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Coexpression cluster:C266: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!6.41e-19!39;DOID:8692!3.70e-18!31;DOID:2531!1.30e-17!51;DOID:0060083!1.30e-17!51
|ontology_enrichment_disease=DOID:1240!6.41e-19!39;DOID:8692!3.70e-18!31;DOID:2531!1.30e-17!51;DOID:0060083!1.30e-17!51
|ontology_enrichment_uberon=UBERON:0002390!5.05e-19!102;UBERON:0003061!5.05e-19!102;UBERON:0002193!2.40e-16!112;UBERON:0002371!6.54e-14!80;UBERON:0001474!1.34e-12!86;UBERON:0004765!2.35e-10!101;UBERON:0001434!2.35e-10!101;UBERON:0002405!1.69e-08!115
|ontology_enrichment_uberon=UBERON:0002390!5.05e-19!102;UBERON:0003061!5.05e-19!102;UBERON:0002193!2.40e-16!112;UBERON:0002371!6.54e-14!80;UBERON:0001474!1.34e-12!86;UBERON:0004765!2.35e-10!101;UBERON:0001434!2.35e-10!101;UBERON:0002405!1.69e-08!115
|tf_chipseq_enrich=GATA1#2623;13:3.59763277284502:3.96023418025606e-05:0.000738576602771004!GATA2#2624;12:3.12120777148261:0.000318891361545543:0.00326452606434571!STAT2#6773;4:5.32765479072985:0.00673933989550124:0.0286432230230844!TAL1#6886;12:7.31476326794454:5.70523040920804e-08:3.56795544136095e-06
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22659,0.827456,0.91194,0.48198,0.633771,0.8766,0.881634,0.847822,0.850993,0.957849,0.377483,0.999781,0.921951,0.476475,0.44041,0.603256,0.720987,0.991599,0.981628,0.857935,0.899244,0.910367,0.987969,0.913149,0.725617,0.597205,0.752237,0.63962,0.961912,0.484156,0.240556,0.183008,0.23715,0.0196177,0.997644,0.801415,0.188153,0.803728,0.962972,0.411607,0.378999,0.848717,0.190102,0.669585,0.707203,0.921914,0.580806,0.819134,0.567606,0.647408,0.722634,0.477031,0.721015,0.431831,0.716037,0.968545,0.972017,0.0768562,0.215048,0.326268,0.343179,0.969553,0.620288,0.999771,0.62034,0.549062,0.568231,0.641474,0.821947,0.692904,0.0345149,0.593303,0.660819,0.446662,0.643555,0.956887,1,1,0.0887541,0.909904,0.846154,0.679803,0.847474,0.562899,0.807129,0.724932,0.72297,0.178059,0.298262,0.69583,0.92126,0.058457,0.466091,0.674612,0.528626,0.595551,0.862128,0.796793,0.814063,0.540406,0.914981,0.61768,0.810098,0.724936,0.996002,0.932803,0.868456,0.910023,0.826239,0.988425,0.202186,0.0223235,0.74864,0.652562,0.860768,0.269908,0.99999,0.763192,0.704343,0.792901,0.269669,0.921557,0.498157,0.812402,0.518888,0.587741,0.466732,0.693883,0.923869,0.511067,0.196761,0.873808,0.760945,0.89331,0.312825,0.580875,0.965752,0.956615,0.8036,0.736141,0.192424,0.236788,0.820363,0.535529,0.832634,0.312445,0.344817,0.801196,0.788231,0.278242,0.9494,0.663068,0.750076,0.964571,0.76467,0.728686,0.946333,0.262366,0.945559,0.830009,0.375298,0.801606,0.999805,0.998405,0.121996,0.863357,0.899253,0.516033,0.678861,0.998581,0.47941,0.636694,0.352922,0.62279,0.971808,0.602929,0.871409,0.799815,0.383096,0.292298,0.131751,0.854758,0.478017,0.263266,0.836344,0.33226,0.220847,0.692171,0.959944,0.212901,0.349059,0.16898,0.0663718,0.998098,1,0.985118,0.646457,0.701