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Coexpression cluster:C606: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0045879!negative regulation of smoothened signaling pathway!0.00156010832450253!64399$GO:0040036!regulation of fibroblast growth factor receptor signaling pathway!0.0023401624867538!64399$GO:0008589!regulation of smoothened signaling pathway!0.00364025275717257!64399$GO:0007224!smoothened signaling pathway!0.00442030691942384!64399$GO:0008543!fibroblast growth factor receptor signaling pathway!0.00442030691942384!64399$GO:0007405!neuroblast proliferation!0.00442030691942384!64399$GO:0009953!dorsal/ventral pattern formation!0.00624043329801013!64399$GO:0030324!lung development!0.00745385088373431!64399$GO:0030323!respiratory tube development!0.00745385088373431!64399$GO:0003002!regionalization!0.013572942423172!64399$GO:0009968!negative regulation of signal transduction!0.0147501150680239!64399$GO:0035295!tube development!0.0148810332491011!64399$GO:0007389!pattern specification process!0.0148810332491011!64399$GO:0009986!cell surface!0.0164925737161696!64399$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0218415165430354!64399$GO:0048699!generation of neurons!0.0235966384081008!64399$GO:0022008!neurogenesis!0.0240440224129214!64399$GO:0007167!enzyme linked receptor protein signaling pathway!0.0260018054083755!64399$GO:0009887!organ morphogenesis!0.0297241691299956!64399
|gostat_on_coexpression_clusters=GO:0045879!negative regulation of smoothened signaling pathway!0.00156010832450253!64399$GO:0040036!regulation of fibroblast growth factor receptor signaling pathway!0.0023401624867538!64399$GO:0008589!regulation of smoothened signaling pathway!0.00364025275717257!64399$GO:0007224!smoothened signaling pathway!0.00442030691942384!64399$GO:0008543!fibroblast growth factor receptor signaling pathway!0.00442030691942384!64399$GO:0007405!neuroblast proliferation!0.00442030691942384!64399$GO:0009953!dorsal/ventral pattern formation!0.00624043329801013!64399$GO:0030324!lung development!0.00745385088373431!64399$GO:0030323!respiratory tube development!0.00745385088373431!64399$GO:0003002!regionalization!0.013572942423172!64399$GO:0009968!negative regulation of signal transduction!0.0147501150680239!64399$GO:0035295!tube development!0.0148810332491011!64399$GO:0007389!pattern specification process!0.0148810332491011!64399$GO:0009986!cell surface!0.0164925737161696!64399$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0218415165430354!64399$GO:0048699!generation of neurons!0.0235966384081008!64399$GO:0022008!neurogenesis!0.0240440224129214!64399$GO:0007167!enzyme linked receptor protein signaling pathway!0.0260018054083755!64399$GO:0009887!organ morphogenesis!0.0297241691299956!64399
|id=C606
|id=C606
