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Coexpression cluster:C3413: Difference between revisions

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|full_id=C3413_Neutrophils_Eosinophils_Mesenchymal_Smooth_Fibroblast_Osteoblast_mesenchymal
|full_id=C3413_Neutrophils_Eosinophils_Mesenchymal_Smooth_Fibroblast_Osteoblast_mesenchymal
|id=C3413
|id=C3413
|ontology_enrichment_celltype=CL:0000222!5.27e-17!119;CL:0002371!5.95e-17!591;CL:0000055!2.70e-15!180;CL:0000220!4.03e-15!246;CL:0002321!2.97e-14!248;CL:0000144!7.07e-14!625;CL:0000192!1.33e-13!42;CL:0000514!1.33e-13!42;CL:0000359!1.74e-13!32;CL:0000548!4.14e-12!679;CL:0000004!4.14e-12!679;CL:0000255!4.14e-12!679;CL:0000183!8.49e-12!59;CL:0000012!4.12e-11!682;CL:0000680!4.86e-11!57;CL:0000056!4.86e-11!57;CL:0000355!4.86e-11!57;CL:0000187!2.89e-10!54;CL:0000057!5.92e-09!75;CL:1000449!5.91e-08!16;CL:0000003!1.82e-07!722;CL:0002078!5.13e-07!44;CL:1000497!5.82e-07!18;CL:0002518!5.82e-07!18;CL:0000393!5.96e-07!60;CL:0000211!5.96e-07!60
|ontology_enrichment_celltype=CL:0000222!1.90e-16!121;CL:0002371!6.15e-16!588;CL:0002321!6.61e-14!250;CL:0000359!1.66e-12!32;CL:0000192!2.15e-12!43;CL:0000514!2.15e-12!43;CL:0000548!1.80e-11!679;CL:0000255!1.80e-11!679;CL:0000183!4.43e-10!59;CL:0000680!1.18e-09!58;CL:0000056!1.18e-09!58;CL:0000355!1.18e-09!58;CL:0000057!6.06e-09!76;CL:0000187!6.56e-09!55;CL:1000449!1.71e-08!15;CL:0002078!1.08e-07!45;CL:1000497!2.46e-07!17;CL:0002518!2.46e-07!17;CL:0000115!3.68e-07!36;CL:0000003!4.09e-07!722;CL:0002681!5.54e-07!12;CL:0002584!5.54e-07!12
|ontology_enrichment_disease=DOID:2394!8.93e-07!14
|ontology_enrichment_disease=DOID:2394!7.66e-07!14
|ontology_enrichment_uberon=UBERON:0003914!1.09e-22!118;UBERON:0000926!1.98e-19!448;UBERON:0004120!1.98e-19!448;UBERON:0006603!1.98e-19!448;UBERON:0001637!3.31e-18!42;UBERON:0003509!3.31e-18!42;UBERON:0004572!3.31e-18!42;UBERON:0002100!4.50e-18!216;UBERON:0000055!1.43e-17!69;UBERON:0002049!2.14e-17!79;UBERON:0007798!2.14e-17!79;UBERON:0001981!2.74e-17!60;UBERON:0007500!2.74e-17!60;UBERON:0004537!2.74e-17!60;UBERON:0006965!2.74e-17!60;UBERON:0004535!2.98e-17!110;UBERON:0001009!1.01e-16!113;UBERON:0004872!1.25e-16!84;UBERON:0005256!3.14e-16!143;UBERON:0004573!1.08e-14!33;UBERON:0004571!1.08e-14!33;UBERON:0000490!9.19e-13!138;UBERON:0003104!6.26e-12!238;UBERON:0009142!6.26e-12!238;UBERON:0000468!4.35e-11!659;UBERON:0009569!6.93e-11!113;UBERON:0000486!1.28e-10!82;UBERON:0003081!1.75e-10!216;UBERON:0000480!1.79e-10!626;UBERON:0000467!1.91e-10!625;UBERON:0000914!4.51e-10!83;UBERON:0002329!4.51e-10!83;UBERON:0003077!4.51e-10!83;UBERON:0003059!4.51e-10!83;UBERON:0007282!4.51e-10!83;UBERON:0009618!4.51e-10!83;UBERON:0007285!4.51e-10!83;UBERON:0001134!2.49e-09!61;UBERON:0002036!2.49e-09!61;UBERON:0003082!2.49e-09!61;UBERON:0002385!2.78e-09!63;UBERON:0001015!2.78e-09!63;UBERON:0000383!2.78e-09!63;UBERON:0004290!2.85e-09!70;UBERON:0000947!5.33e-09!21;UBERON:0010191!5.33e-09!21;UBERON:0000080!2.33e-08!18;UBERON:0002120!2.33e-08!18;UBERON:0004875!2.33e-08!18;UBERON:0005721!2.33e-08!18;UBERON:0005754!2.33e-08!18;UBERON:0007297!2.33e-08!18;UBERON:0004876!2.35e-08!20;UBERON:0006555!3.33e-08!17;UBERON:0005103!3.33e-08!17;UBERON:0000083!3.33e-08!17;UBERON:0009201!3.33e-08!17;UBERON:0004819!3.33e-08!17;UBERON:0006553!3.33e-08!17;UBERON:0003074!3.33e-08!17;UBERON:0003060!3.33e-08!17;UBERON:0000058!3.88e-08!26;UBERON:0000466!5.20e-08!126;UBERON:0004211!5.91e-08!16;UBERON:0001285!5.91e-08!16;UBERON:0007684!5.91e-08!16;UBERON:0003220!5.91e-08!16;UBERON:0004208!5.91e-08!16;UBERON:0000464!9.03e-08!104;UBERON:0003887!2.34e-07!21;UBERON:0002553!2.73e-07!70;UBERON:0001008!3.19e-07!45;UBERON:0003886!3.35e-07!63;UBERON:0006554!3.92e-07!44;UBERON:0002417!4.27e-07!61;UBERON:0000916!4.27e-07!61;UBERON:0000353!4.78e-07!17;UBERON:0003103!5.39e-07!69;UBERON:0003064!6.85e-07!37
