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Coexpression cluster:C3910: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000926!8.85e-16!315;UBERON:0004120!8.85e-16!315;UBERON:0006603!8.85e-16!315;UBERON:0000486!4.29e-11!83;UBERON:0007503!7.33e-11!78;UBERON:0003914!2.45e-10!117;UBERON:0002204!2.48e-10!167;UBERON:0007524!3.33e-10!73;UBERON:0005256!7.27e-10!122;UBERON:0002329!7.78e-10!71;UBERON:0003059!7.78e-10!71;UBERON:0007282!7.78e-10!71;UBERON:0004290!7.78e-10!71;UBERON:0009618!7.78e-10!71;UBERON:0003104!8.00e-10!160;UBERON:0009142!8.00e-10!160;UBERON:0003077!8.42e-10!72;UBERON:0007285!8.42e-10!72;UBERON:0004872!1.91e-09!83;UBERON:0000468!2.33e-09!656;UBERON:0001134!2.95e-09!62;UBERON:0002036!2.95e-09!62;UBERON:0003082!2.95e-09!62;UBERON:0001637!3.66e-09!42;UBERON:0003509!3.66e-09!42;UBERON:0004572!3.66e-09!42;UBERON:0002385!6.77e-09!64;UBERON:0001015!6.77e-09!64;UBERON:0000383!6.77e-09!64;UBERON:0002049!1.02e-08!78;UBERON:0007798!1.02e-08!78;UBERON:0000490!1.72e-08!148;UBERON:0000480!1.86e-08!625;UBERON:0000467!2.21e-08!624;UBERON:0003081!8.55e-08!203;UBERON:0000055!9.62e-08!68;UBERON:0004535!1.56e-07!109;UBERON:0001009!2.16e-07!112;UBERON:0007500!4.04e-07!59;UBERON:0001981!4.04e-07!59;UBERON:0004537!4.04e-07!59;UBERON:0006965!4.04e-07!59;UBERON:0004573!8.37e-07!33;UBERON:0004571!8.37e-07!33
|ontology_enrichment_uberon=UBERON:0000926!8.85e-16!315;UBERON:0004120!8.85e-16!315;UBERON:0006603!8.85e-16!315;UBERON:0000486!4.29e-11!83;UBERON:0007503!7.33e-11!78;UBERON:0003914!2.45e-10!117;UBERON:0002204!2.48e-10!167;UBERON:0007524!3.33e-10!73;UBERON:0005256!7.27e-10!122;UBERON:0002329!7.78e-10!71;UBERON:0003059!7.78e-10!71;UBERON:0007282!7.78e-10!71;UBERON:0004290!7.78e-10!71;UBERON:0009618!7.78e-10!71;UBERON:0003104!8.00e-10!160;UBERON:0009142!8.00e-10!160;UBERON:0003077!8.42e-10!72;UBERON:0007285!8.42e-10!72;UBERON:0004872!1.91e-09!83;UBERON:0000468!2.33e-09!656;UBERON:0001134!2.95e-09!62;UBERON:0002036!2.95e-09!62;UBERON:0003082!2.95e-09!62;UBERON:0001637!3.66e-09!42;UBERON:0003509!3.66e-09!42;UBERON:0004572!3.66e-09!42;UBERON:0002385!6.77e-09!64;UBERON:0001015!6.77e-09!64;UBERON:0000383!6.77e-09!64;UBERON:0002049!1.02e-08!78;UBERON:0007798!1.02e-08!78;UBERON:0000490!1.72e-08!148;UBERON:0000480!1.86e-08!625;UBERON:0000467!2.21e-08!624;UBERON:0003081!8.55e-08!203;UBERON:0000055!9.62e-08!68;UBERON:0004535!1.56e-07!109;UBERON:0001009!2.16e-07!112;UBERON:0007500!4.04e-07!59;UBERON:0001981!4.04e-07!59;UBERON:0004537!4.04e-07!59;UBERON:0006965!4.04e-07!59;UBERON:0004573!8.37e-07!33;UBERON:0004571!8.37e-07!33
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
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,1.44641,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.886337,1.45054,0.430728,1.87308,1.02656,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,1.05469,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3910_Mesenchymal_Smooth_Fibroblast_Hepatic_sacrococcigeal_Prostate_Alveolar



Phase1 CAGE Peaks

Hg19::chr1:180123993..180124029,+p1@QSOX1
Hg19::chr1:180159606..180159619,+p@chr1:180159606..180159619
+
Hg19::chr1:180163451..180163471,+p@chr1:180163451..180163471
+


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
somatic cell2.65e-23588
animal cell7.74e-22679
eukaryotic cell7.74e-22679
fibroblast1.89e-1676
mesodermal cell1.94e-13121
multi fate stem cell3.61e-13427
somatic stem cell8.10e-13433
native cell1.56e-12722
stem cell1.50e-11441
smooth muscle cell3.55e-1143
smooth muscle myoblast3.55e-1143
muscle precursor cell4.95e-1158
myoblast4.95e-1158
multi-potent skeletal muscle stem cell4.95e-1158
contractile cell5.03e-1159
muscle cell1.85e-1055
electrically responsive cell6.73e-0961
electrically active cell6.73e-0961
embryonic cell1.07e-08250
stromal cell8.88e-0828
vascular associated smooth muscle cell1.64e-0732
Uber Anatomy
Ontology termp-valuen
mesoderm8.85e-16315
mesoderm-derived structure8.85e-16315
presumptive mesoderm8.85e-16315
multilaminar epithelium4.29e-1183
epithelial vesicle7.33e-1178
epithelial tube2.45e-10117
musculoskeletal system2.48e-10167
dense mesenchyme tissue3.33e-1073
trunk mesenchyme7.27e-10122
somite7.78e-1071
presomitic mesoderm7.78e-1071
presumptive segmental plate7.78e-1071
dermomyotome7.78e-1071
trunk paraxial mesoderm7.78e-1071
mesenchyme8.00e-10160
entire embryonic mesenchyme8.00e-10160
paraxial mesoderm8.42e-1072
presumptive paraxial mesoderm8.42e-1072
splanchnic layer of lateral plate mesoderm1.91e-0983
multi-cellular organism2.33e-09656
skeletal muscle tissue2.95e-0962
striated muscle tissue2.95e-0962
myotome2.95e-0962
artery3.66e-0942
arterial blood vessel3.66e-0942
arterial system3.66e-0942
muscle tissue6.77e-0964
musculature6.77e-0964
musculature of body6.77e-0964
vasculature1.02e-0878
vascular system1.02e-0878
unilaminar epithelium1.72e-08148
anatomical group1.86e-08625
anatomical system2.21e-08624
lateral plate mesoderm8.55e-08203
vessel9.62e-0868
cardiovascular system1.56e-07109
circulatory system2.16e-07112
epithelial tube open at both ends4.04e-0759
blood vessel4.04e-0759
blood vasculature4.04e-0759
vascular cord4.04e-0759
systemic artery8.37e-0733
systemic arterial system8.37e-0733


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

No analysis results for this cluster

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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