0005605!basal lamina!0.0246949599187639!1756$GO:0008307!structural constituent of muscle!0.0246949599187639!1756$GO:0004089!carbonate dehydratase activity!0.0246949599187639!770$GO:0030016!myofibril!0.0272601251068618!1756$GO:0044449!contractile fiber part!0.0282061916009638!1756$GO:0043292!contractile fiber!0.0282061916009638!1756$GO:0005604!basement membrane!0.0304302166801092!1756$GO:0005200!structural constituent of cytoskeleton!0.0326402487061384!1756$GO:0016836!hydro-lyase activity!0.0326402487061384!770$GO:0016835!carbon-oxygen lyase activity!0.0345834233518151!770$GO:0006979!response to oxidative stress!0.0389048363651696!55074$GO:0044420!extracellular matrix part!0.040334478647165!1756$GO:0006730!one-carbon compound metabolic process!0.0440785620807245!770$GO:0003012!muscle system process!0.0440785620807245!1756$GO:0006936!muscle contraction!0.0440785620807245!1756$GO:0007517!muscle development!0.0440785620807245!1756

Revision as of 13:30, 12 September 2012


Full id: C1062_extraskeletal_pineal_amygdala_middle_medial_parietal_hippocampus



Phase1 CAGE Peaks

Hg19::chr19:49149202..49149212,-p11@CA11
Hg19::chr19:49149234..49149251,-p9@CA11
Hg19::chr8:107282339..107282351,+p6@OXR1
Hg19::chr8:107440851..107440855,+p@chr8:107440851..107440855
+
Hg19::chrX:33357425..33357435,-p23@DMD
Hg19::chrX:33357482..33357512,-p6@DMD
Hg19::chrX:33357525..33357536,-p13@DMD
Hg19::chrX:33357642..33357657,-p16@DMD


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:0043034costamere0.0154520836096565
GO:0043043peptide biosynthetic process0.0154520836096565
GO:0016998cell wall catabolic process0.0194157566529812
GO:0010382cell wall metabolic process0.0194157566529812
GO:0007047cell wall organization and biogenesis0.0194157566529812
GO:0016010dystrophin-associated glycoprotein complex0.0194157566529812
GO:0045229external encapsulating structure organization and biogenesis0.0194157566529812
GO:0006518peptide metabolic process0.0216182731161402
GO:0005605basal lamina0.0246949599187639
GO:0008307structural constituent of muscle0.0246949599187639
GO:0004089carbonate dehydratase activity0.0246949599187639
GO:0030016myofibril0.0272601251068618
GO:0044449contractile fiber part0.0282061916009638
GO:0043292contractile fiber0.0282061916009638
GO:0005604basement membrane0.0304302166801092
GO:0005200structural constituent of cytoskeleton0.0326402487061384
GO:0016836hydro-lyase activity0.0326402487061384
GO:0016835carbon-oxygen lyase activity0.0345834233518151
GO:0006979response to oxidative stress0.0389048363651696
GO:0044420extracellular matrix part0.040334478647165
GO:0006730one-carbon compound metabolic process0.0440785620807245
GO:0003012muscle system process0.0440785620807245
GO:0006936muscle contraction0.0440785620807245
GO:0007517muscle development0.0440785620807245



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
central nervous system2.72e-3182
regional part of nervous system1.22e-3094
nervous system1.22e-3094
neural tube1.56e-2957
neural rod1.56e-2957
future spinal cord1.56e-2957
neural keel1.56e-2957
brain2.50e-2669
future brain2.50e-2669
regional part of forebrain1.44e-2541
forebrain1.44e-2541
future forebrain1.44e-2541
regional part of brain3.22e-2559
anterior neural tube2.05e-2442
adult organism3.12e-23115
gray matter3.73e-2334
brain grey matter3.73e-2334
telencephalon4.18e-2334
regional part of telencephalon2.33e-2233
neurectoderm2.43e-2290
neural plate5.06e-2286
presumptive neural plate5.06e-2286
cerebral hemisphere7.93e-2232
ectoderm1.78e-21173
presumptive ectoderm1.78e-21173
ectoderm-derived structure5.60e-21169
regional part of cerebral cortex4.12e-1822
cerebral cortex5.45e-1725
pallium5.45e-1725
neocortex1.37e-1620
pre-chordal neural plate6.19e-1661
anterior region of body1.27e-15129
craniocervical region1.27e-15129
head1.47e-15123
organism subdivision7.11e-13365
basal ganglion9.34e-089
nuclear complex of neuraxis9.34e-089
aggregate regional part of brain9.34e-089
collection of basal ganglia9.34e-089
cerebral subcortex9.34e-089
nucleus of brain1.25e-079
neural nucleus1.25e-079
temporal lobe2.35e-077
multi-tissue structure5.42e-07347


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#1066453.350160233171890.007643853146021220.0314905281336953



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.