|ontology_enrichment_uberon=UBERON:0003914!1.66e-21!117;UBERON:0001637!2.69e-17!42;UBERON:0003509!2.69e-17!42;UBERON:0004572!2.69e-17!42;UBERON:0000055!1.10e-16!68;UBERON:0002049!1.48e-16!78;UBERON:0007798!1.48e-16!78;UBERON:0004535!1.73e-16!109;UBERON:0007500!2.75e-16!59;UBERON:0001981!2.75e-16!59;UBERON:0004537!2.75e-16!59;UBERON:0006965!2.75e-16!59;UBERON:0002100!4.16e-16!199;UBERON:0001009!6.73e-16!112;UBERON:0000475!7.60e-16!264;UBERON:0004872!4.20e-15!83;UBERON:0004573!7.18e-14!33;UBERON:0004571!7.18e-14!33;UBERON:0000926!7.33e-14!315;UBERON:0004120!7.33e-14!315;UBERON:0006603!7.33e-14!315;UBERON:0003104!8.55e-13!160;UBERON:0009142!8.55e-13!160;UBERON:0000490!6.21e-12!148;UBERON:0000468!1.85e-11!656;UBERON:0005256!2.89e-11!122;UBERON:0000480!4.25e-11!625;UBERON:0000467!4.42e-11!624;UBERON:0009569!9.54e-11!112;UBERON:0007503!2.11e-10!78;UBERON:0000486!2.26e-09!83;UBERON:0006555!9.76e-09!16;UBERON:0004819!9.76e-09!16;UBERON:0000947!1.66e-08!21;UBERON:0010191!1.66e-08!21;UBERON:0004211!1.71e-08!15;UBERON:0009773!1.71e-08!15;UBERON:0001231!1.71e-08!15;UBERON:0001285!1.71e-08!15;UBERON:0007684!1.71e-08!15;UBERON:0004208!1.71e-08!15;UBERON:0003081!2.35e-08!203;UBERON:0002329!4.09e-08!71;UBERON:0003059!4.09e-08!71;UBERON:0007282!4.09e-08!71;UBERON:0004290!4.09e-08!71;UBERON:0009618!4.09e-08!71;UBERON:0007524!4.95e-08!73;UBERON:0001134!5.26e-08!62;UBERON:0002036!5.26e-08!62;UBERON:0003082!5.26e-08!62;UBERON:0002385!5.59e-08!64;UBERON:0001015!5.59e-08!64;UBERON:0000383!5.59e-08!64;UBERON:0003077!8.03e-08!72;UBERON:0007285!8.03e-08!72;UBERON:0001008!3.84e-07!48;UBERON:0002417!3.99e-07!60;UBERON:0000916!3.99e-07!60;UBERON:0000353!4.01e-07!15;UBERON:0006554!5.36e-07!47;UBERON:0001225!5.54e-07!12;UBERON:0008987!5.54e-07!12
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018958326544068!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.0065930867188664!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278812160300055!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324325350025815!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00913563892195144!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319697391458714!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.046095515750836!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00390480342970372!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108509636012215!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122645535356649!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000755696698267432!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127805411238607!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293758223230538!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269064940779881!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245182262148054!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172586330823875!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136341201048679!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0275920256718562!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245897725951602!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0108939130146817!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374384656445566!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00154611523205986!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00628533467505946!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139836772091747
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}}
}}

