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Coexpression cluster:C351: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0001955!blood vessel maturation!0.00182503237960673!4313$GO:0004228!gelatinase A activity!0.00182503237960673!4313$GO:0030574!collagen catabolic process!0.00762948231814427!4313$GO:0044256!protein digestion!0.00762948231814427!4313$GO:0044254!multicellular organismal protein catabolic process!0.00762948231814427!4313$GO:0044266!multicellular organismal macromolecule catabolic process!0.00762948231814427!4313$GO:0044259!multicellular organismal macromolecule metabolic process!0.00762948231814427!4313$GO:0044268!multicellular organismal protein metabolic process!0.00762948231814427!4313$GO:0032963!collagen metabolic process!0.00762948231814427!4313$GO:0044243!multicellular organismal catabolic process!0.00762948231814427!4313$GO:0044236!multicellular organismal metabolic process!0.00762948231814427!4313$GO:0030017!sarcomere!0.0138075264980836!4313$GO:0021700!developmental maturation!0.0138075264980836!4313$GO:0030016!myofibril!0.0138075264980836!4313$GO:0044449!contractile fiber part!0.014586720778938!4313$GO:0043292!contractile fiber!0.014586720778938!4313$GO:0007586!digestion!0.0203692002083057!4313$GO:0001568!blood vessel development!0.031812593175251!4313$GO:0001944!vasculature development!0.031812593175251!4313$GO:0004222!metalloendopeptidase activity!0.0360308646701287!4313
|gostat_on_coexpression_clusters=GO:0001955!blood vessel maturation!0.00182503237960673!4313$GO:0004228!gelatinase A activity!0.00182503237960673!4313$GO:0030574!collagen catabolic process!0.00762948231814427!4313$GO:0044256!protein digestion!0.00762948231814427!4313$GO:0044254!multicellular organismal protein catabolic process!0.00762948231814427!4313$GO:0044266!multicellular organismal macromolecule catabolic process!0.00762948231814427!4313$GO:0044259!multicellular organismal macromolecule metabolic process!0.00762948231814427!4313$GO:0044268!multicellular organismal protein metabolic process!0.00762948231814427!4313$GO:0032963!collagen metabolic process!0.00762948231814427!4313$GO:0044243!multicellular organismal catabolic process!0.00762948231814427!4313$GO:0044236!multicellular organismal metabolic process!0.00762948231814427!4313$GO:0030017!sarcomere!0.0138075264980836!4313$GO:0021700!developmental maturation!0.0138075264980836!4313$GO:0030016!myofibril!0.0138075264980836!4313$GO:0044449!contractile fiber part!0.014586720778938!4313$GO:0043292!contractile fiber!0.014586720778938!4313$GO:0007586!digestion!0.0203692002083057!4313$GO:0001568!blood vessel development!0.031812593175251!4313$GO:0001944!vasculature development!0.031812593175251!4313$GO:0004222!metalloendopeptidase activity!0.0360308646701287!4313
|id=C351
|id=C351
|ontology_enrichment_celltype=CL:0000055!2.31e-42!180;CL:0000057!3.19e-19!75;CL:0000680!2.35e-18!57;CL:0000056!2.35e-18!57;CL:0000355!2.35e-18!57;CL:0000183!1.67e-17!59;CL:0000187!5.11e-17!54;CL:0000393!6.88e-16!60;CL:0000211!6.88e-16!60;CL:0000222!1.25e-15!119;CL:0000192!2.47e-15!42;CL:0000514!2.47e-15!42;CL:0000359!5.94e-12!32;CL:0000220!8.91e-12!246;CL:0002321!1.10e-11!248;CL:0002620!7.55e-08!23;CL:0002334!1.20e-07!12;CL:0000144!2.43e-07!625;CL:0002371!3.91e-07!591
|ontology_enrichment_celltype=CL:0000680!1.14e-20!58;CL:0000056!1.14e-20!58;CL:0000355!1.14e-20!58;CL:0000055!4.13e-20!106;CL:0000187!4.81e-19!55;CL:0000057!5.97e-19!76;CL:0000183!9.41e-19!59;CL:0000192!1.09e-18!43;CL:0000514!1.09e-18!43;CL:0000393!5.65e-16!61;CL:0000211!5.65e-16!61;CL:0000359!4.69e-14!32;CL:0000222!1.55e-12!121;CL:0000048!5.11e-11!427;CL:0002371!3.16e-10!588;CL:0000723!3.92e-10!433;CL:0000034!1.86e-09!441;CL:0000499!9.34e-08!28;CL:0002334!1.14e-07!12;CL:0002539!1.97e-07!10;CL:0002620!2.69e-07!23
|ontology_enrichment_disease=DOID:2394!7.08e-07!14
|ontology_enrichment_disease=DOID:2394!2.43e-08!14
|ontology_enrichment_uberon=UBERON:0000914!7.14e-21!83;UBERON:0002329!7.14e-21!83;UBERON:0003077!7.14e-21!83;UBERON:0003059!7.14e-21!83;UBERON:0007282!7.14e-21!83;UBERON:0009618!7.14e-21!83;UBERON:0007285!7.14e-21!83;UBERON:0000486!3.62e-20!82;UBERON:0004290!7.96e-20!70;UBERON:0004872!2.98e-19!84;UBERON:0002385!1.13e-18!63;UBERON:0001015!1.13e-18!63;UBERON:0000383!1.13e-18!63;UBERON:0001134!1.27e-18!61;UBERON:0002036!1.27e-18!61;UBERON:0003082!1.27e-18!61;UBERON:0001981!5.02e-16!60;UBERON:0007500!5.02e-16!60;UBERON:0004537!5.02e-16!60;UBERON:0006965!5.02e-16!60;UBERON:0005256!5.17e-16!143;UBERON:0002049!5.21e-16!79;UBERON:0007798!5.21e-16!79;UBERON:0001637!4.16e-15!42;UBERON:0003509!4.16e-15!42;UBERON:0004572!4.16e-15!42;UBERON:0000055!3.77e-14!69;UBERON:0004573!5.13e-13!33;UBERON:0004571!5.13e-13!33;UBERON:0003914!7.62e-13!118;UBERON:0000475!1.31e-12!365;UBERON:0000468!1.46e-12!659;UBERON:0000490!1.95e-12!138;UBERON:0002100!9.09e-12!216;UBERON:0001009!3.42e-11!113;UBERON:0004535!5.21e-11!110;UBERON:0003102!6.69e-10!95;UBERON:0000119!1.81e-09!312;UBERON:0000483!2.12e-09!309;UBERON:0002199!2.90e-09!45;UBERON:0002416!2.90e-09!45;UBERON:0000947!3.73e-09!21;UBERON:0010191!3.73e-09!21;UBERON:0000467!5.01e-09!625;UBERON:0000480!8.88e-09!626;UBERON:0000948!2.63e-07!24;UBERON:0005498!2.63e-07!24;UBERON:0004140!2.63e-07!24;UBERON:0009881!2.63e-07!24;UBERON:0004141!2.63e-07!24;UBERON:0003084!2.63e-07!24;UBERON:0007005!2.63e-07!24;UBERON:0004139!2.63e-07!24;UBERON:0004291!2.63e-07!24;UBERON:0007100!2.80e-07!27;UBERON:0002097!3.15e-07!40;UBERON:0001135!3.38e-07!15
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}}
}}

