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Coexpression cluster:C952: Difference between revisions

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|full_id=C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast
|full_id=C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast
|id=C952
|id=C952
|ontology_enrichment_celltype=CL:0000055!3.15e-37!180;CL:0000057!4.64e-21!75;CL:0000680!1.03e-17!57;CL:0000056!1.03e-17!57;CL:0000355!1.03e-17!57;CL:0000222!1.04e-16!119;CL:0000183!1.45e-16!59;CL:0000187!3.29e-16!54;CL:0002321!6.44e-16!248;CL:0000220!6.92e-16!246;CL:0000393!2.37e-15!60;CL:0000211!2.37e-15!60;CL:0000192!8.59e-15!42;CL:0000514!8.59e-15!42;CL:0000359!1.74e-14!32;CL:0002620!1.29e-13!23
|ontology_enrichment_celltype=CL:0000057!5.95e-21!76;CL:0000680!3.45e-18!58;CL:0000056!3.45e-18!58;CL:0000355!3.45e-18!58;CL:0000222!3.48e-17!121;CL:0000187!9.11e-17!55;CL:0000183!1.71e-16!59;CL:0000393!8.03e-16!61;CL:0000211!8.03e-16!61;CL:0002321!1.84e-15!250;CL:0000055!3.80e-15!106;CL:0000192!6.22e-15!43;CL:0000514!6.22e-15!43;CL:0000359!1.92e-14!32;CL:0002620!1.58e-13!23
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.30e-25!365;UBERON:0000914!2.89e-24!83;UBERON:0002329!2.89e-24!83;UBERON:0003077!2.89e-24!83;UBERON:0003059!2.89e-24!83;UBERON:0007282!2.89e-24!83;UBERON:0009618!2.89e-24!83;UBERON:0007285!2.89e-24!83;UBERON:0004290!4.61e-21!70;UBERON:0000486!9.59e-21!82;UBERON:0000119!2.43e-19!312;UBERON:0000483!6.69e-19!309;UBERON:0001637!2.67e-17!42;UBERON:0003509!2.67e-17!42;UBERON:0004572!2.67e-17!42;UBERON:0000481!8.68e-17!347;UBERON:0002385!1.23e-16!63;UBERON:0001015!1.23e-16!63;UBERON:0000383!1.23e-16!63;UBERON:0001134!1.43e-16!61;UBERON:0002036!1.43e-16!61;UBERON:0003082!1.43e-16!61;UBERON:0001981!4.14e-16!60;UBERON:0007500!4.14e-16!60;UBERON:0004537!4.14e-16!60;UBERON:0006965!4.14e-16!60;UBERON:0002049!6.52e-16!79;UBERON:0007798!6.52e-16!79;UBERON:0002199!7.97e-16!45;UBERON:0002416!7.97e-16!45;UBERON:0000055!1.29e-15!69;UBERON:0003102!6.89e-15!95;UBERON:0002097!1.75e-14!40;UBERON:0004573!2.06e-14!33;UBERON:0004571!2.06e-14!33;UBERON:0004872!4.28e-14!84;UBERON:0005256!8.81e-14!143;UBERON:0000468!3.53e-13!659;UBERON:0000467!2.11e-12!625;UBERON:0000480!3.03e-12!626;UBERON:0000490!6.96e-11!138;UBERON:0002100!1.32e-10!216;UBERON:0004111!1.40e-10!241;UBERON:0000477!5.48e-10!286;UBERON:0004535!8.16e-10!110;UBERON:0000025!1.04e-09!194;UBERON:0001009!4.05e-09!113;UBERON:0000947!1.92e-08!21;UBERON:0010191!1.92e-08!21;UBERON:0003914!2.88e-08!118;UBERON:0004121!7.49e-08!169;UBERON:0000922!1.02e-07!612;UBERON:0003104!1.88e-07!238;UBERON:0009142!1.88e-07!238;UBERON:0002050!2.81e-07!605;UBERON:0005423!2.81e-07!605;UBERON:0000923!3.19e-07!604;UBERON:0005291!3.19e-07!604;UBERON:0006598!3.19e-07!604;UBERON:0002532!3.19e-07!604;UBERON:0000924!4.68e-07!173;UBERON:0006601!4.68e-07!173
|ontology_enrichment_uberon=UBERON:0007524!2.25e-22!73;UBERON:0003077!7.75e-22!72;UBERON:0007285!7.75e-22!72;UBERON:0002329!1.02e-21!71;UBERON:0003059!1.02e-21!71;UBERON:0007282!1.02e-21!71;UBERON:0004290!1.02e-21!71;UBERON:0009618!1.02e-21!71;UBERON:0000486!1.19e-20!83;UBERON:0007503!1.53e-19!78;UBERON:0000119!2.80e-19!309;UBERON:0000483!5.26e-19!306;UBERON:0001637!1.46e-17!42;UBERON:0003509!1.46e-17!42;UBERON:0004572!1.46e-17!42;UBERON:0002385!3.22e-17!64;UBERON:0001015!3.22e-17!64;UBERON:0000383!3.22e-17!64;UBERON:0001134!4.58e-17!62;UBERON:0002036!4.58e-17!62;UBERON:0003082!4.58e-17!62;UBERON:0002199!5.77e-16!46;UBERON:0002416!5.77e-16!46;UBERON:0007500!2.82e-15!59;UBERON:0001981!2.82e-15!59;UBERON:0004537!2.82e-15!59;UBERON:0006965!2.82e-15!59;UBERON:0002049!3.87e-15!78;UBERON:0007798!3.87e-15!78;UBERON:0002097!4.32e-15!41;UBERON:0000055!8.71e-15!68;UBERON:0004573!1.34e-14!33;UBERON:0004571!1.34e-14!33;UBERON:0000481!2.16e-14!342;UBERON:0000490!3.08e-14!148;UBERON:0003102!3.33e-14!99;UBERON:0000467!1.25e-13!624;UBERON:0000468!1.81e-13!656;UBERON:0000480!1.88e-13!625;UBERON:0000477!2.12e-13!373;UBERON:0004872!2.53e-13!83;UBERON:0005256!2.30e-11!122;UBERON:0003104!8.93e-11!160;UBERON:0009142!8.93e-11!160;UBERON:0010314!2.09e-10!132;UBERON:0004111!3.43e-10!240;UBERON:0000475!8.34e-10!264;UBERON:0004535!1.40e-09!109;UBERON:0000025!1.44e-09!192;UBERON:0001009!6.88e-09!112;UBERON:0000947!2.79e-08!21;UBERON:0010191!2.79e-08!21;UBERON:0003914!5.59e-08!117;UBERON:0002100!1.27e-07!199;UBERON:0004121!2.64e-07!171;UBERON:0000924!2.64e-07!171;UBERON:0006601!2.64e-07!171;UBERON:0000922!4.02e-07!592
|tf_chipseq_enrich=CTCF#10664;8:4.76467233162225:1.10088565904027e-05:0.000285157235477447!EGR1#1958;7:3.879694851519:0.000318655785854229:0.00326307398949209!RAD21#5885;7:8.05391525202159:2.36147727378579e-06:8.3802353040066e-05!ZBTB7A#51341;7:5.71815168390347:2.40589727322203e-05:0.000524352056172862
|tf_chipseq_enrich=CTCF#10664;8:4.76467233162225:1.10088565904027e-05:0.000285157235477447!EGR1#1958;7:3.879694851519:0.000318655785854229:0.00326307398949209!RAD21#5885;7:8.05391525202159:2.36147727378579e-06:8.3802353040066e-05!ZBTB7A#51341;7:5.71815168390347:2.40589727322203e-05:0.000524352056172862
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}}
}}

