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Coexpression cluster:C4532: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110207476862338!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164486332299403!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115663705748503!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168219398432976!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901128129200808!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435697869406815!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446049887092089!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157499135183587!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187268371603245!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270655608724345!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00885198032122697!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667800903252928!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486399038977351!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109354928353484!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645031885505173!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631596808040091!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422705299068011
|tf_chipseq_enrich=BATF#10538;3:24.3578017923036:6.91705216281876e-05:0.00110207476862338!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00164486332299403!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115663705748503!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168219398432976!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901128129200808!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00435697869406815!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446049887092089!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157499135183587!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0187268371603245!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0270655608724345!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00885198032122697!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667800903252928!RFX5#5993;3:12.0479108271951:0.000571724605031258:0.00486399038977351!SPI1#6688;3:8.20432350852273:0.00181059318941052:0.0109354928353484!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00645031885505173!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00631596808040091!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422705299068011
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.00156205,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.0002288,0.188635,0.00920475,0.081977,0.00465244,0.0415721,0.215492,0.209392,0.0907212,0.0108656,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.688181,0.0429682,0.120351,0.0667043,0.0964797,2.53136e-06,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.000326349,0.154071,0.0541794,0.0701653,0.0929951,0.0212153,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.00129656,0.352278,0.0600088,0.0860723,0.167053,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.000702541,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.58489,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.00361707,0.01474,0.214708,0.140123,0.00378931,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,2.00605e-06,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.0174119,0.0265818,0.0427088,0.117549,0.00286684,0.228385,0.0516985,0.0337251,0.227719,0.00469088,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,5.80919e-07,0.0176328,0.178449,0.0356339,0.0133424,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.000260351,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.0413967,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.00377835,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.0802194,0.117027,0.159052,0.185164,0.185743,0.0980288,0.00497632,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.584917,0.713218,0.782949,0.019623,0.563047,0.823736,0.807281,0.335423,0.00355277,0.261553,0.446302,0.0120704,0.000581634,0.0313047,0.330703,0.395854,0.329568,0.178727,0.615744,0.271958,0.292154,0.405773,0.0921263,0.217139,0.597171,0.187251,0.362792,0.181715,0.0186051,0.109988,0.330894,0.218329,0.0190732,0.0821552,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.484505,0.253571,0.276829,0.00591608,0.481778,0.00695027,0.223503,0.503224,0.603208,0.0447111,0.314747,0.577664,0.291709,0.448095,0.576651,0.416816,0.000455917,0.476744,0.0210941,0.373868,0.213592,0.0694028,0.18237,0.706298,0.821217,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.625945,0.503058,0.513852,0.169228,0.248634,0.281576,0.135034,0.0141151,0.0670502,0.0730934,0.184794,0.596648,0.762864,0.00204647,0.1002,0.305671,0.546839,0.00915612,0.448039,0.218623,0.312808,0.695172,0.0451077,0.0747529,0.00241532,0.650179,0.589326,0.50215,0.294698,0.34331,0.477304,0.0465597,0.327108,0.319027,0.278044,0.807485,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,0.858756,0.0637439,0.144809,0.145539,0.385517,0.376191,0.447325,0.00368553,0.00329638,0.152681,0.0465712,0.00985947,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.0340602,0.00696513,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,4.87051e-05,0.753577,0.206222,0.525396,0.0905337,0.437176,0.269226,0.339277,0.552319,0.281425,0.0105593,0.124432,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.00710886,0.625309,0.347298,0.182325,0.34988,0.136757,0.404569,0.6408,0.630264,0.316179,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.441735,0.191777,0.111931,0.0051519,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.0886747,0.0464827,0.00093131,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.0164446,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.00100412,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,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}}
}}

Revision as of 16:48, 26 November 2012


Full id: C4532_Mast_CD14_Eosinophils_caudate_putamen_Endothelial_diencephalon



Phase1 CAGE Peaks

Hg19::chr5:94417266..94417281,-p3@MCTP1
Hg19::chr5:94417287..94417295,-p4@MCTP1
Hg19::chr5:94417314..94417337,-p2@MCTP1


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><br>


Cell Type
Ontology termp-valuen
myeloid leukocyte3.54e-4072
granulocyte monocyte progenitor cell3.76e-3867
macrophage dendritic cell progenitor1.93e-3461
myeloid lineage restricted progenitor cell2.25e-3466
defensive cell6.73e-3448
phagocyte6.73e-3448
monopoietic cell6.06e-3359
monocyte6.06e-3359
monoblast6.06e-3359
promonocyte6.06e-3359
myeloid cell1.37e-31108
common myeloid progenitor1.37e-31108
classical monocyte1.67e-3042
CD14-positive, CD16-negative classical monocyte1.67e-3042
leukocyte3.10e-24136
hematopoietic stem cell8.13e-23168
angioblastic mesenchymal cell8.13e-23168
hematopoietic oligopotent progenitor cell1.34e-20161
hematopoietic multipotent progenitor cell1.34e-20161
hematopoietic cell1.88e-19177
hematopoietic lineage restricted progenitor cell4.12e-19120
nongranular leukocyte6.63e-18115
stuff accumulating cell6.40e-1787
intermediate monocyte6.71e-079
CD14-positive, CD16-positive monocyte6.71e-079
Uber Anatomy
Ontology termp-valuen
immune system1.62e-3693
hemolymphoid system2.57e-35108
bone marrow7.31e-3476
hematopoietic system1.50e-3398
blood island1.50e-3398
bone element7.40e-3182
skeletal element7.04e-2690
skeletal system6.47e-21100
lateral plate mesoderm2.93e-10203
mesoderm7.39e-10315
mesoderm-derived structure7.39e-10315
presumptive mesoderm7.39e-10315
musculoskeletal system2.04e-09167
regional part of forebrain1.78e-0841
forebrain1.78e-0841
anterior neural tube1.78e-0841
future forebrain1.78e-0841
adult organism2.45e-08114
germ layer8.98e-08560
germ layer / neural crest8.98e-08560
embryonic tissue8.98e-08560
presumptive structure8.98e-08560
germ layer / neural crest derived structure8.98e-08560
epiblast (generic)8.98e-08560
embryonic structure1.56e-07564
cerebral hemisphere8.39e-0732
telencephalon8.52e-0734
developing anatomical structure8.58e-07581
pre-chordal neural plate9.71e-0761


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
BATF#10538324.35780179230366.91705216281876e-050.00110207476862338
BRCA1#672320.18423064322380.0001215704860271640.00164486332299403
CEBPB#105137.971147625824820.001974187055288560.0115663705748503
EP300#203336.77394172622320.003216880500103790.0168219398432976
FOS#235338.99795530889440.001372499272417130.00901128129200808
GTF2F1#2962312.73966087675770.0004835525047438590.00435697869406815
JUN#3725312.51282919233630.0005103313992726250.00446049887092089
JUND#372736.994663941871030.002921845042734990.0157499135183587
MAX#414936.452555509007120.003721913834265510.0187268371603245
NFKB1#479035.488063424193840.006049381815655430.0270655608724345
POU2F2#545239.106124057742520.001324165192682130.00885198032122697
RAD21#5885310.35503389545630.0009004912073565420.00667800903252928
RFX5#5993312.04791082719510.0005717246050312580.00486399038977351
SPI1#668838.204323508522730.001810593189410520.0109354928353484
STAT3#6774310.51946499715420.0008589184530415310.00645031885505173
TCF12#6938310.63446490218640.0008313523990202070.00631596808040091
USF2#7392312.99219738506960.0004558979393427810.00422705299068011



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.