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Coexpression cluster:C4002: Difference between revisions

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|full_id=C4002_Smooth_Fibroblast_Renal_Hair_spindle_Alveolar_Chondrocyte
|full_id=C4002_Smooth_Fibroblast_Renal_Hair_spindle_Alveolar_Chondrocyte
|id=C4002
|id=C4002
|ontology_enrichment_celltype=CL:0000055!2.80e-31!180;CL:0000222!9.39e-28!119;CL:0000220!9.06e-24!246;CL:0002321!1.92e-23!248;CL:0000057!4.44e-16!75;CL:0000680!1.79e-15!57;CL:0000056!1.79e-15!57;CL:0000355!1.79e-15!57;CL:0000183!3.58e-15!59;CL:0000187!5.20e-15!54;CL:0000393!1.79e-14!60;CL:0000211!1.79e-14!60;CL:0000192!2.34e-14!42;CL:0000514!2.34e-14!42;CL:0000359!1.43e-11!32;CL:0000213!4.20e-11!57;CL:0000215!4.20e-11!57;CL:0000548!4.96e-10!679;CL:0000004!4.96e-10!679;CL:0000255!4.96e-10!679;CL:0000012!2.30e-09!682;CL:0002078!2.59e-09!44;CL:0000066!5.54e-09!254;CL:0000144!4.57e-08!625;CL:0002139!9.76e-08!24;CL:0002620!2.39e-07!23;CL:0000115!3.48e-07!35;CL:0002371!5.43e-07!591;CL:0000076!8.61e-07!62
|ontology_enrichment_celltype=CL:0000222!3.01e-30!121;CL:0002321!3.44e-23!250;CL:0000680!2.14e-16!58;CL:0000056!2.14e-16!58;CL:0000355!2.14e-16!58;CL:0000057!2.78e-16!76;CL:0000183!7.70e-16!59;CL:0000187!8.55e-16!55;CL:0000192!1.40e-15!43;CL:0000514!1.40e-15!43;CL:0000393!2.12e-15!61;CL:0000211!2.12e-15!61;CL:0000548!2.37e-15!679;CL:0000255!2.37e-15!679;CL:0000055!3.40e-14!106;CL:0002371!6.77e-13!588;CL:0000359!1.11e-12!32;CL:0000213!1.63e-12!58;CL:0000215!1.63e-12!58;CL:0002078!9.51e-11!45;CL:0002139!2.32e-08!24;CL:0000115!2.47e-08!36;CL:0002620!2.29e-07!23;CL:0000066!5.11e-07!253;CL:0000076!7.78e-07!63
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!3.56e-25!118;UBERON:0005256!1.03e-24!143;UBERON:0002100!2.73e-23!216;UBERON:0002049!4.17e-22!79;UBERON:0007798!4.17e-22!79;UBERON:0000055!1.03e-20!69;UBERON:0000119!5.02e-20!312;UBERON:0000490!8.07e-20!138;UBERON:0004872!1.48e-19!84;UBERON:0000483!1.66e-19!309;UBERON:0000914!1.77e-19!83;UBERON:0002329!1.77e-19!83;UBERON:0003077!1.77e-19!83;UBERON:0003059!1.77e-19!83;UBERON:0007282!1.77e-19!83;UBERON:0009618!1.77e-19!83;UBERON:0007285!1.77e-19!83;UBERON:0000486!2.49e-19!82;UBERON:0000475!1.73e-18!365;UBERON:0001981!2.06e-18!60;UBERON:0007500!2.06e-18!60;UBERON:0004537!2.06e-18!60;UBERON:0006965!2.06e-18!60;UBERON:0003104!3.04e-18!238;UBERON:0009142!3.04e-18!238;UBERON:0004290!5.32e-18!70;UBERON:0000468!9.40e-16!659;UBERON:0001637!3.11e-15!42;UBERON:0003509!3.11e-15!42;UBERON:0004572!3.11e-15!42;UBERON:0001134!3.17e-15!61;UBERON:0002036!3.17e-15!61;UBERON:0003082!3.17e-15!61;UBERON:0000481!3.41e-15!347;UBERON:0002385!5.54e-15!63;UBERON:0001015!5.54e-15!63;UBERON:0000383!5.54e-15!63;UBERON:0000477!7.95e-15!286;UBERON:0004535!2.69e-14!110;UBERON:0001009!7.98e-14!113;UBERON:0000467!1.15e-12!625;UBERON:0000480!1.70e-12!626;UBERON:0004111!3.90e-12!241;UBERON:0004573!1.33e-11!33;UBERON:0004571!1.33e-11!33;UBERON:0000025!4.90e-10!194;UBERON:0009569!1.49e-09!113;UBERON:0000926!1.54e-08!448;UBERON:0004120!1.54e-08!448;UBERON:0006603!1.54e-08!448;UBERON:0004923!2.87e-08!57;UBERON:0000947!9.37e-08!21;UBERON:0010191!9.37e-08!21;UBERON:0003102!1.36e-07!95;UBERON:0002199!1.43e-07!45;UBERON:0002416!1.43e-07!45;UBERON:0006914!1.75e-07!25;UBERON:0000923!2.80e-07!604;UBERON:0005291!2.80e-07!604;UBERON:0006598!2.80e-07!604;UBERON:0002532!2.80e-07!604;UBERON:0002050!3.09e-07!605;UBERON:0005423!3.09e-07!605;UBERON:0000922!4.05e-07!612;UBERON:0000353!4.07e-07!17;UBERON:0000466!4.66e-07!126;UBERON:0000487!5.54e-07!22
|ontology_enrichment_uberon=UBERON:0003914!9.04e-26!117;UBERON:0000490!3.13e-23!148;UBERON:0002049!1.28e-22!78;UBERON:0007798!1.28e-22!78;UBERON:0007503!7.50e-22!78;UBERON:0003104!1.16e-21!160;UBERON:0009142!1.16e-21!160;UBERON:0000055!4.46e-21!68;UBERON:0005256!5.86e-21!122;UBERON:0000486!1.58e-20!83;UBERON:0004872!3.93e-20!83;UBERON:0002100!7.86e-20!199;UBERON:0007500!2.53e-19!59;UBERON:0001981!2.53e-19!59;UBERON:0004537!2.53e-19!59;UBERON:0006965!2.53e-19!59;UBERON:0002329!4.46e-19!71;UBERON:0003059!4.46e-19!71;UBERON:0007282!4.46e-19!71;UBERON:0004290!4.46e-19!71;UBERON:0009618!4.46e-19!71;UBERON:0007524!7.16e-19!73;UBERON:0000475!1.27e-18!264;UBERON:0003077!2.55e-18!72;UBERON:0007285!2.55e-18!72;UBERON:0001637!1.21e-16!42;UBERON:0003509!1.21e-16!42;UBERON:0004572!1.21e-16!42;UBERON:0001134!5.92e-16!62;UBERON:0002036!5.92e-16!62;UBERON:0003082!5.92e-16!62;UBERON:0000119!1.79e-15!309;UBERON:0002385!2.02e-15!64;UBERON:0001015!2.02e-15!64;UBERON:0000383!2.02e-15!64;UBERON:0004535!3.82e-15!109;UBERON:0000483!4.65e-15!306;UBERON:0001009!1.07e-14!112;UBERON:0004573!1.49e-12!33;UBERON:0004571!1.49e-12!33;UBERON:0000468!2.61e-12!656;UBERON:0000467!2.56e-10!624;UBERON:0000480!4.17e-10!625;UBERON:0000477!1.27e-09!373;UBERON:0000481!1.42e-09!342;UBERON:0004111!1.47e-08!240;UBERON:0006914!1.54e-08!25;UBERON:0000947!3.20e-08!21;UBERON:0010191!3.20e-08!21;UBERON:0002199!4.47e-08!46;UBERON:0002416!4.47e-08!46;UBERON:0003102!7.00e-08!99;UBERON:0000487!7.61e-08!22;UBERON:0000926!9.06e-08!315;UBERON:0004120!9.06e-08!315;UBERON:0006603!9.06e-08!315;UBERON:0004923!1.38e-07!66;UBERON:0009569!1.69e-07!112;UBERON:0000353!6.40e-07!15;UBERON:0002097!8.35e-07!41
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279778500515652!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664732832945362!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329158440996695
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279778500515652!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664732832945362!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329158440996695
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689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.000754551,0.0276507,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.0404514,0.00528373,0.222548,0.175934,0.157274,0.00199458,0.035048,0.205954,7.71155e-06
}}
}}

