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Coexpression cluster:C1059: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;5:5.13865102313167:0.00108253124903356:0.00763857044239007
|tf_chipseq_enrich=ZNF263#10127;5:5.13865102313167:0.00108253124903356:0.00763857044239007
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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.360433,1.62205,0.481684,0.301904,0.480078,0.554663,0.19223,1.05889,0.0394821,0.450635,0.597407,0.152895,0.543352,0.300614,0.322799,0.774423,0.698835,2.89962,0.0766963,0.341703,3.24509,0.472508,0.805193,1.00212,0.619829,0.421276,0.470396,0.304828,0.122648,0.429397,0.810962,1.83894,0.154814,0.269459,14.8947,0.266487,0.481208,1.27056,6.55597,0.268162,1.87106,1.18362,0.809926,0.949078,0.371118,0.555735,0.440085,0.732845,0.822946,0.63387,0.567337,0.309329,0.887323,1.03948,0.546236,0.308962,0.514077,1.26716,0.513089,1.98297,0.558065,0.556977,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.197328,0.304852,1.03748,0.149081,0.429044,2.54475,0.730167,0.797419,0.989108,0.167664,0.745864,0.575394,0.19474,0.986227,0.0220225,0.0757344,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.162291,0.87,0.664183,1.16028,0.688301,0.822041,0.864454,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.92894,0.861701,0.893372,0.459808,1.17281,0.732093,1.62816,0.428232,1.69175,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,1.35238,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,1.20791,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.0833399,0.190235,2.20536,3.90629,0.557588,1.36372,0.643609,0.288769,2.6651,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,1.79865,0.553354,1.95084
}}
}}

Revision as of 14:39, 26 November 2012


Full id: C1059_Fibroblast_Adipocyte_Smooth_Chondrocyte_neuroectodermal_Hair_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr19:13050341..13050390,-p@chr19:13050341..13050390
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Hg19::chr19:13051088..13051148,-p@chr19:13051088..13051148
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Hg19::chr19:13051159..13051216,-p@chr19:13051159..13051216
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Hg19::chr19:13051603..13051646,-p@chr19:13051603..13051646
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Hg19::chr19:13054556..13054630,-p3@CALR
Hg19::chr19:13054632..13054644,-p19@CALR
Hg19::chr19:13054647..13054681,-p9@CALR
Hg19::chr19:13054682..13054702,-p14@CALR


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
animal cell1.05e-25679
eukaryotic cell1.05e-25679
somatic cell5.55e-19588
native cell6.38e-14722
embryonic cell1.36e-13250
mesodermal cell2.50e-11121
non-terminally differentiated cell6.33e-10106
fibroblast1.50e-0976
electrically responsive cell1.46e-0861
electrically active cell1.46e-0861
contractile cell1.71e-0859
muscle precursor cell5.81e-0858
myoblast5.81e-0858
multi-potent skeletal muscle stem cell5.81e-0858
muscle cell1.95e-0755
multi fate stem cell6.98e-07427
somatic stem cell8.40e-07433
Uber Anatomy
Ontology termp-valuen
mesenchyme5.04e-10160
entire embryonic mesenchyme5.04e-10160
trunk mesenchyme1.36e-09122
multilaminar epithelium1.95e-0983
epithelial vesicle2.17e-0978
unilaminar epithelium2.48e-09148
epithelial tube7.77e-08117
dense mesenchyme tissue1.00e-0773
somite1.14e-0771
presomitic mesoderm1.14e-0771
presumptive segmental plate1.14e-0771
dermomyotome1.14e-0771
trunk paraxial mesoderm1.14e-0771
paraxial mesoderm2.54e-0772
presumptive paraxial mesoderm2.54e-0772


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
ZNF263#1012755.138651023131670.001082531249033560.00763857044239007



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.