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Coexpression cluster:C229: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;7:3.90047934880916:0.00207323716250547:0.0120172503060777!GTF2B#2959;6:3.09133838074105:0.0129409764714944:0.0465182983997521!POLR2A#5430;42:1.45472634541031:0.000619799458460022:0.00513739965413542!RDBP#7936;4:9.91215509613064:0.000738087004057832:0.00581510777133342
|tf_chipseq_enrich=BCL3#602;7:3.90047934880916:0.00207323716250547:0.0120172503060777!GTF2B#2959;6:3.09133838074105:0.0129409764714944:0.0465182983997521!POLR2A#5430;42:1.45472634541031:0.000619799458460022:0.00513739965413542!RDBP#7936;4:9.91215509613064:0.000738087004057832:0.00581510777133342
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|tfbs_overrepresentation_for_novel_motifs=0.0768018,0.003076,0.0712904,0.425275,0.535284,1.0174,0.602814,0.394636,0.160191,0.000687247,0.357096,0.406009,0.0422556,0.314461,0.205253,0.133565,0.119289,0.50685,0.0539391,0.125359,0.477556,0.313384,0.0826628,0.51569,0.406124,0.05514,0.161338,0.657708,0.213779,0.190464,0.313301,0.138021,0.002829,0.146427,0.0721405,1.28755e-07,0.00733302,0.0882274,0.674962,0.00381975,1.36765,0.0502504,0.785697,0.747292,0.0243818,0.0957998,0.143887,0.335042,0.188244,0.547812,0.0599013,0.635855,0.1376,0.534408,0.768131,0.319102,0.799151,0.111033,0.121184,0.498877,0.160351,0.145852,0.943777,0.344895,0.161182,0.0906885,0.913499,0.652367,0.41389,0.511132,0.0444509,0.178759,0.000494126,0.27936,0.0169642,0.0124199,0.0442451,0.0983574,0.130929,0.883564,0.109736,0.343576,0.160873,0.274579,0.244004,9.68579e-06,0.000676207,0.0339898,0.0692009,0.742187,0.418256,0.226174,0.146997,1.01927,0.00207973,0.0464855,0.0524612,0.170887,0.0709247,0.00371111,0.325353,0.869668,0.167668,0.384308,0.290293,0.0142485,0.113383,0.309042,0.109066,0.00155713,0.0261922,0.166081,0.949804,0.193216,0.990466,0.247247,0.0083361,0.0574421,0.0896888,0.164117,0.273551,0.0683023,0.680308,1.0624,0.469328,1.10862,0.137804,0.149715,0.303903,0.459477,0.64297,0.0594771,0.844198,0.381084,0.428622,0.013041,0.149277,0.207828,0.394746,1.17283,0.79037,0.365644,0.591113,0.504498,0.0865557,0.024611,0.0797291,1.0194,0.0487439,0.0126941,0.0181463,2.80452e-06,0.226872,0.0795979,0.956264,0.537178,0.846492,0.311904,0.0380709,0.0279811,0.956196,0.214937,0.811807,0.189747,0.311046,0.366261,0.00236202,0.940995,0.00101928
}}
}}