|ontology_enrichment_celltype=CL:0000222!3.07e-22!119;CL:0002139!4.64e-17!24;CL:0000359!3.42e-15!32;CL:0000115!1.41e-14!35;CL:0000071!1.24e-13!18;CL:0002546!1.24e-13!18;CL:0002078!1.94e-13!44;CL:0000183!3.17e-13!59;CL:0000680!6.15e-13!57;CL:0000056!6.15e-13!57;CL:0000355!6.15e-13!57;CL:0000055!9.42e-13!180;CL:0000192!3.62e-12!42;CL:0000514!3.62e-12!42;CL:0000187!6.37e-12!54;CL:0000393!3.44e-10!60;CL:0000211!3.44e-10!60;CL:0000213!2.14e-09!57;CL:0000215!2.14e-09!57;CL:1000413!8.55e-08!9
|ontology_enrichment_celltype=CL:0002139!4.38e-29!24;CL:0000115!4.07e-25!36;CL:0000071!4.59e-23!18;CL:0002546!4.59e-23!18;CL:0000222!5.38e-20!121;CL:0002078!2.59e-19!45;CL:0000213!1.36e-15!58;CL:0000215!1.36e-15!58;CL:0000359!2.31e-13!32;CL:1000413!1.17e-12!9;CL:0002544!5.59e-09!6;CL:0002543!1.12e-08!6;CL:0000192!4.08e-08!43;CL:0000514!4.08e-08!43;CL:0005020!1.37e-07!6;CL:0002138!1.37e-07!6;CL:0005022!1.37e-07!6;CL:0000680!2.01e-07!58;CL:0000056!2.01e-07!58;CL:0000355!2.01e-07!58;CL:0002494!2.52e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000025!2.17e-42!194;UBERON:0004111!1.50e-37!241;UBERON:0000477!6.09e-35!286;UBERON:0002049!1.05e-34!79;UBERON:0007798!1.05e-34!79;UBERON:0000119!1.17e-33!312;UBERON:0000483!1.25e-32!309;UBERON:0000055!2.88e-32!69;UBERON:0001981!4.05e-30!60;UBERON:0007500!4.05e-30!60;UBERON:0004537!4.05e-30!60;UBERON:0006965!4.05e-30!60;UBERON:0004872!7.79e-29!84;UBERON:0003914!2.83e-28!118;UBERON:0004535!9.59e-26!110;UBERON:0001009!2.17e-24!113;UBERON:0001637!1.10e-23!42;UBERON:0003509!1.10e-23!42;UBERON:0004572!1.10e-23!42;UBERON:0004573!1.35e-18!33;UBERON:0004571!1.35e-18!33;UBERON:0002616!4.61e-17!59;UBERON:0001049!4.84e-17!57;UBERON:0005068!4.84e-17!57;UBERON:0006241!4.84e-17!57;UBERON:0007135!4.84e-17!57;UBERON:0000490!1.45e-16!138;UBERON:0000955!2.54e-16!69;UBERON:0006238!2.54e-16!69;UBERON:0005743!4.75e-16!86;UBERON:0001017!5.83e-16!82;UBERON:0000073!1.47e-15!94;UBERON:0001016!1.47e-15!94;UBERON:0000475!1.16e-14!365;UBERON:0003075!1.26e-14!86;UBERON:0007284!1.26e-14!86;UBERON:0000481!5.04e-14!347;UBERON:0002346!8.16e-14!90;UBERON:0002385!1.02e-13!63;UBERON:0001015!1.02e-13!63;UBERON:0000383!1.02e-13!63;UBERON:0001986!1.24e-13!18;UBERON:0004638!1.24e-13!18;UBERON:0004852!1.24e-13!18;UBERON:0001134!3.64e-13!61;UBERON:0002036!3.64e-13!61;UBERON:0003082!3.64e-13!61;UBERON:0000468!2.60e-12!659;UBERON:0002780!2.63e-12!41;UBERON:0001890!2.63e-12!41;UBERON:0006240!2.63e-12!41;UBERON:0002020!3.14e-12!34;UBERON:0003528!3.14e-12!34;UBERON:0001893!3.37e-12!34;UBERON:0000947!4.07e-12!21;UBERON:0010191!4.07e-12!21;UBERON:0003080!5.23e-12!42;UBERON:0007023!6.57e-12!115;UBERON:0002791!8.23e-12!33;UBERON:0004290!1.29e-11!70;UBERON:0001869!3.11e-11!32;UBERON:0000467!3.12e-11!625;UBERON:0000480!5.31e-11!626;UBERON:0005256!8.16e-11!143;UBERON:0006914!8.64e-11!25;UBERON:0000487!1.02e-10!22;UBERON:0000922!1.79e-10!612;UBERON:0003056!2.89e-10!61;UBERON:0000914!6.36e-10!83;UBERON:0002329!6.36e-10!83;UBERON:0003077!6.36e-10!83;UBERON:0003059!6.36e-10!83;UBERON:0007282!6.36e-10!83;UBERON:0009618!6.36e-10!83;UBERON:0007285!6.36e-10