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Coexpression cluster:C1276: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223572189986459
|tf_chipseq_enrich=POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223572189986459
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|tfbs_overrepresentation_for_novel_motifs=1.01633,0.247072,1.00019,0.529489,0.343148,0.52784,0.604235,0.226729,1.19284,0.443077,0.497563,0.647852,0.184039,0.592674,0.341795,0.365029,0.827563,0.28906,0.569568,0.66776,0.384762,1.80169,0.520063,0.338096,0.430372,0.670692,1.52633,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,0.186138,0.309012,0.71891,0.305874,0.529001,0.773034,1.7673,0.307642,0.459366,0.254304,0.340293,0.494995,0.415364,0.60533,0.486696,0.876276,0.915545,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.924875,0.562713,1.44118,0.561701,0.905643,0.60771,1.19465,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.531388,0.503161,1.47572,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.310394,0.097572,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.81992,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.873303,1.02467,0.915771,0.379203,0.507004,1.22894,0.304323,0.039977,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,2.05416,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.140417,1.18454,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,1.78463,0.554217,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.877715,0.430431,0.401655,1.2088,0.996724,0.850033,1.04428,0.7715,0.624608,0.24928,0.602897,0.0992692
}}
}}

Revision as of 14:47, 26 November 2012


Full id: C1276_mesothelioma_CD14_leiomyoma_bile_Mesothelial_migratory_mesenchymal



Phase1 CAGE Peaks

Hg19::chr5:179247896..179247913,+p1@SQSTM1
Hg19::chr5:179249956..179250009,+p4@SQSTM1
Hg19::chr5:179251175..179251193,+p@chr5:179251175..179251193
+
Hg19::chr5:179260060..179260092,+p@chr5:179260060..179260092
+
Hg19::chr5:179260110..179260123,+p@chr5:179260110..179260123
+
Hg19::chr5:179260160..179260190,+p@chr5:179260160..179260190
+
Hg19::chr5:179260699..179260713,+p@chr5:179260699..179260713
+


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
mesoderm5.22e-18315
mesoderm-derived structure5.22e-18315
presumptive mesoderm5.22e-18315
musculoskeletal system2.00e-12167
lateral plate mesoderm1.85e-10203
multi-cellular organism3.65e-10656
bone marrow5.21e-0976
anatomical group7.63e-09625
anatomical system7.96e-09624
immune system4.71e-0893
skeletal element1.00e-0790
trunk mesenchyme1.11e-07122
vasculature1.24e-0778
vascular system1.24e-0778
vessel1.54e-0768
epithelial tube2.30e-07117
artery2.52e-0742
arterial blood vessel2.52e-0742
arterial system2.52e-0742
skeletal system3.46e-07100
bone element3.84e-0782
germ layer8.07e-07560
germ layer / neural crest8.07e-07560
embryonic tissue8.07e-07560
presumptive structure8.07e-07560
germ layer / neural crest derived structure8.07e-07560
epiblast (generic)8.07e-07560
embryo8.13e-07592
epithelial vesicle8.19e-0778
mesenchyme8.26e-07160
entire embryonic mesenchyme8.26e-07160
trunk8.54e-07199


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
POLR2A#543072.147453176558070.004747636447610280.0223572189986459



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.