Revision as of 13:51, 26 November 2012


Full id: C229_Mesenchymal_CD4_Melanocyte_acute_skeletal_left_heart



Phase1 CAGE Peaks

Hg19::chr11:17096287..17096292,-p1@SNORD14A
Hg19::chr11:62432889..62432899,+p1@SNORA57
Hg19::chr11:811679..811684,+p2@SNORA52
Hg19::chr11:93465662..93465665,-p1@SNORA8
Hg19::chr11:93466460..93466463,-p1@SNORD5
Hg19::chr11:93468399..93468405,-p19@TAF1D
p1@SNORA40
Hg19::chr12:57038878..57038884,-p1@SNORD59A
Hg19::chr13:27829202..27829226,+p1@SNORD102
Hg19::chr13:45910578..45910583,-p1@ENST00000517242
Hg19::chr14:20791482..20791485,-p1@ENST00000410557
Hg19::chr16:2013101..2013108,-p1@SNORA64
Hg19::chr16:2015179..2015182,+p3@SNORA78
Hg19::chr16:2205102..2205107,-p2@SNORD60
Hg19::chr16:33965418..33965444,+p1@RN5-8S2
Hg19::chr16:70563415..70563420,+p4@SNORD111B
Hg19::chr16:89627836..89627840,+p2@SNORD68
Hg19::chr17:27050447..27050450,+p1@SNORD42A
Hg19::chr17:27050702..27050704,+p1@SNORD4B
Hg19::chr17:7478029..7478035,+p1@SNORA48
Hg19::chr17:7480128..7480132,+p1@SNORD10
Hg19::chr18:47017713..47017717,-p1@SNORD58A
Hg19::chr18:47018091..47018115,-p1@SNORD58B
p4@RPL17
Hg19::chr19:10218330..10218339,+p1@SNORD105
Hg19::chr19:10220437..10220441,+p1@SNORD105B
Hg19::chr19:24187307..24187313,-p1@RN5-8S4
Hg19::chr19:49993222..49993226,+p1@SNORD32A
Hg19::chr19:49993872..49993876,+p1@SNORD33
Hg19::chr19:49994430..49994434,+p1@SNORD35A
Hg19::chr1:173833352..173833357,-p1@SNORD81
Hg19::chr1:173833579..173833584,-p1@SNORD47
Hg19::chr1:173835162..173835166,-p1@SNORD44
Hg19::chr1:173835843..173835856,-p1@SNORD76
Hg19::chr1:173836874..173836885,-p1@SNORD74
Hg19::chr1:235291248..235291252,-p2@SNORA14B
Hg19::chr1:28160911..28160914,+p1@SCARNA1
Hg19::chr1:28833864..28833907,+p1@SNORA73A
Hg19::chr1:28835067..28835078,+p1@SNORA73B
Hg19::chr1:28907004..28907024,-p1@SNORA44
Hg19::chr1:28907560..28907564,-p1@SNORA16A
Hg19::chr20:2634860..2634861,+p1@SNORD110
Hg19::chr20:2637264..2637276,+p1@SNORD56
Hg19::chr20:2637584..2637589,+p2@SNORD57
Hg19::chr20:47896855..47896877,+p1@SNORD12B
Hg19::chr20:47897225..47897227,+p2@SNORD12
Hg19::chr2:29150850..29150852,+p@chr2:29150850..29150852
+
Hg19::chr3:186505086..186505092,+p2@SNORA63
Hg19::chr4:119200341..119200348,+p2@SNORA24
Hg19::chr4:1976361..1976365,+p1@SCARNA22
Hg19::chr5:105889153..105889161,+p1@ENST00000478633
Hg19::chr5:137896795..137896800,-p1@SNORD63
Hg19::chr5:180668885..180668889,-p1@SNORD96A
Hg19::chr5:74063455..74063464,-p4@GFM2
Hg19::chr6:26305727..26305730,-p@chr6:26305727..26305730
-
Hg19::chr6:31804851..31804855,+p1@SNORD52
Hg19::chr8:56986457..56986460,-p1@SNORD54
Hg19::chr9:136216952..136216953,+p2@SNORD36B
Hg19::chr9:136217312..136217315,+p1@SNORD36A
Hg19::chr9:136217702..136217704,+p1@SNORD36C
p6@RPL7A
Hg19::chrM:12203..12214,+p3@uc004cow.1
Hg19::chrX:132286783..132286784,+p1@ENST00000384372
Hg19::chrX:153628621..153628623,+p2@SNORA70
Hg19::chrY:10037751..10037770,+p1@RN5-8S6


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><br><br>disease_data<br>

Disease
Ontology termp-valuen
germ cell and embryonal cancer4.15e-0822
germ cell cancer4.15e-0822
cancer1.98e-07235
disease of cellular proliferation6.42e-07239


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
BCL3#60273.900479348809160.002073237162505470.0120172503060777
GTF2B#295963.091338380741050.01294097647149440.0465182983997521
POLR2A#5430421.454726345410310.0006197994584600220.00513739965413542
RDBP#793649.912155096130640.0007380870040578320.00581510777133342



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

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