!83;UBERON:0002050!8.06e-10!605;UBERON:0005423!8.06e-10!605;UBERON:0000923!9.95e-10!604;UBERON:0005291!9.95e-10!604;UBERON:0006598!9.95e-10!604;UBERON:0002532!9.95e-10!604;UBERON:0000153!8.86e-09!129;UBERON:0007811!8.86e-09!129;UBERON:0000033!9.88e-09!123;UBERON:0000956!1.37e-08!25;UBERON:0000203!1.37e-08!25;UBERON:0000486!1.87e-08!82;UBERON:0002619!1.97e-08!22;UBERON:0003915!8.55e-08!9;UBERON:0004700!8.55e-08!9;UBERON:0001917!8.55e-08!9;UBERON:0001950!1.34e-07!20;UBERON:0003103!2.96e-07!69;UBERON:0004121!7.49e-07!169
|ontology_enrichment_uberon=UBERON:0000025!6.63e-45!192;UBERON:0000055!3.19e-39!68;UBERON:0002049!2.34e-38!78;UBERON:0007798!2.34e-38!78;UBERON:0004111!1.83e-36!240;UBERON:0007500!6.32e-36!59;UBERON:0001981!6.32e-36!59;UBERON:0004537!6.32e-36!59;UBERON:0006965!6.32e-36!59;UBERON:0004872!4.14e-32!83;UBERON:0004535!6.52e-32!109;UBERON:0001009!2.08e-30!112;UBERON:0001637!3.02e-30!42;UBERON:0003509!3.02e-30!42;UBERON:0004572!3.02e-30!42;UBERON:0000119!4.94e-30!309;UBERON:0000483!3.80e-29!306;UBERON:0003914!1.34e-28!117;UBERON:0000477!2.12e-27!373;UBERON:0004638!4.59e-23!18;UBERON:0001986!4.59e-23!18;UBERON:0004852!4.59e-23!18;UBERON:0004573!8.99e-23!33;UBERON:0004571!8.99e-23!33;UBERON:0000487!1.56e-17!22;UBERON:0006914!2.12e-16!25;UBERON:0001049!3.46e-16!56;UBERON:0005068!3.46e-16!56;UBERON:0006241!3.46e-16!56;UBERON:0007135!3.46e-16!56;UBERON:0000947!1.77e-14!21;UBERON:0010191!1.77e-14!21;UBERON:0000073!2.66e-14!53;UBERON:0002616!2.66e-14!53;UBERON:0010314!5.81e-14!132;UBERON:0003075!9.41e-14!82;UBERON:0007284!9.41e-14!82;UBERON:0002346!2.40e-13!86;UBERON:0003915!1.17e-12!9;UBERON:0004700!1.17e-12!9;UBERON:0001917!1.17e-12!9;UBERON:0000490!3.31e-12!148;UBERON:0000955!1.28e-11!68;UBERON:0006238!1.28e-11!68;UBERON:0000481!2.66e-11!342;UBERON:0002780!1.66e-10!41;UBERON:0001890!1.66e-10!41;UBERON:0003080!1.66e-10!41;UBERON:0006240!1.66e-10!41;UBERON:0001893!2.13e-10!34;UBERON:0003528!2.63e-10!34;UBERON:0002020!2.63e-10!34;UBERON:0001017!3.25e-10!81;UBERON:0003056!1.46e-09!61;UBERON:0001016!2.13e-09!89;UBERON:0002791!3.25e-09!32;UBERON:0001869!4.40e-09!32;UBERON:0010371!9.45e-09!104;UBERON:0000923!1.15e-08!560;UBERON:0010316!1.15e-08!560;UBERON:0005291!1.15e-08!560;UBERON:0006598!1.15e-08!560;UBERON:0010317!1.15e-08!560;UBERON:0002532!1.15e-08!560;UBERON:0002050!2.46e-08!564;UBERON:0000125!5.14e-08!9;UBERON:0002308!5.14e-08!9;UBERON:0005423!5.14e-08!581;UBERON:0010260!5.21e-08!9;UBERON:0000467!5.65e-08!624;UBERON:0000480!6.78e-08!625;UBERON:0007023!7.91e-08!114;UBERON:0003081!9.11e-08!203;UBERON:0000922!1.66e-07!592;UBERON:0003076!2.85e-07!15;UBERON:0003057!2.85e-07!15;UBERON:0007503!3.29e-07!78;UBERON:0000468!4.60e-07!656;UBERON:0009663!9.00e-07!7
|tf_chipseq_enrich=EBF1#1879;10:5.93764456437934:5.57766636877494e-07:2.57868923368077e-05!FOS#2353;10:5.99863687259627:5.06473487999527e-07:2.36987386259778e-05
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}}
}}

