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Coexpression cluster:C2833: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!3.65e-30!312;UBERON:0000475!2.16e-29!365;UBERON:0000477!5.75e-29!286;UBERON:0000483!9.80e-29!309;UBERON:0000481!2.52e-26!347;UBERON:0004111!3.19e-24!241;UBERON:0000025!4.20e-23!194;UBERON:0003075!1.41e-21!86;UBERON:0007284!1.41e-21!86;UBERON:0002346!9.73e-21!90;UBERON:0005743!1.71e-19!86;UBERON:0000468!7.63e-19!659;UBERON:0001017!6.43e-18!82;UBERON:0000073!1.27e-17!94;UBERON:0001016!1.27e-17!94;UBERON:0002616!2.46e-17!59;UBERON:0001049!9.62e-17!57;UBERON:0005068!9.62e-17!57;UBERON:0006241!9.62e-17!57;UBERON:0007135!9.62e-17!57;UBERON:0000955!3.76e-16!69;UBERON:0006238!3.76e-16!69;UBERON:0000033!5.64e-15!123;UBERON:0000922!1.15e-14!612;UBERON:0003056!1.38e-14!61;UBERON:0000467!2.55e-14!625;UBERON:0000064!3.26e-14!219;UBERON:0004121!4.33e-14!169;UBERON:0000480!4.87e-14!626;UBERON:0000153!6.35e-14!129;UBERON:0007811!6.35e-14!129;UBERON:0000924!7.76e-14!173;UBERON:0006601!7.76e-14!173;UBERON:0002050!1.10e-13!605;UBERON:0005423!1.10e-13!605;UBERON:0000923!2.21e-13!604;UBERON:0005291!2.21e-13!604;UBERON:0006598!2.21e-13!604;UBERON:0002532!2.21e-13!604;UBERON:0002100!2.29e-13!216;UBERON:0000490!7.67e-12!138;UBERON:0005256!4.73e-11!143;UBERON:0003080!8.34e-11!42;UBERON:0002780!1.46e-10!41;UBERON:0001890!1.46e-10!41;UBERON:0006240!1.46e-10!41;UBERON:0000062!2.82e-10!511;UBERON:0003914!5.08e-10!118;UBERON:0007023!6.08e-10!115;UBERON:0002020!9.49e-10!34;UBERON:0003528!9.49e-10!34;UBERON:0002049!1.84e-09!79;UBERON:0007798!1.84e-09!79;UBERON:0001893!1.85e-09!34;UBERON:0002791!2.13e-09!33;UBERON:0001869!7.29e-09!32;UBERON:0003104!1.70e-08!238;UBERON:0009142!1.70e-08!238;UBERON:0000956!3.09e-08!25;UBERON:0000203!3.09e-08!25;UBERON:0009569!1.23e-07!113;UBERON:0003076!1.44e-07!15;UBERON:0003057!1.44e-07!15;UBERON:0002417!1.92e-07!61;UBERON:0000916!1.92e-07!61;UBERON:0000063!2.71e-07!97;UBERON:0001048!3.64e-07!168;UBERON:0002200!3.94e-07!11;UBERON:0006876!3.94e-07!11;UBERON:0002619!4.87e-07!22;UBERON:0004535!4.94e-07!110
|ontology_enrichment_uberon=UBERON:0000119!3.65e-30!312;UBERON:0000475!2.16e-29!365;UBERON:0000477!5.75e-29!286;UBERON:0000483!9.80e-29!309;UBERON:0000481!2.52e-26!347;UBERON:0004111!3.19e-24!241;UBERON:0000025!4.20e-23!194;UBERON:0003075!1.41e-21!86;UBERON:0007284!1.41e-21!86;UBERON:0002346!9.73e-21!90;UBERON:0005743!1.71e-19!86;UBERON:0000468!7.63e-19!659;UBERON:0001017!6.43e-18!82;UBERON:0000073!1.27e-17!94;UBERON:0001016!1.27e-17!94;UBERON:0002616!2.46e-17!59;UBERON:0001049!9.62e-17!57;UBERON:0005068!9.62e-17!57;UBERON:0006241!9.62e-17!57;UBERON:0007135!9.62e-17!57;UBERON:0000955!3.76e-16!69;UBERON:0006238!3.76e-16!69;UBERON:0000033!5.64e-15!123;UBERON:0000922!1.15e-14!612;UBERON:0003056!1.38e-14!61;UBERON:0000467!2.55e-14!625;UBERON:0000064!3.26e-14!219;UBERON:0004121!4.33e-14!169;UBERON:0000480!4.87e-14!626;UBERON:0000153!6.35e-14!129;UBERON:0007811!6.35e-14!129;UBERON:0000924!7.76e-14!173;UBERON:0006601!7.76e-14!173;UBERON:0002050!1.10e-13!605;UBERON:0005423!1.10e-13!605;UBERON:0000923!2.21e-13!604;UBERON:0005291!2.21e-13!604;UBERON:0006598!2.21e-13!604;UBERON:0002532!2.21e-13!604;UBERON:0002100!2.29e-13!216;UBERON:0000490!7.67e-12!138;UBERON:0005256!4.73e-11!143;UBERON:0003080!8.34e-11!42;UBERON:0002780!1.46e-10!41;UBERON:0001890!1.46e-10!41;UBERON:0006240!1.46e-10!41;UBERON:0000062!2.82e-10!511;UBERON:0003914!5.08e-10!118;UBERON:0007023!6.08e-10!115;UBERON:0002020!9.49e-10!34;UBERON:0003528!9.49e-10!34;UBERON:0002049!1.84e-09!79;UBERON:0007798!1.84e-09!79;UBERON:0001893!1.85e-09!34;UBERON:0002791!2.13e-09!33;UBERON:0001869!7.29e-09!32;UBERON:0003104!1.70e-08!238;UBERON:0009142!1.70e-08!238;UBERON:0000956!3.09e-08!25;UBERON:0000203!3.09e-08!25;UBERON:0009569!1.23e-07!113;UBERON:0003076!1.44e-07!15;UBERON:0003057!1.44e-07!15;UBERON:0002417!1.92e-07!61;UBERON:0000916!1.92e-07!61;UBERON:0000063!2.71e-07!97;UBERON:0001048!3.64e-07!168;UBERON:0002200!3.94e-07!11;UBERON:0006876!3.94e-07!11;UBERON:0002619!4.87e-07!22;UBERON:0004535!4.94e-07!110
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}}
}}

