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Coexpression cluster:C2904: Difference between revisions

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|full_id=C2904_Mesenchymal_adenocarcinoma_Cardiac_small_sacrococcigeal_Preadipocyte_Smooth
|full_id=C2904_Mesenchymal_adenocarcinoma_Cardiac_small_sacrococcigeal_Preadipocyte_Smooth
|id=C2904
|id=C2904
|ontology_enrichment_celltype=CL:0000680!7.54e-18!57;CL:0000056!7.54e-18!57;CL:0000355!7.54e-18!57;CL:0000187!1.54e-17!54;CL:0000055!5.81e-17!180;CL:0000393!1.74e-16!60;CL:0000211!1.74e-16!60;CL:0000183!2.83e-16!59;CL:0000192!1.82e-12!42;CL:0000514!1.82e-12!42;CL:0000048!1.10e-11!430;CL:0000034!9.46e-11!444;CL:0000723!1.15e-10!436;CL:0000057!1.25e-10!75;CL:0000359!9.76e-08!32;CL:0002494!1.35e-07!16
|ontology_enrichment_celltype=CL:0000680!2.53e-19!58;CL:0000056!2.53e-19!58;CL:0000355!2.53e-19!58;CL:0000187!6.90e-19!55;CL:0000183!7.92e-18!59;CL:0000393!2.00e-17!61;CL:0000211!2.00e-17!61;CL:0000192!1.41e-13!43;CL:0000514!1.41e-13!43;CL:0000048!7.01e-11!427;CL:0000057!2.85e-10!76;CL:0000723!4.46e-10!433;CL:0000034!7.31e-10!441;CL:0000359!4.61e-08!32;CL:0000055!4.00e-07!106;CL:0002494!4.47e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!2.75e-20!83;UBERON:0002329!2.75e-20!83;UBERON:0003077!2.75e-20!83;UBERON:0003059!2.75e-20!83;UBERON:0007282!2.75e-20!83;UBERON:0009618!2.75e-20!83;UBERON:0007285!2.75e-20!83;UBERON:0002385!1.82e-18!63;UBERON:0001015!1.82e-18!63;UBERON:0000383!1.82e-18!63;UBERON:0001134!5.16e-18!61;UBERON:0002036!5.16e-18!61;UBERON:0003082!5.16e-18!61;UBERON:0004290!9.54e-18!70;UBERON:0002204!2.27e-16!167;UBERON:0007023!5.17e-14!115;UBERON:0000468!9.63e-13!659;UBERON:0005256!3.57e-12!143;UBERON:0000486!4.47e-12!82;UBERON:0000479!7.48e-12!787;UBERON:0000922!3.88e-11!612;UBERON:0002050!6.56e-11!605;UBERON:0005423!6.56e-11!605;UBERON:0000467!9.09e-11!625;UBERON:0000923!1.27e-10!604;UBERON:0005291!1.27e-10!604;UBERON:0006598!1.27e-10!604;UBERON:0002532!1.27e-10!604;UBERON:0000480!1.46e-10!626;UBERON:0000481!1.89e-10!347;UBERON:0000948!3.64e-10!24;UBERON:0005498!3.64e-10!24;UBERON:0004140!3.64e-10!24;UBERON:0009881!3.64e-10!24;UBERON:0004141!3.64e-10!24;UBERON:0003084!3.64e-10!24;UBERON:0007005!3.64e-10!24;UBERON:0004139!3.64e-10!24;UBERON:0004291!3.64e-10!24;UBERON:0007100!8.83e-10!27;UBERON:0004872!3.99e-09!84;UBERON:0000477!7.14e-09!286;UBERON:0000926!7.59e-09!448;UBERON:0004120!7.59e-09!448;UBERON:0006603!7.59e-09!448;UBERON:0001009!9.34e-09!113;UBERON:0004535!1.17e-08!110;UBERON:0000475!9.47e-08!365;UBERON:0000483!1.80e-07!309;UBERON:0004111!2.03e-07!241;UBERON:0000490!2.47e-07!138;UBERON:0000119!2.75e-07!312;UBERON:0003081!7.24e-07!216;UBERON:0004573!9.24e-07!33;UBERON:0004571!9.24e-07!33
|ontology_enrichment_uberon=UBERON:0002385!7.58e-20!64;UBERON:0001015!7.58e-20!64;UBERON:0000383!7.58e-20!64;UBERON:0007524!9.94e-20!73;UBERON:0001134!2.12e-19!62;UBERON:0002036!2.12e-19!62;UBERON:0003082!2.12e-19!62;UBERON:0003077!3.30e-19!72;UBERON:0007285!3.30e-19!72;UBERON:0002329!4.87e-19!71;UBERON:0003059!4.87e-19!71;UBERON:0007282!4.87e-19!71;UBERON:0004290!4.87e-19!71;UBERON:0009618!4.87e-19!71;UBERON:0002204!1.88e-18!167;UBERON:0000926!3.80e-16!315;UBERON:0004120!3.80e-16!315;UBERON:0006603!3.80e-16!315;UBERON:0007503!1.81e-15!78;UBERON:0000923!2.71e-14!560;UBERON:0010316!2.71e-14!560;UBERON:0005291!2.71e-14!560;UBERON:0006598!2.71e-14!560;UBERON:0010317!2.71e-14!560;UBERON:0002532!2.71e-14!560;UBERON:0000479!4.47e-14!773;UBERON:0002050!4.89e-14!564;UBERON:0000486!9.17e-14!83;UBERON:0005256!2.22e-13!122;UBERON:0005423!5.00e-12!581;UBERON:0000468!9.48e-12!656;UBERON:0000481!1.50e-11!342;UBERON:0000922!1.80e-11!592;UBERON:0003104!2.07e-11!160;UBERON:0009142!2.07e-11!160;UBERON:0000467!3.89e-11!624;UBERON:0000480!5.80e-11!625;UBERON:0007023!9.62e-11!114;UBERON:0000948!9.87e-10!24;UBERON:0005498!9.87e-10!24;UBERON:0004140!9.87e-10!24;UBERON:0009881!9.87e-10!24;UBERON:0004141!9.87e-10!24;UBERON:0003084!9.87e-10!24;UBERON:0007005!9.87e-10!24;UBERON:0004139!9.87e-10!24;UBERON:0004291!9.87e-10!24;UBERON:0007100!1.71e-09!27;UBERON:0004872!8.69e-09!83;UBERON:0000490!4.30e-08!148;UBERON:0001009!5.83e-08!112;UBERON:0003081!7.72e-08!203;UBERON:0004535!8.31e-08!109;UBERON:0010314!9.42e-08!132;UBERON:0000483!2.09e-07!306;UBERON:0000119!2.66e-07!309;UBERON:0000477!2.93e-07!373
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819984522970818!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00130004472819629
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}}
}}

