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Coexpression cluster:C2737: Difference between revisions

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|ontology_enrichment_disease=DOID:1240!1.44e-19!39;DOID:2531!1.80e-19!51;DOID:0060083!1.80e-19!51;DOID:8692!7.15e-16!31
|ontology_enrichment_disease=DOID:1240!1.44e-19!39;DOID:2531!1.80e-19!51;DOID:0060083!1.80e-19!51;DOID:8692!7.15e-16!31
|ontology_enrichment_uberon=UBERON:0002390!9.53e-33!102;UBERON:0003061!9.53e-33!102;UBERON:0002193!1.83e-32!112;UBERON:0002371!4.13e-24!80;UBERON:0001474!1.20e-19!86;UBERON:0002405!7.34e-19!115;UBERON:0003081!3.83e-17!216;UBERON:0004765!1.45e-13!101;UBERON:0001434!1.45e-13!101;UBERON:0007023!1.87e-09!115;UBERON:0002384!2.00e-09!375
|ontology_enrichment_uberon=UBERON:0002390!9.53e-33!102;UBERON:0003061!9.53e-33!102;UBERON:0002193!1.83e-32!112;UBERON:0002371!4.13e-24!80;UBERON:0001474!1.20e-19!86;UBERON:0002405!7.34e-19!115;UBERON:0003081!3.83e-17!216;UBERON:0004765!1.45e-13!101;UBERON:0001434!1.45e-13!101;UBERON:0007023!1.87e-09!115;UBERON:0002384!2.00e-09!375
|tf_chipseq_enrich=GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378753630297247!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000614917924504192!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723236501154275!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466411889683461!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488905916085109!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768801312395728!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444534311756939!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227705118471495!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483253720008202!USF2#7392;3:9.7441480388022:0.00171834184841007:0.010724387731929
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66228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.112715,0.281453,0.0522771,0.0787278,0.0372041,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.0429523,0.245002,0.000952981,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.0180783,0.216557,0.182956,0.116818,0.00167639,0.36316,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,5.07653e-05,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.285695,0.0760151,0.00202402,0.0300882,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.626334,0.0339072,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.00516485,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.00351634,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.00530734,0.0578865,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.00035396,0.335582,0.0567624,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.00200865,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.369553,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.514243,0.459091,0.189333,0.502211,0.296013,0.282366,0.537932,0.459994,0.170061,0.548059,0.0354672,0.031106,0.45013,0.153911,0.472542,0.322168,0.747471,0.529642,0.0943307,0.14198,0.590496,0.603763,0.541914,0.627201,0.526336,0.514482,0.290703,0.622694,0.722684,0.478691,0.360199,0.241059,0.657141,0.253797,0.365494,0.212703,0.56318,0.364079,0.315494,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.829658,0.19941,0.209437,0.55323,0.161672,0.598945,0.882403,0.464001,0.871271,0.0118057,0.150592,0.839946,0.860705,0.261575,0.257956,0.00383258,0.379063,0.326516,0.522925,0.0205071,0.475063,0.202522,0.183837,0.158557,0.126097,0.3955,0.442469,0.0243103,0.294954,0.156999,0.35974,0.00547498,0.39549,0.234254,0.357409,0.86719,0.0408829,0.50338,0.252827,0.0958848,0.416164,0.424691,0.357704,0.479581,0.077723,0.172925,0.642173,0.284496,0.512545,0.512178,0.201413,0.829402,0.321001,0.263302,0.552023,0.180735,0.775168,0.0252414,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.142363,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.391754,0.385425,0.307816,0.461541,0.0866806,0.382854,0.00249494,0.478745,0.0158475,0.319747,0.475047,0.197104,0.00277992,0.282281,0.612712,0.00335455,0.246827,0.564333,0.70712,0.0870695,0.559969,0.358813,0.303004,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.0118751,0.447581,0.42505,0.0355841,0.713293,0.479347,0.416962,0.632833,0.378333,0.0473484,0.00382285,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.000359908,0.215123,0.321224,0.469461,0.325254,0.0392149,0.187728,0.231754,0.249415,0.283107,0.285648,0.0191181,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.00489571,0.0887542,0.267811,0.00865954,0.000605968,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.0217216,0.15696,0.129351,0.141936,0.0786166,0.00446773,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.0025618,0.207281,0.00774558,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.0377937,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.00336176,0.0528669,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.0140513,0.355805,0.279739,0.108118,0.259901,0.000507733,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.00297709,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.0109087,0.433518,0.184359,0.334474,0.325785,0.0364266,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.000968095,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.00460647,0.286696,0.150674,0.00325002,0.246177,9.66518e-05,0.0737175,0.318525,0.0245539,0.287217,0.122782,0.410951,0.0465068,0.00396262,0.125746,0.112897,0.0926658,0.222091,0.205977,0.34423,0.000147325,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.003854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}}
}}

