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Coexpression cluster:C666: Difference between revisions

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|tf_chipseq_enrich=REST#5978;6:4.4538594074437:0.00111223676696847:0.00772141024364667!SMC3#9126;5:5.78651263266648:0.00106075295019698:0.00749502586872485!TAF7#6879;6:5.27680126381104:0.000446292320197271:0.00415384757410951!TCF7L2#6934;5:4.14237560120667:0.00468850344400493:0.022119646347221!ZNF263#10127;6:3.79469614015877:0.00258517358054671:0.0142989589862683
|tf_chipseq_enrich=REST#5978;6:4.4538594074437:0.00111223676696847:0.00772141024364667!SMC3#9126;5:5.78651263266648:0.00106075295019698:0.00749502586872485!TAF7#6879;6:5.27680126381104:0.000446292320197271:0.00415384757410951!TCF7L2#6934;5:4.14237560120667:0.00468850344400493:0.022119646347221!ZNF263#10127;6:3.79469614015877:0.00258517358054671:0.0142989589862683
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|tfbs_overrepresentation_for_novel_motifs=0.208137,1.96828,0.585688,0.320418,0.509452,0.854581,0.385011,0.0904943,0.0889928,0.437382,0.797059,0.423573,0.499876,0.37489,0.169864,0.187326,0.587543,1.32622,0.0716493,0.0231345,1.1081,0.0548422,0.312425,0.500259,0.670559,0.443987,0.442433,0.310589,0.515041,0.70699,0.275306,0.622056,0.110199,0.0661331,0.145955,13.7468,0.868674,0.320003,1.29937,9.02509,0.144976,0.261903,0.171949,0.16875,1.04897,0.226447,0.385972,0.776485,0.312409,0.173249,0.456831,0.396393,0.0308939,0.694739,0.841347,0.377467,0.176395,0.92117,0.0468732,0.348003,0.660716,0.388062,0.299793,1.38047,0.403967,0.529794,0.927044,1.28869,0.612294,1.12869,0.700198,1.58863,1.68323,0.839414,0.840426,2.22254,0.0498505,0.546008,0.609242,0.233499,1.39633,0.560705,0.403653,0.636937,0.789807,0.00329133,1.08786,0.687175,0.480498,1.38705,1.01818,0.763867,0.637885,0.114875,2.2319,0.390718,0.248364,0.67819,0.484706,2.96422,1.30514,1.52942,0.672898,1.44218,0.519171,0.289709,0.576179,0.371864,2.70962,0.933941,0.211112,0.670274,0.198172,0.301413,0.971251,0.142611,1.05642,0.274314,0.527634,0.116746,0.831412,0.478284,1.5335,0.413695,1.0796,0.546713,0.379419,0.642598,0.872646,0.124214,0.76453,0.761072,0.886589,0.410725,1.03079,0.659572,0.270369,1.51346,0.989273,1.83943,1.43902,3.59882,0.38094,0.674844,0.52079,0.904915,0.505455,1.68078,0.718674,1.75815,0.0262543,0.817179,0.764896,0.598654,0.387634,1.15881,1.17612,0.160686,0.670668,0.617071,0.951654,0.747146,0.608503,0.21815,1.3253,0.402951,0.341994,0.383837,0.00658855
}}
}}

Revision as of 14:23, 26 November 2012


Full id: C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr1:56962127..56962135,-p@chr1:56962127..56962135
-
Hg19::chr1:56962213..56962224,-p@chr1:56962213..56962224
-
Hg19::chr1:56977768..56977801,-p@chr1:56977768..56977801
-
Hg19::chr1:56977818..56977827,-p@chr1:56977818..56977827
-
Hg19::chr1:56990054..56990076,-p@chr1:56990054..56990076
-
Hg19::chr1:56990149..56990181,-p@chr1:56990149..56990181
-
Hg19::chr1:56990206..56990220,-p@chr1:56990206..56990220
-
Hg19::chr1:57044697..57044720,-p9@PPAP2B
Hg19::chr1:57044945..57044953,-p13@PPAP2B
Hg19::chr1:57044980..57045112,-p1@PPAP2B
Hg19::chr1:57045115..57045143,-p6@PPAP2B
Hg19::chr1:57045207..57045226,-p2@PPAP2B
Hg19::chr1:57045228..57045242,-p3@PPAP2B


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
fibroblast2.40e-1176
skin fibroblast3.83e-1023
fat cell3.89e-0815
Uber Anatomy
Ontology termp-valuen
adult organism6.89e-22114
multi-cellular organism4.14e-11656
structure with developmental contribution from neural crest1.37e-10132
neural tube2.44e-1056
neural rod2.44e-1056
future spinal cord2.44e-1056
neural keel2.44e-1056
brain grey matter2.81e-0934
gray matter2.81e-0934
regional part of nervous system3.65e-0953
regional part of brain3.65e-0953
telencephalon4.60e-0934
central nervous system1.12e-0881
regional part of telencephalon1.27e-0832
cerebral hemisphere1.28e-0832
surface structure2.22e-0899
organ2.43e-08503
regional part of forebrain8.61e-0841
forebrain8.61e-0841
anterior neural tube8.61e-0841
future forebrain8.61e-0841
anatomical system9.04e-08624
neural plate9.21e-0882
presumptive neural plate9.21e-0882
anatomical group1.15e-07625
integument1.25e-0746
integumental system1.25e-0746
multi-tissue structure1.93e-07342
brain2.60e-0768
future brain2.60e-0768
skin of body2.97e-0741
neurectoderm8.05e-0786


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
REST#597864.45385940744370.001112236766968470.00772141024364667
SMC3#912655.786512632666480.001060752950196980.00749502586872485
TAF7#687965.276801263811040.0004462923201972710.00415384757410951
TCF7L2#693454.142375601206670.004688503444004930.022119646347221
ZNF263#1012763.794696140158770.002585173580546710.0142989589862683



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.