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Coexpression cluster:C609: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!2.48e-07!14
|ontology_enrichment_disease=DOID:2394!2.48e-07!14
|ontology_enrichment_uberon=UBERON:0002204!4.35e-20!167;UBERON:0000926!6.18e-20!448;UBERON:0004120!6.18e-20!448;UBERON:0006603!6.18e-20!448;UBERON:0004290!2.00e-18!70;UBERON:0000914!3.17e-18!83;UBERON:0002329!3.17e-18!83;UBERON:0003077!3.17e-18!83;UBERON:0003059!3.17e-18!83;UBERON:0007282!3.17e-18!83;UBERON:0009618!3.17e-18!83;UBERON:0007285!3.17e-18!83;UBERON:0001134!4.56e-17!61;UBERON:0002036!4.56e-17!61;UBERON:0003082!4.56e-17!61;UBERON:0002385!2.75e-16!63;UBERON:0001015!2.75e-16!63;UBERON:0000383!2.75e-16!63;UBERON:0000486!7.12e-15!82;UBERON:0005256!5.76e-14!143;UBERON:0004872!1.88e-12!84;UBERON:0003081!3.31e-12!216;UBERON:0002384!1.24e-11!375;UBERON:0001009!2.13e-10!113;UBERON:0004535!2.41e-10!110;UBERON:0001637!3.18e-10!42;UBERON:0003509!3.18e-10!42;UBERON:0004572!3.18e-10!42;UBERON:0002100!3.49e-10!216;UBERON:0003914!5.11e-10!118;UBERON:0002049!1.94e-09!79;UBERON:0007798!1.94e-09!79;UBERON:0000468!2.66e-09!659;UBERON:0004573!3.78e-09!33;UBERON:0004571!3.78e-09!33;UBERON:0000948!9.59e-09!24;UBERON:0005498!9.59e-09!24;UBERON:0004140!9.59e-09!24;UBERON:0009881!9.59e-09!24;UBERON:0004141!9.59e-09!24;UBERON:0003084!9.59e-09!24;UBERON:0007005!9.59e-09!24;UBERON:0004139!9.59e-09!24;UBERON:0004291!9.59e-09!24;UBERON:0000490!1.37e-08!138;UBERON:0001981!2.05e-08!60;UBERON:0007500!2.05e-08!60;UBERON:0004537!2.05e-08!60;UBERON:0006965!2.05e-08!60;UBERON:0007100!2.08e-08!27;UBERON:0000055!9.01e-08!69;UBERON:0001013!1.42e-07!14;UBERON:0000480!2.21e-07!626;UBERON:0000467!2.72e-07!625
|ontology_enrichment_uberon=UBERON:0002204!4.35e-20!167;UBERON:0000926!6.18e-20!448;UBERON:0004120!6.18e-20!448;UBERON:0006603!6.18e-20!448;UBERON:0004290!2.00e-18!70;UBERON:0000914!3.17e-18!83;UBERON:0002329!3.17e-18!83;UBERON:0003077!3.17e-18!83;UBERON:0003059!3.17e-18!83;UBERON:0007282!3.17e-18!83;UBERON:0009618!3.17e-18!83;UBERON:0007285!3.17e-18!83;UBERON:0001134!4.56e-17!61;UBERON:0002036!4.56e-17!61;UBERON:0003082!4.56e-17!61;UBERON:0002385!2.75e-16!63;UBERON:0001015!2.75e-16!63;UBERON:0000383!2.75e-16!63;UBERON:0000486!7.12e-15!82;UBERON:0005256!5.76e-14!143;UBERON:0004872!1.88e-12!84;UBERON:0003081!3.31e-12!216;UBERON:0002384!1.24e-11!375;UBERON:0001009!2.13e-10!113;UBERON:0004535!2.41e-10!110;UBERON:0001637!3.18e-10!42;UBERON:0003509!3.18e-10!42;UBERON:0004572!3.18e-10!42;UBERON:0002100!3.49e-10!216;UBERON:0003914!5.11e-10!118;UBERON:0002049!1.94e-09!79;UBERON:0007798!1.94e-09!79;UBERON:0000468!2.66e-09!659;UBERON:0004573!3.78e-09!33;UBERON:0004571!3.78e-09!33;UBERON:0000948!9.59e-09!24;UBERON:0005498!9.59e-09!24;UBERON:0004140!9.59e-09!24;UBERON:0009881!9.59e-09!24;UBERON:0004141!9.59e-09!24;UBERON:0003084!9.59e-09!24;UBERON:0007005!9.59e-09!24;UBERON:0004139!9.59e-09!24;UBERON:0004291!9.59e-09!24;UBERON:0000490!1.37e-08!138;UBERON:0001981!2.05e-08!60;UBERON:0007500!2.05e-08!60;UBERON:0004537!2.05e-08!60;UBERON:0006965!2.05e-08!60;UBERON:0007100!2.08e-08!27;UBERON:0000055!9.01e-08!69;UBERON:0001013!1.42e-07!14;UBERON:0000480!2.21e-07!626;UBERON:0000467!2.72e-07!625
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}}
}}

Revision as of 20:36, 8 August 2012


Full id: C609_Smooth_mesenchymal_Preadipocyte_Cardiac_Fibroblast_Osteoblast_tenocyte