407,0.684153,0.794973,0.97189,0.658187,0.722717,0.199567,0.790084,0.560183,0.803386,0.73673,0.270902,0.797308,0.239883,0.121022,0.49923,0.832551,0.999968,0.960384,0.982322,0.770278,0.943802,0.588133,0.792741,0.784643,0.977438,0.357255,0.99993,0.182905,0.999925,0.794615,0.999997,0.508899,0.496361,0.178429,0.930373,0.117429,0.683775,0.27299,0.270416,0.0232966,0.45323,0.0163267,0.229934,0.73656,0.291583,0.0762945,0.260231,0.876577,0.793962,0.980733,0.279157,0.634428,0.301056,0.933136,0.498123,0.15773,0.904655,0.987188,0.573517,0.905571,0.839927,0.547141,0.161216,0.993966,0.87993,0.230832,0.178244,0.992646,0.320015,0.990874,0.833863,0.8877,0.926487,0.700594,0.999141,0.0326384,0.293645,0.758795,0.742591,0.279098,0.821626,0.221958,0.149971,0.915275,0.054907,0.612209,0.274739,0.698339,0.744152,0.0783441,0.717265,0.270108,0.365281,0.628107,0.175944,0.895633,0.490544,0.251024,0.46919,0.981,0.253523,0.703056,0.15994,0.182239,0.00410772,0.105789,0.532213,0.135575,0.0753171,0.982803,0.81848,0.153555,0.138759,0.880703,0.931525,0.714638,0.213794,0.100977,0.699542,0.356603,0.8373,0.269707,0.758265,0.768904,0.955553,0.119541,0.850224,0.805981,0.484769,0.756797,0.406786,0.64659,0.680802,0.979814,0.157359,0.323531,0.390712,0.734111,0.60961,0.888574,0.42888,0.967772,0.540494,0.853927,0.704497,0.877539,0.00984273,0.860122,0.555729,0.768592,0.0405717,0.456038,0.805433,0.569442,0.852303,0.657065,0.1152,0.730964,0.749689,0.960429,0.865642,0.772984,0.916872,0.810772,0.566554,0.909629,0.875915,0.655891,0.633015,0.703195,0.417958,0.798094,0.885053,0.628209,0.605092,0.442877,0.18141,0.899302,0.733751,0.681791,0.392106,0.679716,0.187189,0.570513,0.31256,0.727177,0.421207,0.328038,0.98569,0.951138,0.473325,0.672727,0.583401,0.53303,0.254391,0.881717,0.557341,0.51847,0.618215,0.816737,0.559159,0.633229,0.365926,0.534878,0.579101,0.283524,0.637146,0.722103,0.556209,0.631138,0.941896,0.359215,0.74558,0.761579,0.172998,0.425749,0.964845,0.706618,0.221184,0.728827,0.718279,0.103439,0.0159783,0.455915,0.0655198,0.327954,0.866461,0.783623,0.183855,0.599496,0.496098,0.103459,0.694733,0.295831,0.52557,0.899228,0.0267456,0.778531,0.813254,0.392477,0.810876,0.712592,0.724242,0.970775,0.375019,0.753814,0.974951,0.550022,0.593387,0.594567,0.280667,0.734652,0.492912,0.5943,0.600814,0.871606,0.0983228,0.852713,0.631071,0.261948,0.402906,0.502615,0.294673,0.626386,0.292912,0.270621,0.67402,0.726239,0.657665,0.848653,0.521375,0.677573,0.453288,0.457453,0.906351,0.319473,0.349981,0.192751,0.823495,0.917612,0.557385,0.86019,0.87884,0.791845,0.227345,0.110989,0.396343,0.10133,0.9601,0.670921,0.54486,0.726642,0.490966,0.913012,0.987804,0.461361,0.326161,0.569935,0.593134,0.864741,0.686951,0.860021,0.0977374,0.100515,0.504988,0.174463,0.782734,0.476602,0.0659095,0.786983,0.333037,0.228649,0.769493,0.287399,0.811996,0.940713,0.15159,0.700262,0.0785972,0.82438,0.916267,0.388696,0.938876,0.36501,0.699628,0.325691,0.597652
}}
}}