Revision as of 15:35, 19 October 2012


Full id: C4002_Smooth_Fibroblast_Renal_Hair_spindle_Alveolar_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr1:86046433..86046453,+p1@CYR61
Hg19::chr1:86047201..86047223,+p2@CYR61
Hg19::chr1:86048263..86048315,-p@chr1:86048263..86048315
-


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

No GOStat results

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
epithelial tube9.04e-26117
unilaminar epithelium3.13e-23148
vasculature1.28e-2278
vascular system1.28e-2278
epithelial vesicle7.50e-2278
mesenchyme1.16e-21160
entire embryonic mesenchyme1.16e-21160
vessel4.46e-2168
trunk mesenchyme5.86e-21122
multilaminar epithelium1.58e-2083
splanchnic layer of lateral plate mesoderm3.93e-2083
trunk7.86e-20199
epithelial tube open at both ends2.53e-1959
blood vessel2.53e-1959
blood vasculature2.53e-1959
vascular cord2.53e-1959
somite4.46e-1971
presomitic mesoderm4.46e-1971
presumptive segmental plate4.46e-1971
dermomyotome4.46e-1971
trunk paraxial mesoderm4.46e-1971
dense mesenchyme tissue7.16e-1973
organism subdivision1.27e-18264
paraxial mesoderm2.55e-1872
presumptive paraxial mesoderm2.55e-1872
artery1.21e-1642
arterial blood vessel1.21e-1642
arterial system1.21e-1642
skeletal muscle tissue5.92e-1662
striated muscle tissue5.92e-1662
myotome5.92e-1662
cell layer1.79e-15309
muscle tissue2.02e-1564
musculature2.02e-1564
musculature of body2.02e-1564
cardiovascular system3.82e-15109
epithelium4.65e-15306
circulatory system1.07e-14112
systemic artery1.49e-1233
systemic arterial system1.49e-1233
multi-cellular organism2.61e-12656
anatomical system2.56e-10624
anatomical group4.17e-10625
anatomical cluster1.27e-09373
multi-tissue structure1.42e-09342
anatomical conduit1.47e-08240
squamous epithelium1.54e-0825
aorta3.20e-0821
aortic system3.20e-0821
integument4.47e-0846
integumental system4.47e-0846
surface structure7.00e-0899
simple squamous epithelium7.61e-0822
mesoderm9.06e-08315
mesoderm-derived structure9.06e-08315
presumptive mesoderm9.06e-08315
organ component layer1.38e-0766
subdivision of trunk1.69e-07112
parenchyma6.40e-0715
skin of body8.35e-0741


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#1066435.360256373075030.0064925092527670.0279778500515652
RAD21#5885310.35503389545630.0009004912073565420.00664732832945362
TRIM28#10155212.39368336350830.008368344129438470.0329158440996695



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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