Revision as of 13:24, 5 September 2012


Full id: C2833_Mesenchymal_Fibroblast_small_Pericytes_ductal_alveolar_lung



Phase1 CAGE Peaks

Hg19::chr5:92918894..92918912,+p2@NR2F1
Hg19::chr5:92918919..92918942,+p1@NR2F1
Hg19::chr5:92918956..92918969,+p4@NR2F1
Hg19::chr5:92919312..92919334,+p13@NR2F1


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>

Cell Type
Ontology termp-valuen
mesodermal cell2.19e-10119
non-terminally differentiated cell2.48e-09180
contractile cell7.87e-0859
muscle precursor cell7.95e-0757
myoblast7.95e-0757
multi-potent skeletal muscle stem cell7.95e-0757
Uber Anatomy
Ontology termp-valuen
cell layer3.65e-30312
organism subdivision2.16e-29365
anatomical cluster5.75e-29286
epithelium9.80e-29309
multi-tissue structure2.52e-26347
anatomical conduit3.19e-24241
tube4.20e-23194
neural plate1.41e-2186
presumptive neural plate1.41e-2186
neurectoderm9.73e-2190
multi-cellular organism7.63e-19659
central nervous system6.43e-1882
regional part of nervous system1.27e-1794
nervous system1.27e-1794
regional part of brain2.46e-1759
neural tube9.62e-1757
neural rod9.62e-1757
future spinal cord9.62e-1757
neural keel9.62e-1757
brain3.76e-1669
future brain3.76e-1669
head5.64e-15123
embryo1.15e-14612
pre-chordal neural plate1.38e-1461
anatomical system2.55e-14625
organ part3.26e-14219
ectoderm-derived structure4.33e-14169
anatomical group4.87e-14626
anterior region of body6.35e-14129
craniocervical region6.35e-14129
ectoderm7.76e-14173
presumptive ectoderm7.76e-14173
embryonic structure1.10e-13605
developing anatomical structure1.10e-13605
germ layer2.21e-13604
embryonic tissue2.21e-13604
presumptive structure2.21e-13604
epiblast (generic)2.21e-13604
trunk2.29e-13216
unilaminar epithelium7.67e-12138
trunk mesenchyme4.73e-11143
anterior neural tube8.34e-1142
regional part of forebrain1.46e-1041
forebrain1.46e-1041
future forebrain1.46e-1041
organ2.82e-10511
epithelial tube5.08e-10118
adult organism6.08e-10115
gray matter9.49e-1034
brain grey matter9.49e-1034
vasculature1.84e-0979
vascular system1.84e-0979
telencephalon1.85e-0934
regional part of telencephalon2.13e-0933
cerebral hemisphere7.29e-0932
mesenchyme1.70e-08238
entire embryonic mesenchyme1.70e-08238
cerebral cortex3.09e-0825
pallium3.09e-0825
subdivision of trunk1.23e-07113
posterior neural tube1.44e-0715
chordal neural plate1.44e-0715
abdominal segment of trunk1.92e-0761
abdomen1.92e-0761
organ segment2.71e-0797
primordium3.64e-07168
vasculature of head3.94e-0711
vasculature of organ3.94e-0711
regional part of cerebral cortex4.87e-0722
cardiovascular system4.94e-07110


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
EP300#203335.08045629466740.01144298405398240.0419169377297838
FOXA1#316938.311064812039090.002740138182109850.0150413797751167
FOXA2#3170212.31523187633260.009361916285467240.0353526837667829
GATA1#2623310.17023110785030.001515158168498270.0096677421774066
GATA2#262439.55869880016550.001818151618357440.0109060902228265
GTF2F1#296239.554745657568240.001820362319304780.0109036946699858
HDAC2#3066413.41562023662633.0859005065161e-050.000628119982459628
HEY1#2346244.040111043105710.00375304636917980.0186525368683149
HNF4A#3172423.13229036295373.48990320893214e-060.000115818875512445
HNF4G#3174321.56506689483510.0001638032421292610.00203732842738333
JUND#372746.994663941871030.000417684217818580.00392394729016413
MXI1#460149.96157162875930.0001015224754950450.00142723190445914
PRDM1#639398.87321683309561.73225752892158e-066.52652395609817e-05
REST#597837.237521537096020.004104697304192610.0195919053860688
RFX5#599339.035933120396320.002144561191324070.0123900993671901
RXRA#6256315.055962854350.0004758307997303580.00434057934256607
SIN3A#2594245.408884726815140.001168172384885160.00797872969099606
SP1#666745.69838137814090.0009482606065333980.00685603250160897
SRF#6722310.34788369662590.001439893778401260.00924113969903824
TAL1#6886322.40146250808020.0001462756395930170.0018897676303136
TCF7L2#693438.077632422353010.002978381685834620.0158703675962695
TRIM28#10155313.94289378394690.0005972858184258420.0049975912186009
ZNF263#1012748.221841637010680.0002187871180958320.00249834986079276
ZZZ3#260094239.4132124352333.02023811776815e-103.05353967842776e-08



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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