Revision as of 14:21, 5 September 2012


Full id: C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14



Phase1 CAGE Peaks

Hg19::chr3:196366555..196366572,+p2@LRRC33
Hg19::chr3:196366587..196366604,+p3@LRRC33
Hg19::chr3:196366616..196366690,+p1@LRRC33
p2@PIGX
Hg19::chr3:196366873..196366890,-p@chr3:196366873..196366890
-


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>disease_data<br>


Cell Type
Ontology termp-valuen
hematopoietic stem cell3.84e-70172
angioblastic mesenchymal cell3.84e-70172
hematopoietic cell4.79e-67182
hematopoietic oligopotent progenitor cell8.23e-66165
hematopoietic multipotent progenitor cell8.23e-66165
leukocyte1.46e-51140
myeloid cell2.67e-46112
common myeloid progenitor2.67e-46112
hematopoietic lineage restricted progenitor cell9.95e-44124
nongranular leukocyte5.56e-42119
myeloid leukocyte3.66e-2876
granulocyte monocyte progenitor cell2.85e-2771
myeloid lineage restricted progenitor cell3.56e-2670
macrophage dendritic cell progenitor2.65e-2465
monopoietic cell1.69e-2363
monocyte1.69e-2363
monoblast1.69e-2363
promonocyte1.69e-2363
CD14-positive, CD16-negative classical monocyte1.15e-2042
classical monocyte2.77e-1745
lymphocyte2.66e-1653
common lymphoid progenitor2.66e-1653
lymphoid lineage restricted progenitor cell8.78e-1652
mesenchymal cell3.50e-12358
connective tissue cell1.13e-10365
motile cell1.53e-09390
lymphocyte of B lineage2.49e-0824
pro-B cell2.49e-0824
stem cell3.13e-08444
multi fate stem cell4.67e-08430
T cell6.55e-0825
pro-T cell6.55e-0825
somatic stem cell4.62e-07436
intermediate monocyte7.24e-079
CD14-positive, CD16-positive monocyte7.24e-079
dendritic cell8.68e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.53e-33102
blood island9.53e-33102
hemolymphoid system1.83e-32112
bone marrow4.13e-2480
bone element1.20e-1986
immune system7.34e-19115
lateral plate mesoderm3.83e-17216
skeletal element1.45e-13101
skeletal system1.45e-13101
adult organism1.87e-09115
connective tissue2.00e-09375
Disease
Ontology termp-valuen
leukemia1.44e-1939
hematologic cancer1.80e-1951
immune system cancer1.80e-1951
myeloid leukemia7.15e-1631


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
GABPB1#255335.300762877136630.01012678824234270.0378753630297247
GATA1#2623413.56030814380042.95627390049268e-050.000614917924504192
GATA2#2624412.7449317335543.78864877853583e-050.000723236501154275
MAX#414934.839416631755340.01315737137836840.0466411889683461
MEF2A#4205314.0574231822330.0005830038854186610.00488905916085109
NFKB1#479045.488063424193840.001102199566301980.00768801312395728
PAX5#507946.669565531177830.0005052774169483260.00444534311756939
POU2F2#545236.829593043306890.004860473775203740.0227705118471495
USF1#739134.771124457905970.01370465887188020.0483253720008202
USF2#739239.74414803880220.001718341848410070.010724387731929



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.