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Coexpression cluster:C3301: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus
|full_id=C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus
|gostat_on_coexpression_clusters=GO:0030049!muscle filament sliding!0.0107137600063315!140465$GO:0033275!actin-myosin filament sliding!0.0107137600063315!140465$GO:0016461!unconventional myosin complex!0.0107137600063315!140465$GO:0030048!actin filament-based movement!0.0183640125820119!140465$GO:0005859!muscle myosin complex!0.0198914181804517!140465$GO:0016460!myosin II complex!0.0198914181804517!140465$GO:0008307!structural constituent of muscle!0.0275354752527976!140465$GO:0044449!contractile fiber part!0.0307366264913492!140465$GO:0043292!contractile fiber!0.0307366264913492!140465$GO:0007519!skeletal muscle development!0.0307366264913492!140465$GO:0014706!striated muscle development!0.03668909487398!140465$GO:0016459!myosin complex!0.0408816032450061!140465
|gostat_on_coexpression_clusters=GO:0030049!muscle filament sliding!0.0107137600063315!140465$GO:0033275!actin-myosin filament sliding!0.0107137600063315!140465$GO:0016461!unconventional myosin complex!0.0107137600063315!140465$GO:0030048!actin filament-based movement!0.0183640125820119!140465$GO:0005859!muscle myosin complex!0.0198914181804517!140465$GO:0016460!myosin II complex!0.0198914181804517!140465$GO:0008307!structural constituent of muscle!0.0275354752527976!140465$GO:0044449!contractile fiber part!0.0307366264913492!140465$GO:0043292!contractile fiber!0.0307366264913492!140465$GO:0007519!skeletal muscle development!0.0307366264913492!140465$GO:0014706!striated muscle development!0.03668909487398!140465$GO:0016459!myosin complex!0.0408816032450061!140465

Revision as of 16:12, 12 September 2012


Full id: C3301_Renal_Placental_Mesenchymal_Pericytes_Osteoblast_Astrocyte_Nucleus



Phase1 CAGE Peaks

Hg19::chr12:56546363..56546397,+p1@MYL6B
Hg19::chr19:50354393..50354422,+p1@PTOV1
Hg19::chr19:50354430..50354447,+p2@PTOV1


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:0030049muscle filament sliding0.0107137600063315
GO:0033275actin-myosin filament sliding0.0107137600063315
GO:0016461unconventional myosin complex0.0107137600063315
GO:0030048actin filament-based movement0.0183640125820119
GO:0005859muscle myosin complex0.0198914181804517
GO:0016460myosin II complex0.0198914181804517
GO:0008307structural constituent of muscle0.0275354752527976
GO:0044449contractile fiber part0.0307366264913492
GO:0043292contractile fiber0.0307366264913492
GO:0007519skeletal muscle development0.0307366264913492
GO:0014706striated muscle development0.03668909487398
GO:0016459myosin complex0.0408816032450061



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
cell layer2.97e-31312
epithelium9.54e-31309
multi-tissue structure4.57e-23347
anatomical cluster9.11e-23286
tube3.07e-21194
organism subdivision7.11e-21365
anatomical conduit5.75e-19241
vasculature3.12e-1679
vascular system3.12e-1679
epithelial tube1.57e-15118
trunk mesenchyme1.60e-15143
dermomyotome1.68e-1570
somite3.13e-1583
paraxial mesoderm3.13e-1583
presomitic mesoderm3.13e-1583
presumptive segmental plate3.13e-1583
trunk paraxial mesoderm3.13e-1583
presumptive paraxial mesoderm3.13e-1583
multilaminar epithelium7.43e-1582
ectoderm2.59e-14173
presumptive ectoderm2.59e-14173
splanchnic layer of lateral plate mesoderm3.84e-1484
skeletal muscle tissue4.08e-1461
striated muscle tissue4.08e-1461
myotome4.08e-1461
unilaminar epithelium5.24e-14138
ectoderm-derived structure1.88e-13169
neurectoderm7.35e-1390
muscle tissue7.77e-1363
musculature7.77e-1363
musculature of body7.77e-1363
regional part of nervous system1.05e-1294
nervous system1.05e-1294
embryo1.14e-12612
vessel3.30e-1269
blood vessel3.56e-1260
epithelial tube open at both ends3.56e-1260
blood vasculature3.56e-1260
vascular cord3.56e-1260
central nervous system4.29e-1282
organ part4.76e-12219
neural plate5.92e-1286
presumptive neural plate5.92e-1286
multi-cellular organism7.25e-12659
head1.41e-11123
pre-chordal neural plate2.44e-1161
artery5.93e-1142
arterial blood vessel5.93e-1142
arterial system5.93e-1142
anterior region of body1.10e-10129
craniocervical region1.10e-10129
embryonic structure1.41e-10605
developing anatomical structure1.41e-10605
germ layer1.64e-10604
embryonic tissue1.64e-10604
presumptive structure1.64e-10604
epiblast (generic)1.64e-10604
circulatory system3.62e-10113
cardiovascular system3.69e-10110
trunk5.79e-10216
brain6.96e-1069
future brain6.96e-1069
regional part of brain2.45e-0959
mesenchyme4.75e-09238
entire embryonic mesenchyme4.75e-09238
anatomical system3.26e-08625
neural tube4.06e-0857
neural rod4.06e-0857
future spinal cord4.06e-0857
neural keel4.06e-0857
anatomical group4.61e-08626
systemic artery1.14e-0733
systemic arterial system1.14e-0733
telencephalon2.14e-0734
compound organ2.36e-0769
gray matter2.66e-0734
brain grey matter2.66e-0734
cerebral hemisphere3.20e-0732
regional part of telencephalon3.73e-0733


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
BRCA1#672213.45615376214920.007119807716084560.0296119468782667
CCNT2#90536.336201576962630.003930750035764890.0189469517231388
E2F1#186934.907389214879320.008460985347239390.032412311509384
E2F6#187635.017155731697390.00791769806886330.0320970565778059
EGR1#195834.988179094810140.008056488137383440.0319491025432939
EP300#203336.77394172622320.003216880500103790.0167048420122484
FOXA1#3169311.08141974938550.000734755275698670.00580023478750516
HMGN3#932438.178547723350590.001827766942164210.0108447989815185
IRF1#365937.63716375356390.002244692747297240.0127756657130778
JUND#372736.994663941871030.002921845042734990.0156329187714242
MYC#460935.22228187160940.007020843755740150.0293558291698993
PAX5#507936.669565531177830.003370290999677260.0172484844276618
SIN3A#2594235.408884726815140.006318961977991520.0275770368985607
SIX5#147912317.0867153554590.0002004060546325010.0023917504216391
SP1#666735.69838137814090.005403962701712170.0245726428336867
SRF#6722313.79717826216780.0003806615025800190.00374173239227808
THAP1#55145220.91276306856750.002983447413736940.0158625599166763
USF1#739136.361499277207960.00388404057290560.0189722329822594
ZBTB7A#5134137.35190930787590.002516255860282270.0139777270247338



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.