Revision as of 14:10, 5 September 2012


Full id: C266_acute_chronic_leukemia_small_choriocarcinoma_hepatoma_Mast



Phase1 CAGE Peaks

Hg19::chr10:126826943..126826984,-p28@CTBP2
Hg19::chr10:127505042..127505063,-p8@UROS
Hg19::chr10:25820836..25820845,+p@chr10:25820836..25820845
+
Hg19::chr10:25820884..25820895,+p@chr10:25820884..25820895
+
Hg19::chr10:25820904..25820913,+p@chr10:25820904..25820913
+
Hg19::chr10:25821044..25821091,+p@chr10:25821044..25821091
+
Hg19::chr11:33914678..33914683,-p@chr11:33914678..33914683
-
Hg19::chr11:74807933..74807937,-p@chr11:74807933..74807937
-
Hg19::chr12:115758751..115758760,-p@chr12:115758751..115758760
-
Hg19::chr12:115758858..115758876,-p@chr12:115758858..115758876
-
Hg19::chr12:115758891..115758908,-p@chr12:115758891..115758908
-
Hg19::chr12:71617078..71617086,-p@chr12:71617078..71617086
-
Hg19::chr12:78870953..78870955,+p@chr12:78870953..78870955
+
Hg19::chr14:105166013..105166017,+p@chr14:105166013..105166017
+
Hg19::chr14:67859531..67859537,-p9@PLEK2
Hg19::chr16:24124312..24124336,+p@chr16:24124312..24124336
+
Hg19::chr16:24127820..24127835,-p@chr16:24127820..24127835
-
Hg19::chr16:88558406..88558427,+p@chr16:88558406..88558427
+
Hg19::chr16:88858526..88858538,-p@chr16:88858526..88858538
-
Hg19::chr17:25899255..25899265,+p@chr17:25899255..25899265
+
Hg19::chr17:72864739..72864767,-p5@FDXR
Hg19::chr18:31319109..31319114,+p9@ASXL3
Hg19::chr18:43620002..43620017,-p@chr18:43620002..43620017
-
Hg19::chr19:51105300..51105305,+p@chr19:51105300..51105305
+
Hg19::chr19:5131212..5131221,+p4@KDM4B
Hg19::chr19:5131887..5131896,+p@chr19:5131887..5131896
+
Hg19::chr19:59067834..59067852,-p@chr19:59067834..59067852
-
Hg19::chr1:159253361..159253368,+p@chr1:159253361..159253368
+
Hg19::chr1:176849256..176849268,+p@chr1:176849256..176849268
+
Hg19::chr1:179011968..179011976,-p@chr1:179011968..179011976
-
Hg19::chr22:36007795..36007820,-p@chr22:36007795..36007820
-
Hg19::chr2:219258788..219258830,+p@chr2:219258788..219258830
+
Hg19::chr2:220386017..220386029,+p@chr2:220386017..220386029
+
Hg19::chr2:225249514..225249517,-p@chr2:225249514..225249517
-
Hg19::chr2:5211564..5211614,+p@chr2:5211564..5211614
+
Hg19::chr3:139059704..139059754,-p@chr3:139059704..139059754
-
Hg19::chr3:50211282..50211296,+p@chr3:50211282..50211296
+
Hg19::chr3:52334122..52334129,-p@chr3:52334122..52334129
-
Hg19::chr3:52334165..52334173,-p@chr3:52334165..52334173
-
Hg19::chr4:124087446..124087458,+p@chr4:124087446..124087458
+
Hg19::chr4:134160987..134160994,-p@chr4:134160987..134160994
-
Hg19::chr4:171901111..171901116,+p@chr4:171901111..171901116
+
Hg19::chr5:1201575..1201595,+p3@SLC6A19
Hg19::chr5:1201599..1201625,+p2@SLC6A19
Hg19::chr6:31615512..31615544,-p@chr6:31615512..31615544
-
Hg19::chr6:42072634..42072643,-p13@C6orf132
Hg19::chrX:11327532..11327554,-p@chrX:11327532..11327554
-
Hg19::chrX:48559008..48559045,-p@chrX:48559008..48559045
-
Hg19::chrX:48650688..48650735,+p5@GATA1


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


GO IDGO nameFDR corrected p-value
GO:0016730oxidoreductase activity, acting on iron-sulfur proteins as donors0.00715294948781349
GO:0004324ferredoxin-NADP+ reductase activity0.00715294948781349
GO:0008937ferredoxin reductase activity0.00715294948781349
GO:0016731oxidoreductase activity, acting on iron-sulfur proteins as donors, NAD or NADP as acceptor0.00715294948781349
GO:0046502uroporphyrinogen III metabolic process0.00953656411554144
GO:0006780uroporphyrinogen III biosynthetic process0.00953656411554144
GO:0004852uroporphyrinogen-III synthase activity0.0163459895047015
GO:0015804neutral amino acid transport0.0485828177802072
GO:0006783heme biosynthetic process0.0485828177802072
GO:0015175neutral amino acid transmembrane transporter activity0.0485828177802072



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
hematopoietic system5.05e-19102
blood island5.05e-19102
hemolymphoid system2.40e-16112
bone marrow6.54e-1480
bone element1.34e-1286
skeletal element2.35e-10101
skeletal system2.35e-10101
immune system1.69e-08115
Disease
Ontology termp-valuen
leukemia6.41e-1939
myeloid leukemia3.70e-1831
hematologic cancer1.30e-1751
immune system cancer1.30e-1751


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
GATA1#2623133.597632772845023.96023418025606e-050.000738576602771004
GATA2#2624123.121207771482610.0003188913615455430.00326452606434571
STAT2#677345.327654790729850.006739339895501240.0286432230230844
TAL1#6886127.314763267944545.70523040920804e-083.56795544136095e-06



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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