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Coexpression cluster:C2737: Difference between revisions

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|full_id=C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14
|full_id=C2737_Monocytederived_granulocyte_chronic_Dendritic_Basophils_Macrophage_CD14
|id=C2737
|id=C2737
|ontology_enrichment_celltype=CL:0000037!3.84e-70!172;CL:0000566!3.84e-70!172;CL:0000988!4.79e-67!182;CL:0002032!8.23e-66!165;CL:0000837!8.23e-66!165;CL:0000738!1.46e-51!140;CL:0000763!2.67e-46!112;CL:0000049!2.67e-46!112;CL:0002031!9.95e-44!124;CL:0002087!5.56e-42!119;CL:0000766!3.66e-28!76;CL:0000557!2.85e-27!71;CL:0000839!3.56e-26!70;CL:0002009!2.65e-24!65;CL:0002194!1.69e-23!63;CL:0000576!1.69e-23!63;CL:0000040!1.69e-23!63;CL:0000559!1.69e-23!63;CL:0002057!1.15e-20!42;CL:0000860!2.77e-17!45;CL:0000542!2.66e-16!53;CL:0000051!2.66e-16!53;CL:0000838!8.78e-16!52;CL:0000134!3.50e-12!358;CL:0002320!1.13e-10!365;CL:0000219!1.53e-09!390;CL:0000945!2.49e-08!24;CL:0000826!2.49e-08!24;CL:0000034!3.13e-08!444;CL:0000048!4.67e-08!430;CL:0000084!6.55e-08!25;CL:0000827!6.55e-08!25;CL:0000723!4.62e-07!436;CL:0002393!7.24e-07!9;CL:0002397!7.24e-07!9;CL:0000451!8.68e-07!10
|ontology_enrichment_celltype=CL:0000037!2.21e-77!168;CL:0000566!2.21e-77!168;CL:0000988!7.46e-74!177;CL:0002032!7.98e-73!161;CL:0000837!7.98e-73!161;CL:0000738!1.22e-57!136;CL:0000763!2.38e-51!108;CL:0000049!2.38e-51!108;CL:0002031!9.99e-50!120;CL:0002087!4.77e-48!115;CL:0000766!4.59e-32!72;CL:0000557!1.67e-31!67;CL:0000839!1.98e-30!66;CL:0002009!1.09e-28!61;CL:0002194!8.06e-28!59;CL:0000576!8.06e-28!59;CL:0000040!8.06e-28!59;CL:0000559!8.06e-28!59;CL:0000473!5.61e-24!48;CL:0000234!5.61e-24!48;CL:0000860!4.52e-20!42;CL:0002057!4.52e-20!42;CL:0002242!1.88e-18!55;CL:0000542!6.37e-18!53;CL:0000051!6.37e-18!53;CL:0000838!2.41e-17!52;CL:0000134!3.14e-12!354;CL:0002320!7.56e-11!361;CL:0000325!1.57e-10!87;CL:0000219!1.08e-09!386;CL:0000945!5.33e-09!24;CL:0000826!5.33e-09!24;CL:0000084!8.95e-09!25;CL:0000827!8.95e-09!25;CL:0000034!1.34e-07!441;CL:0000048!2.70e-07!427;CL:0000451!4.15e-07!10
|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:2531!4.32e-21!51;DOID:0060083!4.32e-21!51;DOID:1240!1.22e-20!39;DOID:8692!1.25e-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!6.22e-36!98;UBERON:0003061!6.22e-36!98;UBERON:0002193!3.83e-34!108;UBERON:0002405!5.92e-28!93;UBERON:0002371!8.43e-27!76;UBERON:0001474!2.35e-22!82;UBERON:0004765!2.52e-17!90;UBERON:0003081!2.50e-16!203;UBERON:0001434!9.92e-14!100;UBERON:0002384!8.43e-10!371;UBERON:0007023!2.93e-08!114;UBERON:0000178!5.79e-07!15;UBERON:0000179!5.79e-07!15;UBERON:0000463!5.79e-07!15
|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
|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 14:22, 19 October 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 cell2.21e-77168
angioblastic mesenchymal cell2.21e-77168
hematopoietic cell7.46e-74177
hematopoietic oligopotent progenitor cell7.98e-73161
hematopoietic multipotent progenitor cell7.98e-73161
leukocyte1.22e-57136
myeloid cell2.38e-51108
common myeloid progenitor2.38e-51108
hematopoietic lineage restricted progenitor cell9.99e-50120
nongranular leukocyte4.77e-48115
myeloid leukocyte4.59e-3272
granulocyte monocyte progenitor cell1.67e-3167
myeloid lineage restricted progenitor cell1.98e-3066
macrophage dendritic cell progenitor1.09e-2861
monopoietic cell8.06e-2859
monocyte8.06e-2859
monoblast8.06e-2859
promonocyte8.06e-2859
defensive cell5.61e-2448
phagocyte5.61e-2448
classical monocyte4.52e-2042
CD14-positive, CD16-negative classical monocyte4.52e-2042
nucleate cell1.88e-1855
lymphocyte6.37e-1853
common lymphoid progenitor6.37e-1853
lymphoid lineage restricted progenitor cell2.41e-1752
mesenchymal cell3.14e-12354
connective tissue cell7.56e-11361
stuff accumulating cell1.57e-1087
motile cell1.08e-09386
lymphocyte of B lineage5.33e-0924
pro-B cell5.33e-0924
T cell8.95e-0925
pro-T cell8.95e-0925
stem cell1.34e-07441
multi fate stem cell2.70e-07427
dendritic cell4.15e-0710
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.22e-3698
blood island6.22e-3698
hemolymphoid system3.83e-34108
immune system5.92e-2893
bone marrow8.43e-2776
bone element2.35e-2282
skeletal element2.52e-1790
lateral plate mesoderm2.50e-16203
skeletal system9.92e-14100
connective tissue8.43e-10371
adult organism2.93e-08114
blood5.79e-0715
haemolymphatic fluid5.79e-0715
organism substance5.79e-0715
Disease
Ontology termp-valuen
hematologic cancer4.32e-2151
immune system cancer4.32e-2151
leukemia1.22e-2039
myeloid leukemia1.25e-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.