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Coexpression cluster:C3505: Difference between revisions

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|full_id=C3505_Cardiac_Retinal_lung_Chondrocyte_Synoviocyte_tenocyte_seminal
|full_id=C3505_Cardiac_Retinal_lung_Chondrocyte_Synoviocyte_tenocyte_seminal
|id=C3505
|id=C3505
|ontology_enrichment_celltype=CL:0000055!1.70e-07!180;CL:0000136!3.46e-07!15
|ontology_enrichment_celltype=CL:0000136!3.06e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!4.91e-12!659;UBERON:0000477!2.56e-11!286;UBERON:0000481!6.88e-10!347;UBERON:0003914!9.70e-10!118;UBERON:0000062!1.43e-09!511;UBERON:0000025!1.75e-09!194;UBERON:0000475!1.13e-08!365;UBERON:0000467!5.81e-08!625;UBERON:0002417!7.47e-08!61;UBERON:0000916!7.47e-08!61;UBERON:0000480!8.57e-08!626;UBERON:0003103!1.57e-07!69;UBERON:0000483!1.67e-07!309;UBERON:0000119!1.72e-07!312;UBERON:0004111!1.78e-07!241;UBERON:0009569!5.52e-07!113;UBERON:0007100!7.27e-07!27
|ontology_enrichment_uberon=UBERON:0000477!5.23e-15!373;UBERON:0000468!1.83e-11!656;UBERON:0000481!1.32e-10!342;UBERON:0003914!1.02e-09!117;UBERON:0000025!1.82e-09!192;UBERON:0000062!1.78e-08!503;UBERON:0000119!8.48e-08!309;UBERON:0000483!8.77e-08!306;UBERON:0000467!1.07e-07!624;UBERON:0004111!1.07e-07!240;UBERON:0002417!1.25e-07!60;UBERON:0000916!1.25e-07!60;UBERON:0000480!1.50e-07!625;UBERON:0003103!1.70e-07!68;UBERON:0007100!4.95e-07!27;UBERON:0003104!7.07e-07!160;UBERON:0009142!7.07e-07!160;UBERON:0009569!9.76e-07!112
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129492670630165!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115082675746417!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324575518339884!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321419702496993!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167239674722654!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000675147351480339!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00580462225708724!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00107175954885687!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.01085466573824!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0293958427279404!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000736617438443744!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245399285615324!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00308432257452368!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276047212121745!SIX5#147912;3:17.086715355459:0.000200406054632501:0.00239421275906701!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.000301454341870981!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.0061274411819033!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247832716886012!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614368476463874!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189971111035306!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421172267908189!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109181444907998
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}}
}}

Revision as of 15:10, 19 October 2012


Full id: C3505_Cardiac_Retinal_lung_Chondrocyte_Synoviocyte_tenocyte_seminal



Phase1 CAGE Peaks

Hg19::chr15:66994561..66994597,+p2@SMAD6
Hg19::chr15:66994615..66994630,+p3@SMAD6
Hg19::chr15:66994663..66994680,+p1@SMAD6


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
fat cell3.06e-0715
Uber Anatomy
Ontology termp-valuen
anatomical cluster5.23e-15373
multi-cellular organism1.83e-11656
multi-tissue structure1.32e-10342
epithelial tube1.02e-09117
tube1.82e-09192
organ1.78e-08503
cell layer8.48e-08309
epithelium8.77e-08306
anatomical system1.07e-07624
anatomical conduit1.07e-07240
abdominal segment of trunk1.25e-0760
abdomen1.25e-0760
anatomical group1.50e-07625
compound organ1.70e-0768
primary circulatory organ4.95e-0727
mesenchyme7.07e-07160
entire embryonic mesenchyme7.07e-07160
subdivision of trunk9.76e-07112


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-050.00129492670630165
CEBPB#105137.971147625824820.001974187055288560.0115082675746417
E2F1#186934.907389214879320.008460985347239390.0324575518339884
E2F6#187635.017155731697390.00791769806886330.0321419702496993
EP300#203336.77394172622320.003216880500103790.0167239674722654
ESR1#2099330.76860329615453.43136389821584e-050.000675147351480339
FOXA1#3169311.08141974938550.000734755275698670.00580462225708724
FOXA2#3170324.63046375266526.68983856509345e-050.00107175954885687
HMGN3#932438.178547723350590.001827766942164210.01085466573824
MYC#460935.22228187160940.007020843755740150.0293958427279404
NANOG#79923329.24477848101273.99627955670032e-050.000736617438443744
NFYB#4801316.75979325353650.0002123649923296180.00245399285615324
NR3C1#2908314.9730233311730.0002978331194675480.00308432257452368
SIN3A#2594235.408884726815140.006318961977991520.0276047212121745
SIX5#147912317.0867153554590.0002004060546325010.00239421275906701
SMARCC1#6599343.66335931963151.20046018043203e-050.000301454341870981
TCF7L2#6934310.77017656313730.0008003181298398380.0061274411819033
TFAP2A#7020316.5186343730450.0002218033880766340.00247832716886012
TFAP2C#7022310.80922860986020.0007916746575753130.00614368476463874
USF1#739136.361499277207960.00388404057290560.0189971111035306
USF2#7392312.99219738506960.0004558979393427810.00421172267908189
ZNF263#1012738.221841637010680.001799043925565870.0109181444907998



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.