Revision as of 15:05, 19 October 2012


Full id: C3413_Neutrophils_Eosinophils_Mesenchymal_Smooth_Fibroblast_Osteoblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:23341013..23341067,+p1@LRP10
Hg19::chr14:23341077..23341094,+p4@LRP10
Hg19::chr14:23341106..23341120,+p7@LRP10


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
epithelial tube1.66e-21117
artery2.69e-1742
arterial blood vessel2.69e-1742
arterial system2.69e-1742
vessel1.10e-1668
vasculature1.48e-1678
vascular system1.48e-1678
cardiovascular system1.73e-16109
epithelial tube open at both ends2.75e-1659
blood vessel2.75e-1659
blood vasculature2.75e-1659
vascular cord2.75e-1659
trunk4.16e-16199
circulatory system6.73e-16112
organism subdivision7.60e-16264
splanchnic layer of lateral plate mesoderm4.20e-1583
systemic artery7.18e-1433
systemic arterial system7.18e-1433
mesoderm7.33e-14315
mesoderm-derived structure7.33e-14315
presumptive mesoderm7.33e-14315
mesenchyme8.55e-13160
entire embryonic mesenchyme8.55e-13160
unilaminar epithelium6.21e-12148
multi-cellular organism1.85e-11656
trunk mesenchyme2.89e-11122
anatomical group4.25e-11625
anatomical system4.42e-11624
subdivision of trunk9.54e-11112
epithelial vesicle2.11e-1078
multilaminar epithelium2.26e-0983
excretory tube9.76e-0916
kidney epithelium9.76e-0916
aorta1.66e-0821
aortic system1.66e-0821
nephron epithelium1.71e-0815
renal tubule1.71e-0815
nephron tubule1.71e-0815
nephron1.71e-0815
uriniferous tubule1.71e-0815
nephrogenic mesenchyme1.71e-0815
lateral plate mesoderm2.35e-08203
somite4.09e-0871
presomitic mesoderm4.09e-0871
presumptive segmental plate4.09e-0871
dermomyotome4.09e-0871
trunk paraxial mesoderm4.09e-0871
dense mesenchyme tissue4.95e-0873
skeletal muscle tissue5.26e-0862
striated muscle tissue5.26e-0862
myotome5.26e-0862
muscle tissue5.59e-0864
musculature5.59e-0864
musculature of body5.59e-0864
paraxial mesoderm8.03e-0872
presumptive paraxial mesoderm8.03e-0872
renal system3.84e-0748
abdominal segment of trunk3.99e-0760
abdomen3.99e-0760
parenchyma4.01e-0715
urinary system structure5.36e-0747
cortex of kidney5.54e-0712
renal parenchyma5.54e-0712
Disease
Ontology termp-valuen
ovarian cancer7.66e-0714


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
CCNT2#90536.336201576962630.003930750035764890.018958326544068
CHD2#1106310.34402283411690.0009033701102746880.0065930867188664
CTCF#1066435.360256373075030.0064925092527670.0278812160300055
E2F1#186934.907389214879320.008460985347239390.0324325350025815
EBF1#187938.9064668465690.00141523283560980.00913563892195144
EGR1#195834.988179094810140.008056488137383440.0319697391458714
ELF1#199734.258097958807540.01295179875054610.046095515750836
HDAC2#3066313.41562023662630.0004140761399857210.00390480342970372
HMGN3#932438.178547723350590.001827766942164210.0108509636012215
HNF4A#3172323.13229036295378.07584663437677e-050.00122645535356649
HNF4G#3174328.75342252644684.20470658818262e-050.000755696698267432
IRF1#365937.63716375356390.002244692747297240.0127805411238607
MYC#460935.22228187160940.007020843755740150.0293758223230538
NFKB1#479035.488063424193840.006049381815655430.0269064940779881
NFYB#4801316.75979325353650.0002123649923296180.00245182262148054
PAX5#507936.669565531177830.003370290999677260.0172586330823875
PBX3#5090321.91451268674419.49854535978121e-050.00136341201048679
SIN3A#2594235.408884726815140.006318961977991520.0275920256718562
SP1#666735.69838137814090.005403962701712170.0245897725951602
SPI1#668838.204323508522730.001810593189410520.0108939130146817
SRF#6722313.79717826216780.0003806615025800190.00374384656445566
STAT1#6772320.70658749719920.0001125992441046670.00154611523205986
TCF12#6938310.63446490218640.0008313523990202070.00628533467505946
ZBTB7A#5134137.35190930787590.002516255860282270.0139836772091747



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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