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Coexpression cluster:C3722: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!7.27e-25!365;UBERON:0000119!1.61e-23!312;UBERON:0000483!2.29e-22!309;UBERON:0000477!1.04e-19!286;UBERON:0000468!1.29e-19!659;UBERON:0004111!1.71e-19!241;UBERON:0000025!7.65e-18!194;UBERON:0000467!2.68e-16!625;UBERON:0004872!3.12e-16!84;UBERON:0000480!5.80e-16!626;UBERON:0002049!1.51e-15!79;UBERON:0007798!1.51e-15!79;UBERON:0000481!5.49e-14!347;UBERON:0003914!8.11e-14!118;UBERON:0005256!2.16e-13!143;UBERON:0000914!6.61e-13!83;UBERON:0002329!6.61e-13!83;UBERON:0003077!6.61e-13!83;UBERON:0003059!6.61e-13!83;UBERON:0007282!6.61e-13!83;UBERON:0009618!6.61e-13!83;UBERON:0007285!6.61e-13!83;UBERON:0000055!1.47e-12!69;UBERON:0001981!2.05e-12!60;UBERON:0007500!2.05e-12!60;UBERON:0004537!2.05e-12!60;UBERON:0006965!2.05e-12!60;UBERON:0002100!5.33e-12!216;UBERON:0000486!1.15e-11!82;UBERON:0001637!1.20e-11!42;UBERON:0003509!1.20e-11!42;UBERON:0004572!1.20e-11!42;UBERON:0004121!1.28e-11!169;UBERON:0000924!2.85e-11!173;UBERON:0006601!2.85e-11!173;UBERON:0001134!6.26e-11!61;UBERON:0002036!6.26e-11!61;UBERON:0003082!6.26e-11!61;UBERON:0004290!6.63e-11!70;UBERON:0000490!7.03e-11!138;UBERON:0002385!7.12e-11!63;UBERON:0001015!7.12e-11!63;UBERON:0000383!7.12e-11!63;UBERON:0004535!8.33e-11!110;UBERON:0001009!2.95e-10!113;UBERON:0000923!3.25e-10!604;UBERON:0005291!3.25e-10!604;UBERON:0006598!3.25e-10!604;UBERON:0002532!3.25e-10!604;UBERON:0002050!3.64e-10!605;UBERON:0005423!3.64e-10!605;UBERON:0004573!4.46e-10!33;UBERON:0004571!4.46e-10!33;UBERON:0000922!1.09e-09!612;UBERON:0000033!6.20e-09!123;UBERON:0000064!6.49e-09!219;UBERON:0000153!1.26e-07!129;UBERON:0007811!1.26e-07!129;UBERON:0003075!1.75e-07!86;UBERON:0007284!1.75e-07!86;UBERON:0002616!2.01e-07!59;UBERON:0003102!2.80e-07!95;UBERON:0000947!3.72e-07!21;UBERON:0010191!3.72e-07!21;UBERON:0005631!3.80e-07!14;UBERON:0000158!3.80e-07!14;UBERON:0000955!4.27e-07!69;UBERON:0006238!4.27e-07!69;UBERON:0002346!4.47e-07!90;UBERON:0000073!6.20e-07!94;UBERON:0001016!6.20e-07!94;UBERON:0001017!7.94e-07!82
|ontology_enrichment_uberon=UBERON:0000475!7.27e-25!365;UBERON:0000119!1.61e-23!312;UBERON:0000483!2.29e-22!309;UBERON:0000477!1.04e-19!286;UBERON:0000468!1.29e-19!659;UBERON:0004111!1.71e-19!241;UBERON:0000025!7.65e-18!194;UBERON:0000467!2.68e-16!625;UBERON:0004872!3.12e-16!84;UBERON:0000480!5.80e-16!626;UBERON:0002049!1.51e-15!79;UBERON:0007798!1.51e-15!79;UBERON:0000481!5.49e-14!347;UBERON:0003914!8.11e-14!118;UBERON:0005256!2.16e-13!143;UBERON:0000914!6.61e-13!83;UBERON:0002329!6.61e-13!83;UBERON:0003077!6.61e-13!83;UBERON:0003059!6.61e-13!83;UBERON:0007282!6.61e-13!83;UBERON:0009618!6.61e-13!83;UBERON:0007285!6.61e-13!83;UBERON:0000055!1.47e-12!69;UBERON:0001981!2.05e-12!60;UBERON:0007500!2.05e-12!60;UBERON:0004537!2.05e-12!60;UBERON:0006965!2.05e-12!60;UBERON:0002100!5.33e-12!216;UBERON:0000486!1.15e-11!82;UBERON:0001637!1.20e-11!42;UBERON:0003509!1.20e-11!42;UBERON:0004572!1.20e-11!42;UBERON:0004121!1.28e-11!169;UBERON:0000924!2.85e-11!173;UBERON:0006601!2.85e-11!173;UBERON:0001134!6.26e-11!61;UBERON:0002036!6.26e-11!61;UBERON:0003082!6.26e-11!61;UBERON:0004290!6.63e-11!70;UBERON:0000490!7.03e-11!138;UBERON:0002385!7.12e-11!63;UBERON:0001015!7.12e-11!63;UBERON:0000383!7.12e-11!63;UBERON:0004535!8.33e-11!110;UBERON:0001009!2.95e-10!113;UBERON:0000923!3.25e-10!604;UBERON:0005291!3.25e-10!604;UBERON:0006598!3.25e-10!604;UBERON:0002532!3.25e-10!604;UBERON:0002050!3.64e-10!605;UBERON:0005423!3.64e-10!605;UBERON:0004573!4.46e-10!33;UBERON:0004571!4.46e-10!33;UBERON:0000922!1.09e-09!612;UBERON:0000033!6.20e-09!123;UBERON:0000064!6.49e-09!219;UBERON:0000153!1.26e-07!129;UBERON:0007811!1.26e-07!129;UBERON:0003075!1.75e-07!86;UBERON:0007284!1.75e-07!86;UBERON:0002616!2.01e-07!59;UBERON:0003102!2.80e-07!95;UBERON:0000947!3.72e-07!21;UBERON:0010191!3.72e-07!21;UBERON:0005631!3.80e-07!14;UBERON:0000158!3.80e-07!14;UBERON:0000955!4.27e-07!69;UBERON:0006238!4.27e-07!69;UBERON:0002346!4.47e-07!90;UBERON:0000073!6.20e-07!94;UBERON:0001016!6.20e-07!94;UBERON:0001017!7.94e-07!82
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}}
}}

