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Coexpression cluster:C3858: Difference between revisions

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|full_id=C3858_cerebellum_Skeletal_Fibroblast_myxofibrosarcoma_Preadipocyte_Adipocyte_mesenchymal
|full_id=C3858_cerebellum_Skeletal_Fibroblast_myxofibrosarcoma_Preadipocyte_Adipocyte_mesenchymal
|id=C3858
|id=C3858
|ontology_enrichment_celltype=CL:0000055!2.18e-28!180;CL:0000057!3.02e-18!75;CL:0000680!1.82e-11!57;CL:0000056!1.82e-11!57;CL:0000355!1.82e-11!57;CL:0000187!3.42e-10!54;CL:0000183!1.75e-09!59;CL:0000393!1.02e-08!60;CL:0000211!1.02e-08!60;CL:0002620!6.96e-07!23;CL:0002334!8.72e-07!12
|ontology_enrichment_celltype=CL:0000057!2.51e-19!76;CL:0000680!5.64e-13!58;CL:0000056!5.64e-13!58;CL:0000355!5.64e-13!58;CL:0000187!1.59e-11!55;CL:0000183!3.12e-11!59;CL:0000055!9.97e-11!106;CL:0000393!1.35e-09!61;CL:0000211!1.35e-09!61;CL:0000192!1.84e-07!43;CL:0000514!1.84e-07!43;CL:0002334!2.96e-07!12;CL:0002620!5.38e-07!23
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.69e-24!57;UBERON:0005068!8.69e-24!57;UBERON:0006241!8.69e-24!57;UBERON:0007135!8.69e-24!57;UBERON:0000475!1.06e-23!365;UBERON:0002616!2.34e-23!59;UBERON:0000073!5.43e-23!94;UBERON:0001016!5.43e-23!94;UBERON:0000955!1.76e-22!69;UBERON:0006238!1.76e-22!69;UBERON:0002346!4.82e-22!90;UBERON:0003075!1.69e-21!86;UBERON:0007284!1.69e-21!86;UBERON:0001017!3.25e-21!82;UBERON:0005743!8.24e-21!86;UBERON:0000033!2.09e-20!123;UBERON:0000924!8.05e-19!173;UBERON:0006601!8.05e-19!173;UBERON:0003080!9.30e-19!42;UBERON:0000153!1.03e-18!129;UBERON:0007811!1.03e-18!129;UBERON:0002780!1.47e-18!41;UBERON:0001890!1.47e-18!41;UBERON:0006240!1.47e-18!41;UBERON:0004121!3.50e-18!169;UBERON:0001893!4.19e-17!34;UBERON:0002020!4.23e-17!34;UBERON:0003528!4.23e-17!34;UBERON:0001869!1.15e-16!32;UBERON:0002791!1.89e-16!33;UBERON:0003056!1.77e-15!61;UBERON:0000914!2.84e-15!83;UBERON:0002329!2.84e-15!83;UBERON:0003077!2.84e-15!83;UBERON:0003059!2.84e-15!83;UBERON:0007282!2.84e-15!83;UBERON:0009618!2.84e-15!83;UBERON:0007285!2.84e-15!83;UBERON:0002619!1.60e-14!22;UBERON:0000468!2.29e-14!659;UBERON:0000119!1.09e-13!312;UBERON:0000483!1.56e-13!309;UBERON:0000956!1.67e-13!25;UBERON:0000203!1.67e-13!25;UBERON:0001950!1.98e-13!20;UBERON:0004290!6.60e-13!70;UBERON:0000486!1.99e-12!82;UBERON:0000481!2.42e-12!347;UBERON:0001134!3.09e-11!61;UBERON:0002036!3.09e-11!61;UBERON:0003082!3.09e-11!61;UBERON:0007023!4.16e-11!115;UBERON:0002385!5.40e-11!63;UBERON:0001015!5.40e-11!63;UBERON:0000383!5.40e-11!63;UBERON:0000467!2.41e-10!625;UBERON:0000480!4.05e-10!626;UBERON:0002050!8.16e-10!605;UBERON:0005423!8.16e-10!605;UBERON:0000923!1.07e-09!604;UBERON:0005291!1.07e-09!604;UBERON:0006598!1.07e-09!604;UBERON:0002532!1.07e-09!604;UBERON:0000922!1.74e-09!612;UBERON:0000025!1.58e-08!194;UBERON:0004111!1.81e-07!241;UBERON:0000477!3.39e-07!286;UBERON:0005256!4.23e-07!143;UBERON:0000062!6.22e-07!511
|ontology_enrichment_uberon=UBERON:0010314!1.20e-24!132;UBERON:0001049!1.64e-21!56;UBERON:0005068!1.64e-21!56;UBERON:0006241!1.64e-21!56;UBERON:0007135!1.64e-21!56;UBERON:0001016!2.72e-21!89;UBERON:0000073!9.71e-21!53;UBERON:0002616!9.71e-21!53;UBERON:0000955!2.04e-20!68;UBERON:0006238!2.04e-20!68;UBERON:0002346!7.24e-20!86;UBERON:0003075!2.56e-19!82;UBERON:0007284!2.56e-19!82;UBERON:0001017!6.48e-19!81;UBERON:0002780!4.27e-17!41;UBERON:0001890!4.27e-17!41;UBERON:0003080!4.27e-17!41;UBERON:0006240!4.27e-17!41;UBERON:0004121!7.02e-17!171;UBERON:0000924!7.02e-17!171;UBERON:0006601!7.02e-17!171;UBERON:0001893!4.18e-16!34;UBERON:0003528!7.84e-16!34;UBERON:0002020!7.84e-16!34;UBERON:0001869!1.04e-15!32;UBERON:0000481!1.51e-15!342;UBERON:0010371!2.86e-15!104;UBERON:0002791!3.16e-15!32;UBERON:0003077!4.90e-15!72;UBERON:0007285!4.90e-15!72;UBERON:0007524!7.25e-15!73;UBERON:0003056!1.35e-14!61;UBERON:0002329!1.51e-14!71;UBERON:0003059!1.51e-14!71;UBERON:0007282!1.51e-14!71;UBERON:0004290!1.51e-14!71;UBERON:0009618!1.51e-14!71;UBERON:0002619!6.22e-14!22;UBERON:0000486!4.13e-13!83;UBERON:0001950!5.55e-13!20;UBERON:0000956!6.69e-13!25;UBERON:0000203!6.69e-13!25;UBERON:0001134!1.16e-12!62;UBERON:0002036!1.16e-12!62;UBERON:0003082!1.16e-12!62;UBERON:0000468!1.44e-12!656;UBERON:0000119!1.60e-12!309;UBERON:0000483!2.18e-12!306;UBERON:0002385!2.20e-12!64;UBERON:0001015!2.20e-12!64;UBERON:0000383!2.20e-12!64;UBERON:0007503!2.56e-12!78;UBERON:0007023!2.28e-10!114;UBERON:0000467!1.25e-09!624;UBERON:0000480!1.98e-09!625;UBERON:0000477!2.07e-09!373;UBERON:0002050!3.18e-09!564;UBERON:0005423!4.72e-09!581;UBERON:0000923!5.87e-09!560;UBERON:0010316!5.87e-09!560;UBERON:0005291!5.87e-09!560;UBERON:0006598!5.87e-09!560;UBERON:0010317!5.87e-09!560;UBERON:0002532!5.87e-09!560;UBERON:0000922!1.05e-07!592;UBERON:0000479!1.10e-07!773;UBERON:0000025!3.52e-07!192;UBERON:0003104!5.05e-07!160;UBERON:0009142!5.05e-07!160
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129813723894958!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664216407974503!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767723421065015!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222390887578281!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109442188107045!ZNF274#10782;2:947.83076923077:1.47205921117966e-06:5.6835634734341e-05
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129813723894958!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00664216407974503!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767723421065015!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222390887578281!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109442188107045!ZNF274#10782;2:947.83076923077:1.47205921117966e-06:5.6835634734341e-05
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}}
}}