Phase1 CAGE Peaks

Hg19::chrX:47441825..47441846,+p1@TIMP1
Hg19::chrX:47442857..47442871,+p5@TIMP1
Hg19::chrX:47442876..47442906,+p3@TIMP1
Hg19::chrX:47444329..47444370,+p4@TIMP1
Hg19::chrX:47444375..47444387,-p@chrX:47444375..47444387
-
Hg19::chrX:47444394..47444423,-p@chrX:47444394..47444423
-
Hg19::chrX:47444675..47444713,-p@chrX:47444675..47444713
-
Hg19::chrX:47444716..47444731,-p@chrX:47444716..47444731
-
Hg19::chrX:47445998..47446031,+p@chrX:47445998..47446031
+
Hg19::chrX:47446039..47446094,+p@chrX:47446039..47446094
+
Hg19::chrX:47446043..47446074,-p4@CU674427
Hg19::chrX:47446081..47446133,-p1@CU674427
Hg19::chrX:47446099..47446146,+p@chrX:47446099..47446146
+
Hg19::chrX:47446141..47446157,-p7@CU674427
Hg19::chrX:47446158..47446174,-p3@CU674427


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:0051045negative regulation of membrane protein ectodomain proteolysis0.000809490168373955
GO:0051043regulation of membrane protein ectodomain proteolysis0.000809490168373955
GO:0043249erythrocyte maturation0.00202372542093489
GO:0045861negative regulation of proteolysis0.00202372542093489
GO:0048821erythrocyte development0.00226657247144707
GO:0033619membrane protein proteolysis0.00300667776824612
GO:0006509membrane protein ectodomain proteolysis0.00300667776824612
GO:0030162regulation of proteolysis0.00305807396941272
GO:0008191metalloendopeptidase inhibitor activity0.00305807396941272
GO:0030218erythrocyte differentiation0.0053426351112681
GO:0048469cell maturation0.00662310137760508
GO:0021700developmental maturation0.00715049648730327
GO:0030099myeloid cell differentiation0.00958934507150685
GO:0051248negative regulation of protein metabolic process0.0120267110729845
GO:0030097hemopoiesis0.0173326130169482
GO:0048534hemopoietic or lymphoid organ development0.0173326130169482
GO:0002520immune system development0.0173326130169482
GO:0008284positive regulation of cell proliferation0.0209568010256813
GO:0004866endopeptidase inhibitor activity0.0214727918347617
GO:0030414protease inhibitor activity0.0215324384787472
GO:0031324negative regulation of cellular metabolic process0.0282350170728835
GO:0004857enzyme inhibitor activity0.0282350170728835
GO:0005578proteinaceous extracellular matrix0.0282350170728835
GO:0051246regulation of protein metabolic process0.0282350170728835
GO:0009892negative regulation of metabolic process0.0282350170728835
GO:0042127regulation of cell proliferation0.0292039145359527
GO:0008283cell proliferation0.0446718648473034



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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.37e-31180
multi fate stem cell4.50e-23430
somatic stem cell8.67e-22436
somatic cell4.82e-20591
stem cell1.24e-19444
muscle precursor cell6.69e-1957
myoblast6.69e-1957
multi-potent skeletal muscle stem cell6.69e-1957
fibroblast3.03e-1875
contractile cell9.37e-1859
muscle cell1.04e-1754
smooth muscle cell1.58e-1442
smooth muscle myoblast1.58e-1442
electrically responsive cell4.66e-1460
electrically active cell4.66e-1460
animal cell1.41e-12679
eukaryotic cell1.41e-12679
vascular associated smooth muscle cell9.50e-1232
connective tissue cell1.82e-11365
mesodermal cell1.21e-10119
mesenchymal cell3.59e-10358
cardiocyte2.04e-0816
preadipocyte6.16e-0812
motile cell1.32e-07390
CD14-positive, CD16-negative classical monocyte2.71e-0742
classical monocyte3.54e-0745
Uber Anatomy
Ontology termp-valuen
musculoskeletal system4.35e-20167
mesoderm6.18e-20448
mesoderm-derived structure6.18e-20448
presumptive mesoderm6.18e-20448
dermomyotome2.00e-1870
somite3.17e-1883
paraxial mesoderm3.17e-1883
presomitic mesoderm3.17e-1883
presumptive segmental plate3.17e-1883
trunk paraxial mesoderm3.17e-1883
presumptive paraxial mesoderm3.17e-1883
skeletal muscle tissue4.56e-1761
striated muscle tissue4.56e-1761
myotome4.56e-1761
muscle tissue2.75e-1663
musculature2.75e-1663
musculature of body2.75e-1663
multilaminar epithelium7.12e-1582
trunk mesenchyme5.76e-14143
splanchnic layer of lateral plate mesoderm1.88e-1284
lateral plate mesoderm3.31e-12216
connective tissue1.24e-11375
circulatory system2.13e-10113
cardiovascular system2.41e-10110
artery3.18e-1042
arterial blood vessel3.18e-1042
arterial system3.18e-1042
trunk3.49e-10216
epithelial tube5.11e-10118
vasculature1.94e-0979
vascular system1.94e-0979
multi-cellular organism2.66e-09659
systemic artery3.78e-0933
systemic arterial system3.78e-0933
heart9.59e-0924
primitive heart tube9.59e-0924
primary heart field9.59e-0924
anterior lateral plate mesoderm9.59e-0924
heart tube9.59e-0924
heart primordium9.59e-0924
cardiac mesoderm9.59e-0924
cardiogenic plate9.59e-0924
heart rudiment9.59e-0924
unilaminar epithelium1.37e-08138
blood vessel2.05e-0860
epithelial tube open at both ends2.05e-0860
blood vasculature2.05e-0860
vascular cord2.05e-0860
primary circulatory organ2.08e-0827
vessel9.01e-0869
adipose tissue1.42e-0714
anatomical group2.21e-07626
anatomical system2.72e-07625
Disease
Ontology termp-valuen
ovarian cancer2.48e-0714


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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