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Coexpression cluster:C4332: Difference between revisions

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|ontology_enrichment_disease=DOID:2531!1.11e-07!51;DOID:0060083!1.11e-07!51;DOID:1240!1.64e-07!39
|ontology_enrichment_disease=DOID:2531!1.11e-07!51;DOID:0060083!1.11e-07!51;DOID:1240!1.64e-07!39
|ontology_enrichment_uberon=UBERON:0002390!2.23e-23!102;UBERON:0003061!2.23e-23!102;UBERON:0002193!1.07e-22!112;UBERON:0002371!8.55e-16!80;UBERON:0001474!4.82e-14!86;UBERON:0002405!4.47e-13!115;UBERON:0003081!1.23e-10!216;UBERON:0004765!7.35e-09!101;UBERON:0001434!7.35e-09!101;UBERON:0000178!1.26e-07!15;UBERON:0000179!1.26e-07!15;UBERON:0000463!1.26e-07!15
|ontology_enrichment_uberon=UBERON:0002390!2.23e-23!102;UBERON:0003061!2.23e-23!102;UBERON:0002193!1.07e-22!112;UBERON:0002371!8.55e-16!80;UBERON:0001474!4.82e-14!86;UBERON:0002405!4.47e-13!115;UBERON:0003081!1.23e-10!216;UBERON:0004765!7.35e-09!101;UBERON:0001434!7.35e-09!101;UBERON:0000178!1.26e-07!15;UBERON:0000179!1.26e-07!15;UBERON:0000463!1.26e-07!15
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190675152338713!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280565695899426!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00438175776276113!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00917761577884212!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463943239713364!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763972335148664!GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000628919691707225!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108968005293235!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.012847781324874!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157263746865698!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295462747715576!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00310150385472605!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247363455734624!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109279092758232!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00630633448585643!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158738735770173!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330478372546805!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140629981159105!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.0039003151717112!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109755446312386
|tfbs_overrepresentation=0.147255,0.0586687,5.24277e-05,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.00169471,0.114046,0.0180314,0.208242,0.0665252,0.0844722,3.84895e-06,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.00472557,0.226912,0.0425,0.114846,0.0472875,0.0347684,0.064341,0.209032,0.000428223,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.0177901,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,5.12341e-06,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.12972,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.00112574,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.00664287,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.0133328,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.00958651,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.21774,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.00909613,0.782949,0.00381937,0.00163772,0.00210428,0.00690237,0.335423,0.0185583,0.261553,0.446302,0.373681,0.053682,0.49143,0.330703,0.395854,0.329568,0.53472,0.248224,0.271958,0.292154,0.405773,0.0921263,0.00204348,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.107929,0.376924,0.00381454,1.32381e-09,0.528324,0.168255,0.370782,0.0173702,0.142924,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.236436,0.283727,0.314747,0.0116619,0.291709,0.00324826,0.000269721,0.416816,0.0478086,0.476744,0.439556,0.0807167,0.57762,0.00280546,0.18237,6.93298e-07,2.05465e-06,0.0512465,0.275351,0.236471,0.185661,0.0684159,0.0427964,0.270984,0.625945,0.155555,0.513852,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.0641718,0.00012837,0.0583074,0.0002295,0.671377,0.188159,0.551561,0.00324632,0.218623,0.312808,0.00743804,0.0451077,0.0747529,0.229003,1.6473e-08,0.0129683,0.154921,0.294698,0.0671437,0.00441816,0.0465597,0.000749204,4.0585e-08,0.278044,0.000315884,0.108847,0.228096,0.336314,0.19763,0.15631,2.87559e-06,0.421464,0.141711,0.420626,0.516462,2.91338e-09,0.335105,0.144809,0.145539,0.385517,0.001421,0.119597,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.155572,0.169823,0.284629,0.00375279,0.359455,0.226257,0.405955,0.0175765,0.0760312,0.130283,1.63525e-05,0.206222,0.03988,0.284166,0.437176,0.269226,0.339277,0.0014397,0.281425,0.141758,0.455379,0.00680512,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.000539973,0.347298,0.539392,0.34988,0.475069,0.404569,0.6408,0.262389,0.000642687,0.0697683,0.0556835,0.00138994,0.0779981,0.0575676,0.144322,0.223391,0.00166084,0.000351837,2.73054e-06,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.00427764,0.0627924,0.381386,0.0179103,0.303939,1.3117e-06,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.0205132,0.132201,0.188694,0.0481795,0.199971,1.3111e-06,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237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}}
}}