Revision as of 15:27, 19 October 2012


Full id: C3858_cerebellum_Skeletal_Fibroblast_myxofibrosarcoma_Preadipocyte_Adipocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:145075847..145075982,-p4@PDE4DIP
Hg19::chr1:145075992..145076044,-p5@PDE4DIP
Hg19::chr1:145076048..145076059,-p19@PDE4DIP


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
structure with developmental contribution from neural crest1.20e-24132
neural tube1.64e-2156
neural rod1.64e-2156
future spinal cord1.64e-2156
neural keel1.64e-2156
nervous system2.72e-2189
regional part of nervous system9.71e-2153
regional part of brain9.71e-2153
brain2.04e-2068
future brain2.04e-2068
neurectoderm7.24e-2086
neural plate2.56e-1982
presumptive neural plate2.56e-1982
central nervous system6.48e-1981
regional part of forebrain4.27e-1741
forebrain4.27e-1741
anterior neural tube4.27e-1741
future forebrain4.27e-1741
ectoderm-derived structure7.02e-17171
ectoderm7.02e-17171
presumptive ectoderm7.02e-17171
telencephalon4.18e-1634
brain grey matter7.84e-1634
gray matter7.84e-1634
cerebral hemisphere1.04e-1532
multi-tissue structure1.51e-15342
ecto-epithelium2.86e-15104
regional part of telencephalon3.16e-1532
paraxial mesoderm4.90e-1572
presumptive paraxial mesoderm4.90e-1572
dense mesenchyme tissue7.25e-1573
pre-chordal neural plate1.35e-1461
somite1.51e-1471
presomitic mesoderm1.51e-1471
presumptive segmental plate1.51e-1471
dermomyotome1.51e-1471
trunk paraxial mesoderm1.51e-1471
regional part of cerebral cortex6.22e-1422
multilaminar epithelium4.13e-1383
neocortex5.55e-1320
cerebral cortex6.69e-1325
pallium6.69e-1325
skeletal muscle tissue1.16e-1262
striated muscle tissue1.16e-1262
myotome1.16e-1262
multi-cellular organism1.44e-12656
cell layer1.60e-12309
epithelium2.18e-12306
muscle tissue2.20e-1264
musculature2.20e-1264
musculature of body2.20e-1264
epithelial vesicle2.56e-1278
adult organism2.28e-10114
anatomical system1.25e-09624
anatomical group1.98e-09625
anatomical cluster2.07e-09373
embryonic structure3.18e-09564
developing anatomical structure4.72e-09581
germ layer5.87e-09560
germ layer / neural crest5.87e-09560
embryonic tissue5.87e-09560
presumptive structure5.87e-09560
germ layer / neural crest derived structure5.87e-09560
epiblast (generic)5.87e-09560
embryo1.05e-07592
tissue1.10e-07773
tube3.52e-07192
mesenchyme5.05e-07160
entire embryonic mesenchyme5.05e-07160


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
CTBP2#1488362.71700033932814.049570681927e-060.000129813723894958
RAD21#5885310.35503389545630.0009004912073565420.00664216407974503
REST#597839.650028716128020.001112636247114590.00767723421065015
SUZ12#23512350.11578091106297.93834897779404e-060.000222390887578281
ZNF263#1012738.221841637010680.001799043925565870.0109442188107045
ZNF274#107822947.830769230771.47205921117966e-065.6835634734341e-05



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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