Revision as of 12:12, 5 September 2012


Full id: C3722_Preadipocyte_mature_Adipocyte_Fibroblast_Hepatic_Smooth_Pericytes



Phase1 CAGE Peaks

Hg19::chr18:46065483..46065540,+p2@CTIF
Hg19::chr18:46065541..46065568,+p3@CTIF
Hg19::chr18:46065570..46065579,+p6@CTIF


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
organism subdivision7.27e-25365
cell layer1.61e-23312
epithelium2.29e-22309
anatomical cluster1.04e-19286
multi-cellular organism1.29e-19659
anatomical conduit1.71e-19241
tube7.65e-18194
anatomical system2.68e-16625
splanchnic layer of lateral plate mesoderm3.12e-1684
anatomical group5.80e-16626
vasculature1.51e-1579
vascular system1.51e-1579
multi-tissue structure5.49e-14347
epithelial tube8.11e-14118
trunk mesenchyme2.16e-13143
somite6.61e-1383
paraxial mesoderm6.61e-1383
presomitic mesoderm6.61e-1383
presumptive segmental plate6.61e-1383
trunk paraxial mesoderm6.61e-1383
presumptive paraxial mesoderm6.61e-1383
vessel1.47e-1269
blood vessel2.05e-1260
epithelial tube open at both ends2.05e-1260
blood vasculature2.05e-1260
vascular cord2.05e-1260
trunk5.33e-12216
multilaminar epithelium1.15e-1182
artery1.20e-1142
arterial blood vessel1.20e-1142
arterial system1.20e-1142
ectoderm-derived structure1.28e-11169
ectoderm2.85e-11173
presumptive ectoderm2.85e-11173
skeletal muscle tissue6.26e-1161
striated muscle tissue6.26e-1161
myotome6.26e-1161
dermomyotome6.63e-1170
unilaminar epithelium7.03e-11138
muscle tissue7.12e-1163
musculature7.12e-1163
musculature of body7.12e-1163
cardiovascular system8.33e-11110
circulatory system2.95e-10113
germ layer3.25e-10604
embryonic tissue3.25e-10604
presumptive structure3.25e-10604
epiblast (generic)3.25e-10604
embryonic structure3.64e-10605
developing anatomical structure3.64e-10605
systemic artery4.46e-1033
systemic arterial system4.46e-1033
embryo1.09e-09612
head6.20e-09123
organ part6.49e-09219
anterior region of body1.26e-07129
craniocervical region1.26e-07129
neural plate1.75e-0786
presumptive neural plate1.75e-0786
regional part of brain2.01e-0759
surface structure2.80e-0795
aorta3.72e-0721
aortic system3.72e-0721
extraembryonic membrane3.80e-0714
membranous layer3.80e-0714
brain4.27e-0769
future brain4.27e-0769
neurectoderm4.47e-0790
regional part of nervous system6.20e-0794
nervous system6.20e-0794
central nervous system7.94e-0782


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
ATF3#467322.46317452600878.81932387510763e-050.00129583760015808
BHLHE40#8553344.87181354697741.10603738662898e-050.000284445798133819
E2F6#187635.017155731697390.00791769806886330.0321982894094702
ELF1#199734.258097958807540.01295179875054610.0461994231260727
ETS1#211339.728760922202340.001085840092584840.00761816830777024
IRF1#365937.63716375356390.002244692747297240.0127993811877581
MAX#414936.452555509007120.003721913834265510.0186388376378257
MXI1#460139.96157162875930.001011470541259020.00719990266211498
MYC#460935.22228187160940.007020843755740150.029431239504124
NFKB1#479035.488063424193840.006049381815655430.0269466598756819
SIN3A#2594235.408884726815140.006318961977991520.0276521440551184
SIX5#147912317.0867153554590.0002004060546325010.00239585713596197
SP1#666735.69838137814090.005403962701712170.0246316266138924
SRF#6722313.79717826216780.0003806615025800190.0037491424620855
TCF7L2#6934310.77017656313730.0008003181298398380.00613373634419482
TFAP2C#7022310.80922860986020.0007916746575753130.00615695208597127
USF1#739136.361499277207960.00388404057290560.0190158125536137
USF2#7392312.99219738506960.0004558979393427810.00421433217268727
YY1#752834.911170749853860.008441455341808260.0329170426928691
ZNF143#7702313.50087655222790.0004062804962997170.00388851986373223



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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