Revision as of 12:22, 5 September 2012


Full id: C4332_CD14CD16_Alveolar_Eosinophils_CD14_immature_Natural_CD4



Phase1 CAGE Peaks

Hg19::chr3:47021200..47021229,+p3@NBEAL2
Hg19::chr3:47021263..47021333,+p1@NBEAL2
Hg19::chr3:47021336..47021347,+p9@NBEAL2


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 cell4.37e-50172
angioblastic mesenchymal cell4.37e-50172
hematopoietic oligopotent progenitor cell1.76e-48165
hematopoietic multipotent progenitor cell1.76e-48165
hematopoietic cell1.14e-47182
leukocyte1.54e-44140
nongranular leukocyte1.93e-35119
hematopoietic lineage restricted progenitor cell1.50e-34124
myeloid cell8.73e-32112
common myeloid progenitor8.73e-32112
myeloid leukocyte1.27e-2476
granulocyte monocyte progenitor cell8.77e-2271
CD14-positive, CD16-negative classical monocyte1.67e-2142
classical monocyte6.09e-2145
macrophage dendritic cell progenitor5.25e-2065
monopoietic cell6.09e-1963
monocyte6.09e-1963
monoblast6.09e-1963
promonocyte6.09e-1963
myeloid lineage restricted progenitor cell9.88e-1970
lymphocyte1.71e-1453
common lymphoid progenitor1.71e-1453
lymphoid lineage restricted progenitor cell2.80e-1452
T cell2.73e-1025
pro-T cell2.73e-1025
mature alpha-beta T cell1.68e-0918
alpha-beta T cell1.68e-0918
immature T cell1.68e-0918
mature T cell1.68e-0918
immature alpha-beta T cell1.68e-0918
intermediate monocyte2.53e-079
CD14-positive, CD16-positive monocyte2.53e-079
endothelial cell3.15e-0735
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.23e-23102
blood island2.23e-23102
hemolymphoid system1.07e-22112
bone marrow8.55e-1680
bone element4.82e-1486
immune system4.47e-13115
lateral plate mesoderm1.23e-10216
skeletal element7.35e-09101
skeletal system7.35e-09101
blood1.26e-0715
haemolymphatic fluid1.26e-0715
organism substance1.26e-0715
Disease
Ontology termp-valuen
hematologic cancer1.11e-0751
immune system cancer1.11e-0751
leukemia1.64e-0739


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
CCNT2#90536.336201576962630.003930750035764890.0190675152338713
CTCF#1066435.360256373075030.0064925092527670.0280565695899426
E2F4#1874312.66806031528440.0004917987006298980.00438175776276113
EBF1#187938.9064668465690.00141523283560980.00917761577884212
ELF1#199734.258097958807540.01295179875054610.0463943239713364
ETS1#211339.728760922202340.001085840092584840.00763972335148664
GTF2B#2959331.94382993432423.06634405746243e-050.000628919691707225
HMGN3#932438.178547723350590.001827766942164210.0108968005293235
IRF1#365937.63716375356390.002244692747297240.012847781324874
JUND#372736.994663941871030.002921845042734990.0157263746865698
MYC#460935.22228187160940.007020843755740150.0295462747715576
SMC3#9126315.04493284493280.0002935825420371870.00310150385472605
SP1#666735.69838137814090.005403962701712170.0247363455734624
SPI1#668838.204323508522730.001810593189410520.0109279092758232
TCF12#6938310.63446490218640.0008313523990202070.00630633448585643
THAP1#55145220.91276306856750.002983447413736940.0158738735770173
YY1#752834.911170749853860.008441455341808260.0330478372546805
ZBTB7A#5134137.35190930787590.002516255860282270.0140629981159105
ZNF143#7702313.50087655222790.0004062804962997170.0039003151717112
ZNF263#1012738.221841637010680.001799043925565870.0109755446312386



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.

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