Revision as of 16:54, 19 October 2012


Full id: C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr5:98104978..98105010,+p5@RGMB
Hg19::chr5:98105021..98105033,+p11@RGMB
Hg19::chr5:98105080..98105096,+p9@RGMB
Hg19::chr5:98105123..98105126,+p26@RGMB
Hg19::chr5:98105127..98105145,+p8@RGMB
Hg19::chr5:98105219..98105258,+p6@RGMB
Hg19::chr5:98105268..98105295,+p2@RGMB
Hg19::chr5:98105586..98105654,+p@chr5:98105586..98105654
+
Hg19::chr5:98109470..98109495,+p3@RGMB


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
dense mesenchyme tissue2.25e-2273
paraxial mesoderm7.75e-2272
presumptive paraxial mesoderm7.75e-2272
somite1.02e-2171
presomitic mesoderm1.02e-2171
presumptive segmental plate1.02e-2171
dermomyotome1.02e-2171
trunk paraxial mesoderm1.02e-2171
multilaminar epithelium1.19e-2083
epithelial vesicle1.53e-1978
cell layer2.80e-19309
epithelium5.26e-19306
artery1.46e-1742
arterial blood vessel1.46e-1742
arterial system1.46e-1742
muscle tissue3.22e-1764
musculature3.22e-1764
musculature of body3.22e-1764
skeletal muscle tissue4.58e-1762
striated muscle tissue4.58e-1762
myotome4.58e-1762
integument5.77e-1646
integumental system5.77e-1646
epithelial tube open at both ends2.82e-1559
blood vessel2.82e-1559
blood vasculature2.82e-1559
vascular cord2.82e-1559
vasculature3.87e-1578
vascular system3.87e-1578
skin of body4.32e-1541
vessel8.71e-1568
systemic artery1.34e-1433
systemic arterial system1.34e-1433
multi-tissue structure2.16e-14342
unilaminar epithelium3.08e-14148
surface structure3.33e-1499
anatomical system1.25e-13624
multi-cellular organism1.81e-13656
anatomical group1.88e-13625
anatomical cluster2.12e-13373
splanchnic layer of lateral plate mesoderm2.53e-1383
trunk mesenchyme2.30e-11122
mesenchyme8.93e-11160
entire embryonic mesenchyme8.93e-11160
structure with developmental contribution from neural crest2.09e-10132
anatomical conduit3.43e-10240
organism subdivision8.34e-10264
cardiovascular system1.40e-09109
tube1.44e-09192
circulatory system6.88e-09112
aorta2.79e-0821
aortic system2.79e-0821
epithelial tube5.59e-08117
trunk1.27e-07199
ectoderm-derived structure2.64e-07171
ectoderm2.64e-07171
presumptive ectoderm2.64e-07171
embryo4.02e-07592


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#1066484.764672331622251.10088565904027e-050.000285157235477447
EGR1#195873.8796948515190.0003186557858542290.00326307398949209
RAD21#588578.053915252021592.36147727378579e-068.3802353040066e-05
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524352056172862



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.