Revision as of 15:10, 19 October 2012


Full id: C351_Fibroblast_Smooth_mesenchymal_Adipocyte_tenocyte_Synoviocyte_Hair



Phase1 CAGE Peaks

Hg19::chr14:75070388..75070409,-p@chr14:75070388..75070409
-
Hg19::chr16:4431001..4431014,+p4@VASN
Hg19::chr16:55513074..55513088,+p2@MMP2
Hg19::chr16:55513101..55513124,+p1@MMP2
Hg19::chr16:55516814..55516833,+p@chr16:55516814..55516833
+
Hg19::chr16:55516984..55517009,+p@chr16:55516984..55517009
+
Hg19::chr16:55519282..55519295,+p@chr16:55519282..55519295
+
Hg19::chr16:55519314..55519342,-p@chr16:55519314..55519342
-
Hg19::chr16:55519541..55519560,+p@chr16:55519541..55519560
+
Hg19::chr16:55519569..55519597,+p@chr16:55519569..55519597
+
Hg19::chr16:55519605..55519627,+p@chr16:55519605..55519627
+
Hg19::chr16:55522512..55522527,+p6@MMP2
Hg19::chr16:55522536..55522599,+p4@MMP2
Hg19::chr16:55523690..55523729,-p@chr16:55523690..55523729
-
Hg19::chr16:55525707..55525728,+p@chr16:55525707..55525728
+
Hg19::chr16:55525755..55525774,+p@chr16:55525755..55525774
+
Hg19::chr16:55525781..55525812,+p@chr16:55525781..55525812
+
Hg19::chr16:55527062..55527078,+p7@MMP2
Hg19::chr16:55527084..55527124,+p5@MMP2
Hg19::chr16:55532232..55532249,+p@chr16:55532232..55532249
+
Hg19::chr16:55536741..55536782,+p@chr16:55536741..55536782
+
Hg19::chr16:55539240..55539261,+p@chr16:55539240..55539261
+
Hg19::chr16:55539265..55539280,+p@chr16:55539265..55539280
+
Hg19::chr16:55539338..55539366,+p@chr16:55539338..55539366
+
Hg19::chr16:55539371..55539383,+p@chr16:55539371..55539383
+
Hg19::chr16:55539430..55539443,+p@chr16:55539430..55539443
+
Hg19::chr16:55539539..55539552,+p@chr16:55539539..55539552
+
Hg19::chr16:55539559..55539581,+p@chr16:55539559..55539581
+
Hg19::chr16:55539785..55539877,+p@chr16:55539785..55539877
+
Hg19::chr16:55539883..55539894,+p@chr16:55539883..55539894
+
Hg19::chr16:55539899..55539914,+p@chr16:55539899..55539914
+
Hg19::chr16:55540311..55540323,+p@chr16:55540311..55540323
+