Revision as of 16:28, 19 October 2012


Full id: C606_Endothelial_extraskeletal_Smooth_mesothelioma_Lymphatic_Fibroblast_lung



Phase1 CAGE Peaks

Hg19::chr4:145566841..145566862,+p10@HHIP
Hg19::chr4:145566874..145566889,+p15@HHIP
Hg19::chr4:145566965..145566978,-p2@ENST00000503066
Hg19::chr4:145567278..145567296,+p3@HHIP
Hg19::chr4:145567297..145567355,+p1@HHIP
Hg19::chr4:145567356..145567368,+p7@HHIP
Hg19::chr4:145567374..145567390,+p6@HHIP
Hg19::chr4:145567391..145567425,+p4@HHIP
Hg19::chr4:145567426..145567455,+p5@HHIP
Hg19::chr4:145567461..145567482,+p9@HHIP
Hg19::chr4:145567538..145567544,+p13@HHIP
Hg19::chr4:145567563..145567572,+p8@HHIP
Hg19::chr4:145608930..145608933,+p@chr4:145608930..145608933
+
Hg19::chr4:145629311..145629322,+p17@HHIP
Hg19::chr4:145662551..145662554,+p@chr4:145662551..145662554
+


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:0045879negative regulation of smoothened signaling pathway0.00156010832450253
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0023401624867538
GO:0008589regulation of smoothened signaling pathway0.00364025275717257
GO:0007224smoothened signaling pathway0.00442030691942384
GO:0008543fibroblast growth factor receptor signaling pathway0.00442030691942384
GO:0007405neuroblast proliferation0.00442030691942384
GO:0009953dorsal/ventral pattern formation0.00624043329801013
GO:0030324lung development0.00745385088373431
GO:0030323respiratory tube development0.00745385088373431
GO:0003002regionalization0.013572942423172
GO:0009968negative regulation of signal transduction0.0147501150680239
GO:0035295tube development0.0148810332491011
GO:0007389pattern specification process0.0148810332491011
GO:0009986cell surface0.0164925737161696
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0218415165430354
GO:0048699generation of neurons0.0235966384081008
GO:0022008neurogenesis0.0240440224129214
GO:0007167enzyme linked receptor protein signaling pathway0.0260018054083755
GO:0009887organ morphogenesis0.0297241691299956



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
tube6.63e-45192
vessel3.19e-3968
vasculature2.34e-3878
vascular system2.34e-3878
anatomical conduit1.83e-36240
epithelial tube open at both ends6.32e-3659
blood vessel6.32e-3659
blood vasculature6.32e-3659
vascular cord6.32e-3659
splanchnic layer of lateral plate mesoderm4.14e-3283
cardiovascular system6.52e-32109
circulatory system2.08e-30112
artery3.02e-3042
arterial blood vessel3.02e-3042
arterial system3.02e-3042
cell layer4.94e-30309
epithelium3.80e-29306
epithelial tube1.34e-28117
anatomical cluster2.12e-27373
blood vessel endothelium4.59e-2318
endothelium4.59e-2318
cardiovascular system endothelium4.59e-2318
systemic artery8.99e-2333
systemic arterial system8.99e-2333
simple squamous epithelium1.56e-1722
squamous epithelium2.12e-1625
neural tube3.46e-1656
neural rod3.46e-1656
future spinal cord3.46e-1656
neural keel3.46e-1656
aorta1.77e-1421
aortic system1.77e-1421
regional part of nervous system2.66e-1453
regional part of brain2.66e-1453
structure with developmental contribution from neural crest5.81e-14132
neural plate9.41e-1482
presumptive neural plate9.41e-1482
neurectoderm2.40e-1386
endothelial tube1.17e-129
arterial system endothelium1.17e-129
endothelium of artery1.17e-129
unilaminar epithelium3.31e-12148
brain1.28e-1168
future brain1.28e-1168
multi-tissue structure2.66e-11342
regional part of forebrain1.66e-1041
forebrain1.66e-1041
anterior neural tube1.66e-1041
future forebrain1.66e-1041
telencephalon2.13e-1034
brain grey matter2.63e-1034
gray matter2.63e-1034
central nervous system3.25e-1081
pre-chordal neural plate1.46e-0961
nervous system2.13e-0989
regional part of telencephalon3.25e-0932
cerebral hemisphere4.40e-0932
ecto-epithelium9.45e-09104
germ layer1.15e-08560
germ layer / neural crest1.15e-08560
embryonic tissue1.15e-08560
presumptive structure1.15e-08560
germ layer / neural crest derived structure1.15e-08560
epiblast (generic)1.15e-08560
embryonic structure2.46e-08564
neural nucleus5.14e-089
nucleus of brain5.14e-089
developing anatomical structure5.14e-08581
umbilical blood vessel5.21e-089
anatomical system5.65e-08624
anatomical group6.78e-08625
adult organism7.91e-08114
lateral plate mesoderm9.11e-08203
embryo1.66e-07592
posterior neural tube2.85e-0715
chordal neural plate2.85e-0715
epithelial vesicle3.29e-0778
multi-cellular organism4.60e-07656
telencephalic nucleus9.00e-077


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
EBF1#1879105.937644564379345.57766636877494e-072.57868923368077e-05
FOS#2353105.998636872596275.06473487999527e-072.36987386259778e-05



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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