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Coexpression cluster:C2151: Difference between revisions

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|full_id=C2151_CD4_CD19_CD8_Whole_Dendritic_Neutrophils_Eosinophils
|full_id=C2151_CD4_CD19_CD8_Whole_Dendritic_Neutrophils_Eosinophils
|id=C2151
|id=C2151
|ontology_enrichment_celltype=CL:0000037!7.09e-58!172;CL:0000566!7.09e-58!172;CL:0000738!8.72e-55!140;CL:0000988!8.29e-54!182;CL:0002032!3.12e-53!165;CL:0000837!3.12e-53!165;CL:0002087!1.24e-44!119;CL:0002031!1.24e-44!124;CL:0000542!6.93e-32!53;CL:0000051!6.93e-32!53;CL:0000838!1.80e-31!52;CL:0000763!3.88e-22!112;CL:0000049!3.88e-22!112;CL:0000766!5.51e-18!76;CL:0000084!1.49e-15!25;CL:0000827!1.49e-15!25;CL:0002057!1.51e-15!42;CL:0000945!4.94e-15!24;CL:0000826!4.94e-15!24;CL:0000839!1.52e-14!70;CL:0000557!3.43e-14!71;CL:0002009!1.25e-13!65;CL:0000791!1.68e-13!18;CL:0000789!1.68e-13!18;CL:0002420!1.68e-13!18;CL:0002419!1.68e-13!18;CL:0000790!1.68e-13!18;CL:0000860!2.81e-13!45;CL:0002194!4.36e-13!63;CL:0000576!4.36e-13!63;CL:0000040!4.36e-13!63;CL:0000559!4.36e-13!63;CL:0000236!8.75e-10!14;CL:0000625!5.38e-09!11;CL:0000134!2.70e-07!358
|ontology_enrichment_celltype=CL:0000037!1.26e-78!168;CL:0000566!1.26e-78!168;CL:0000738!7.84e-77!136;CL:0000988!4.34e-76!177;CL:0002032!4.90e-72!161;CL:0000837!4.90e-72!161;CL:0002087!5.63e-64!115;CL:0002031!1.09e-63!120;CL:0002242!1.24e-45!55;CL:0000542!7.16e-45!53;CL:0000051!7.16e-45!53;CL:0000838!2.38e-44!52;CL:0000763!2.71e-28!108;CL:0000049!2.71e-28!108;CL:0000766!7.68e-24!72;CL:0000084!2.54e-21!25;CL:0000827!2.54e-21!25;CL:0000945!6.22e-21!24;CL:0000826!6.22e-21!24;CL:0000860!2.41e-20!42;CL:0002057!2.41e-20!42;CL:0000839!4.49e-20!66;CL:0000557!1.26e-19!67;CL:0002009!3.16e-19!61;CL:0000791!9.94e-19!18;CL:0000789!9.94e-19!18;CL:0002420!9.94e-19!18;CL:0002419!9.94e-19!18;CL:0000790!9.94e-19!18;CL:0002194!2.62e-18!59;CL:0000576!2.62e-18!59;CL:0000040!2.62e-18!59;CL:0000559!2.62e-18!59;CL:0000473!3.17e-16!48;CL:0000234!3.17e-16!48;CL:0000134!1.06e-14!354;CL:0002320!1.09e-13!361;CL:0000236!1.17e-13!14;CL:0000625!3.59e-12!11;CL:0000219!2.94e-10!386;CL:0002393!1.01e-07!9;CL:0002397!1.01e-07!9;CL:0000624!2.94e-07!6
|ontology_enrichment_disease=DOID:2531!1.10e-10!51;DOID:0060083!1.10e-10!51;DOID:1240!1.35e-07!39
|ontology_enrichment_disease=DOID:2531!3.40e-12!51;DOID:0060083!3.40e-12!51;DOID:1240!1.70e-08!39;DOID:0060058!8.57e-07!10
|ontology_enrichment_uberon=UBERON:0002390!3.88e-23!102;UBERON:0003061!3.88e-23!102;UBERON:0002193!3.73e-20!112;UBERON:0007023!1.46e-16!115;UBERON:0002371!1.42e-12!80;UBERON:0001474!7.02e-11!86;UBERON:0000178!6.71e-10!15;UBERON:0000179!6.71e-10!15;UBERON:0000463!6.71e-10!15;UBERON:0002405!2.78e-08!115;UBERON:0004765!1.99e-07!101;UBERON:0001434!1.99e-07!101
|ontology_enrichment_uberon=UBERON:0002390!5.64e-33!98;UBERON:0003061!5.64e-33!98;UBERON:0002193!5.31e-30!108;UBERON:0002405!1.20e-19!93;UBERON:0002371!1.68e-17!76;UBERON:0001474!4.74e-15!82;UBERON:0000178!9.78e-14!15;UBERON:0000179!9.78e-14!15;UBERON:0000463!9.78e-14!15;UBERON:0004765!2.35e-12!90;UBERON:0002384!2.45e-12!371;UBERON:0001434!3.31e-10!100;UBERON:0003081!4.70e-07!203;UBERON:0004177!7.32e-07!7;UBERON:0005057!7.32e-07!7
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296137352554954!BCL3#602;2:17.2735514018692:0.00483449420807607:0.022670157174805!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240331347782383!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160569119225915!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389785965763311!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428171166675547!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00766548714823282!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443115863201496!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227531609416631!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249061993352095!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119889448112185!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106630170456648!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00612925184437507