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:0001955blood vessel maturation0.00182503237960673
GO:0004228gelatinase A activity0.00182503237960673
GO:0030574collagen catabolic process0.00762948231814427
GO:0044256protein digestion0.00762948231814427
GO:0044254multicellular organismal protein catabolic process0.00762948231814427
GO:0044266multicellular organismal macromolecule catabolic process0.00762948231814427
GO:0044259multicellular organismal macromolecule metabolic process0.00762948231814427
GO:0044268multicellular organismal protein metabolic process0.00762948231814427
GO:0032963collagen metabolic process0.00762948231814427
GO:0044243multicellular organismal catabolic process0.00762948231814427
GO:0044236multicellular organismal metabolic process0.00762948231814427
GO:0030017sarcomere0.0138075264980836
GO:0021700developmental maturation0.0138075264980836
GO:0030016myofibril0.0138075264980836
GO:0044449contractile fiber part0.014586720778938
GO:0043292contractile fiber0.014586720778938
GO:0007586digestion0.0203692002083057
GO:0001568blood vessel development0.031812593175251
GO:0001944vasculature development0.031812593175251
GO:0004222metalloendopeptidase activity0.0360308646701287



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
muscle tissue5.19e-2164
musculature5.19e-2164
musculature of body5.19e-2164
skeletal muscle tissue8.88e-2162
striated muscle tissue8.88e-2162
myotome8.88e-2162
dense mesenchyme tissue2.56e-2073
somite2.89e-2071
presomitic mesoderm2.89e-2071
presumptive segmental plate2.89e-2071
dermomyotome2.89e-2071
trunk paraxial mesoderm2.89e-2071
paraxial mesoderm1.19e-1972
presumptive paraxial mesoderm1.19e-1972
multilaminar epithelium1.80e-1983
splanchnic layer of lateral plate mesoderm1.89e-1883
epithelial vesicle6.20e-1878
artery9.81e-1842
arterial blood vessel9.81e-1842
arterial system9.81e-1842
trunk mesenchyme8.28e-16122
epithelial tube open at both ends1.57e-1559
blood vessel1.57e-1559
blood vasculature1.57e-1559
vascular cord1.57e-1559
systemic artery8.32e-1533
systemic arterial system8.32e-1533
mesoderm2.90e-14315
mesoderm-derived structure2.90e-14315
presumptive mesoderm2.90e-14315
unilaminar epithelium1.53e-13148
vasculature1.55e-1378
vascular system1.55e-1378
vessel7.68e-1368
mesenchyme9.93e-13160
entire embryonic mesenchyme9.93e-13160
cardiovascular system1.28e-11109
epithelial tube2.01e-11117
circulatory system3.34e-11112
trunk7.63e-10199
aorta1.36e-0921
aortic system1.36e-0921
smooth muscle tissue9.70e-0915
integument4.48e-0846
integumental system4.48e-0846
organism subdivision1.22e-07264
blood vessel smooth muscle1.97e-0710
arterial system smooth muscle1.97e-0710
artery smooth muscle tissue1.97e-0710
aorta smooth muscle tissue1.97e-0710
surface structure4.87e-0799
heart8.34e-0724
primitive heart tube8.34e-0724
primary heart field8.34e-0724
anterior lateral plate mesoderm8.34e-0724
heart tube8.34e-0724
heart primordium8.34e-0724
cardiac mesoderm8.34e-0724
cardiogenic plate8.34e-0724
heart rudiment8.34e-0724
multi-cellular organism8.62e-07656
Disease
Ontology termp-valuen
ovarian cancer2.43e-0814


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

No analysis results for this cluster

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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