Revision as of 14:33, 19 October 2012


Full id: C2904_Mesenchymal_adenocarcinoma_Cardiac_small_sacrococcigeal_Preadipocyte_Smooth



Phase1 CAGE Peaks

Hg19::chr7:81399311..81399323,-p6@HGF
Hg19::chr7:81399376..81399392,-p5@HGF
Hg19::chr7:81399411..81399432,-p4@HGF
Hg19::chr7:81399438..81399454,-p2@HGF


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
muscle tissue7.58e-2064
musculature7.58e-2064
musculature of body7.58e-2064
dense mesenchyme tissue9.94e-2073
skeletal muscle tissue2.12e-1962
striated muscle tissue2.12e-1962
myotome2.12e-1962
paraxial mesoderm3.30e-1972
presumptive paraxial mesoderm3.30e-1972
somite4.87e-1971
presomitic mesoderm4.87e-1971
presumptive segmental plate4.87e-1971
dermomyotome4.87e-1971
trunk paraxial mesoderm4.87e-1971
musculoskeletal system1.88e-18167
mesoderm3.80e-16315
mesoderm-derived structure3.80e-16315
presumptive mesoderm3.80e-16315
epithelial vesicle1.81e-1578
germ layer2.71e-14560
germ layer / neural crest2.71e-14560
embryonic tissue2.71e-14560
presumptive structure2.71e-14560
germ layer / neural crest derived structure2.71e-14560
epiblast (generic)2.71e-14560
tissue4.47e-14773
embryonic structure4.89e-14564
multilaminar epithelium9.17e-1483
trunk mesenchyme2.22e-13122
developing anatomical structure5.00e-12581
multi-cellular organism9.48e-12656
multi-tissue structure1.50e-11342
embryo1.80e-11592
mesenchyme2.07e-11160
entire embryonic mesenchyme2.07e-11160
anatomical system3.89e-11624
anatomical group5.80e-11625
adult organism9.62e-11114
heart9.87e-1024
primitive heart tube9.87e-1024
primary heart field9.87e-1024
anterior lateral plate mesoderm9.87e-1024
heart tube9.87e-1024
heart primordium9.87e-1024
cardiac mesoderm9.87e-1024
cardiogenic plate9.87e-1024
heart rudiment9.87e-1024
primary circulatory organ1.71e-0927
splanchnic layer of lateral plate mesoderm8.69e-0983
unilaminar epithelium4.30e-08148
circulatory system5.83e-08112
lateral plate mesoderm7.72e-08203
cardiovascular system8.31e-08109
structure with developmental contribution from neural crest9.42e-08132
epithelium2.09e-07306
cell layer2.66e-07309
anatomical cluster2.93e-07373


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)

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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
CTCF#1066445.360256373075030.001211145381643620.00819984522970818
RAD21#5885410.35503389545638.6948481184721e-050.00130004472819629



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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