|tf_chipseq_enrich=BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296137352554954!BCL3#602;2:17.2735514018692:0.00483449420807607:0.022670157174805!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.0240331347782383!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160569119225915!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389785965763311!IRF4#3662;2:10.9572563433721:0.0117453018068803:0.0428171166675547!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00766548714823282!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00443115863201496!POU2F2#5452;3:6.82959304330689:0.00486047377520374:0.0227531609416631!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249061993352095!TCF12#6938;4:10.6344649021864:7.8163066689251e-05:0.00119889448112185!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106630170456648!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00612925184437507
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00852994,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.0593965,0.0262915,0.258624,0.064656,0.226143,0.460406,0.0438521,0.00283228,0.0439557,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.0188872,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.051371,0.363016,0.100188,0.223102,0.107653,0.235857,0.103852,0.191914,0.184022,0.216557,0.0178622,0.116818,0.389792,0.0757944,0.0625685,0.00808856,0.186295,0.173134,0.101893,0.142875,0.167635,0.171311,0.0721023,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.00252788,0.00342886,0.278645,0.0769795,0.155708,0.248017,0.028736,0.652972,0.0760151,0.00202402,0.486024,0.0803251,0.00233636,0.0832234,0.0939463,0.0457255,0.0779623,0.0471607,0.163865,0.226359,0.404165,0.307186,0.0388045,0.279778,2.01063e-05,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.00442486,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.0988568,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.0277041,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.00966571,0.147842,0.0339286,0.0255494,0.119015,0.0315791,0.21618,0.243266,0.107021,0.0310605,0.20272,0.0896967,0.61565,0.0780061,0.315336,0.00015932,0.279823,0.00552386,0.502112,0.0420826,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.0368787,0.1267,0.54832,0.154964,0.296013,0.000760863,0.181196,0.127256,0.0392766,0.0465928,0.25423,0.146971,0.45013,0.500698,0.472542,0.111549,0.747471,0.529642,0.0301009,0.0046877,0.061678,0.000398101,0.541914,0.00346025,0.00784768,0.293249,0.290703,0.254935,0.138899,0.478691,0.0744652,0.241059,0.0937029,0.00893555,0.365494,0.212703,0.0515679,0.364079,0.00628541,0.0575699,0.421038,0.0537414,0.328518,0.545608,0.0541711,0.324103,0.142433,0.00234287,0.00493585,0.209437,0.0118712,9.66019e-05,0.0141441,0.00647536,0.0255132,0.336867,3.44513e-07,0.150592,0.0112416,0.0500888,0.261575,0.257956,0.264245,0.379063,0.326516,0.0391986,0.113006,0.000543832,0.202522,0.183837,0.507324,0.126097,0.3955,2.77082e-06,0.212239,0.00548706,0.156999,0.35974,0.301684,0.00017745,0.0298727,0.0103854,0.146291,1.21826e-08,0.50338,0.0171443,0.0958848,0.416164,0.106633,0.0388817,0.139684,0.077723,0.635682,0.642173,0.284496,0.16228,0.00087777,0.0102074,0.034169,0.0299859,0.263302,0.552023,0.180735,0.189249,0.216102,0.254659,0.109605,0.397869,0.0121932,0.02784,0.417131,0.463987,0.260097,0.503881,0.0237654,0.0202528,0.483658,0.122467,0.301581,0.261657,0.0686105,0.0260085,0.545655,0.438176,0.00959742,0.0485429,0.0862349,0.307816,0.128211,0.0866806,0.382854,0.0650585,0.478745,0.07062,0.319747,0.475047,0.557967,0.608127,0.0442299,0.000452027,0.000241621,0.246827,0.564333,0.0362483,0.387134,0.559969,0.358813,0.0261538,0.0113028,0.493455,0.346636,0.125876,0.0694762,0.476541,0.215342,0.447581,0.42505,0.254628,0.0382032,0.479347,0.102411,0.264955,0.378333,7.96957e-05,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.133173,0.0597961,0.266651,0.187728,0.231754,0.249415,0.283107,0.285648,0.10809,0.391071,0.0433305,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.0713545,0.00657048,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.0227344,0.282389,0.251421,0.162089,0.330223,0.0136966,0.233244,0.207281,0.0606443,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.0181825,0.248707,0.0567862,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.0604859,0.00492748,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.00258221,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 12:07, 19 October 2012


Full id: C2151_CD4_CD19_CD8_Whole_Dendritic_Neutrophils_Eosinophils



Phase1 CAGE Peaks

Hg19::chr11:64107543..64107574,-p@chr11:64107543..64107574
-
Hg19::chr16:30195531..30195557,+p@chr16:30195531..30195557
+
Hg19::chr16:30195571..30195586,+p@chr16:30195571..30195586
+
Hg19::chr16:3179653..3179678,-p@chr16:3179653..3179678
-


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 cell1.26e-78168
angioblastic mesenchymal cell1.26e-78168
leukocyte7.84e-77136
hematopoietic cell4.34e-76177
hematopoietic oligopotent progenitor cell4.90e-72161
hematopoietic multipotent progenitor cell4.90e-72161
nongranular leukocyte5.63e-64115
hematopoietic lineage restricted progenitor cell1.09e-63120
nucleate cell1.24e-4555
lymphocyte7.16e-4553
common lymphoid progenitor7.16e-4553
lymphoid lineage restricted progenitor cell2.38e-4452
myeloid cell2.71e-28108
common myeloid progenitor2.71e-28108
myeloid leukocyte7.68e-2472
T cell2.54e-2125
pro-T cell2.54e-2125
lymphocyte of B lineage6.22e-2124
pro-B cell6.22e-2124
classical monocyte2.41e-2042
CD14-positive, CD16-negative classical monocyte2.41e-2042
myeloid lineage restricted progenitor cell4.49e-2066
granulocyte monocyte progenitor cell1.26e-1967
macrophage dendritic cell progenitor3.16e-1961
mature alpha-beta T cell9.94e-1918
alpha-beta T cell9.94e-1918
immature T cell9.94e-1918
mature T cell9.94e-1918
immature alpha-beta T cell9.94e-1918
monopoietic cell2.62e-1859
monocyte2.62e-1859
monoblast2.62e-1859
promonocyte2.62e-1859
defensive cell3.17e-1648
phagocyte3.17e-1648
mesenchymal cell1.06e-14354
connective tissue cell1.09e-13361
B cell1.17e-1314
CD8-positive, alpha-beta T cell3.59e-1211
motile cell2.94e-10386
intermediate monocyte1.01e-079
CD14-positive, CD16-positive monocyte1.01e-079
CD4-positive, alpha-beta T cell2.94e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.64e-3398
blood island5.64e-3398
hemolymphoid system5.31e-30108
immune system1.20e-1993
bone marrow1.68e-1776
bone element4.74e-1582
blood9.78e-1415
haemolymphatic fluid9.78e-1415
organism substance9.78e-1415
skeletal element2.35e-1290
connective tissue2.45e-12371
skeletal system3.31e-10100
lateral plate mesoderm4.70e-07203
hemopoietic organ7.32e-077
immune organ7.32e-077
Disease
Ontology termp-valuen
hematologic cancer3.40e-1251
immune system cancer3.40e-1251
leukemia1.70e-0839
lymphoma8.57e-0710


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
BCL11A#53335214.18472755180350.007108328585298740.0296137352554954
BCL3#602217.27355140186920.004834494208076070.022670157174805
EBF1#187936.679850134926750.005184294118278910.0240331347782383
ELF1#199744.258097958807540.003041525565781240.0160569119225915
GABPB1#255347.067683836182170.0004006876864423170.00389785965763311
IRF4#3662210.95725634337210.01174530180688030.0428171166675547
NFKB1#479045.488063424193840.001102199566301980.00766548714823282
PAX5#507946.669565531177830.0005052774169483260.00443115863201496
POU2F2#545236.829593043306890.004860473775203740.0227531609416631
SPI1#668848.204323508522730.000220661881527680.00249061993352095
TCF12#6938410.63446490218647.8163066689251e-050.00119889448112185
YY1#752844.911170749853860.00171871838055440.0106630170456648
ZEB1#6935312.66632401315790.000793336075912850.00612925184437507



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.