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Coexpression cluster:C2424: Difference between revisions

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|ontology_enrichment_disease=DOID:162!9.41e-19!235;DOID:14566!2.15e-17!239;DOID:0050686!1.64e-15!137;DOID:2531!6.59e-10!51;DOID:0060083!6.59e-10!51;DOID:0050687!3.34e-08!143;DOID:305!4.88e-08!106
|ontology_enrichment_disease=DOID:162!9.41e-19!235;DOID:14566!2.15e-17!239;DOID:0050686!1.64e-15!137;DOID:2531!6.59e-10!51;DOID:0060083!6.59e-10!51;DOID:0050687!3.34e-08!143;DOID:305!4.88e-08!106
|ontology_enrichment_uberon=UBERON:0002371!2.83e-10!80;UBERON:0002384!5.31e-10!375;UBERON:0001474!2.27e-09!86;UBERON:0002390!2.85e-07!102;UBERON:0003061!2.85e-07!102
|ontology_enrichment_uberon=UBERON:0002371!2.83e-10!80;UBERON:0002384!5.31e-10!375;UBERON:0001474!2.27e-09!86;UBERON:0002390!2.85e-07!102;UBERON:0003061!2.85e-07!102
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936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.833813,0.758305,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.626334,0.709625,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.649813,0.537932,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.472542,0.685908,0.747471,0.529642,0.818701,0.483077,0.590496,0.603763,0.541914,0.627201,0.765905,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.594773,0.483764,0.829658,0.784052,0.209437,0.843495,0.748403,0.598945,0.630688,0.464001,0.60737,0.579004,0.870272,0.839946,0.860705,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.048546,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.512178,0.563206,0.829402,0.684899,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.627953,0.503881,0.454761,0.639483,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.611661,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.632833,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
}}
}}

Revision as of 11:36, 5 September 2012


Full id: C2424_CD14_CD133_Dendritic_Natural_Basophils_chronic_Peripheral



Phase1 CAGE Peaks

Hg19::chr17:56709188..56709203,-p1@ENST00000390893
Hg19::chr1:145382755..145382759,+p1@ENST00000364688
Hg19::chr1:63266602..63266609,-p@chr1:63266602..63266609
-
Hg19::chr2:88316053..88316067,-p1@ENST00000410792


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 cell2.98e-27172
angioblastic mesenchymal cell2.98e-27172
hematopoietic cell2.78e-24182
hematopoietic oligopotent progenitor cell3.14e-24165
hematopoietic multipotent progenitor cell3.14e-24165
leukocyte8.70e-23140
nongranular leukocyte8.66e-22119
hematopoietic lineage restricted progenitor cell4.95e-21124
CD14-positive, CD16-negative classical monocyte1.33e-1542
classical monocyte3.98e-1545
lymphocyte1.47e-1453
common lymphoid progenitor1.47e-1453
lymphoid lineage restricted progenitor cell4.41e-1452
animal cell3.47e-12679
eukaryotic cell3.47e-12679
myeloid cell7.89e-11112
common myeloid progenitor7.89e-11112
lymphocyte of B lineage8.06e-1124
pro-B cell8.06e-1124
native cell9.04e-10722
connective tissue cell9.62e-10365
mesenchymal cell2.18e-09358
stem cell2.68e-09444
motile cell4.36e-09390
granulocyte monocyte progenitor cell1.61e-0871
multi fate stem cell1.67e-08430
somatic stem cell1.88e-08436
macrophage dendritic cell progenitor2.61e-0865
myeloid lineage restricted progenitor cell1.25e-0770
B cell1.27e-0714
monopoietic cell1.34e-0763
monocyte1.34e-0763
monoblast1.34e-0763
promonocyte1.34e-0763
myeloid leukocyte5.86e-0776
Uber Anatomy
Ontology termp-valuen
bone marrow2.83e-1080
connective tissue5.31e-10375
bone element2.27e-0986
hematopoietic system2.85e-07102
blood island2.85e-07102
Disease
Ontology termp-valuen
cancer9.41e-19235
disease of cellular proliferation2.15e-17239
organ system cancer1.64e-15137
hematologic cancer6.59e-1051
immune system cancer6.59e-1051
cell type cancer3.34e-08143
carcinoma4.88e-08106


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#10538212.17890089615180.009566758805047810.0360155260197674
BCL11A#53335428.36945510360711.542446414682e-065.89215658752646e-05
BCL3#602325.91032710280379.48553136097325e-050.00137381695993439
BCLAF1#9774316.23948570759140.000380256706766480.00376646720390595
BRCA1#672210.09211532161190.0137713969900260.0484706949159615
BRF2#552902537.2877906976745.15958263355146e-060.000158163090890954
CCNT2#90534.752151182721970.01386206996689490.0487192329140037
CHD2#110637.758017125587640.003351522464536340.0172948097570884
EBF1#187936.679850134926750.005184294118278910.0240438071592403
EP300#203335.08045629466740.01144298405398240.0418875542958139
ETS1#211337.296570691651750.00400857377511390.019203313448884
FOSL1#8061219.85678985818650.003677050009233230.0185601191781117
FOSL2#2355312.69765045342130.000787568572975710.00616680718196207
FOXA1#316938.311064812039090.002740138182109850.0150358478222755
FOXA2#3170212.31523187633260.009361916285467240.0353437382496354
GATA1#2623310.17023110785030.001515158168498270.00966301929407616
GATA2#262439.55869880016550.001818151618357440.0108967024486189
GATA3#2625320.42738726790450.0001924415576258320.00231976036898479
GTF2B#2959323.95787245074320.0001197754562855920.00162436422269977
GTF2F1#296239.554745657568240.001820362319304780.010898069376089
HNF4A#3172211.56614518147680.01057585681762490.0390708139432589
HNF4G#3174214.37671126322340.006924169980439180.0293059405327885
IRF1#365935.727872815172930.008097114790333330.0320081215589562
IRF4#3662421.91451268674414.33289161192893e-060.000136343135600556
JUNB#3726322.95797449486590.0001359772504018780.001778946267659
JUND#372735.245997956403270.01043432751748420.0386861703148331
KAT2A#26483462.06751.69143680699618e-081.22419936719247e-06
MAFF#23764228.15767824497260.001846876180367150.0109246659153469
MAFK#7975320.32554985337240.0001953213688931110.00235094715291317
MEF2A#4205314.0574231822330.0005830038854186610.00488709710163251
MEF2C#4208330.9835158694685.56692972943475e-050.000941393416470913
NR2C2#7182324.46095817893070.0001125906063438030.00155519776959932
PAX5#507935.002174148383370.01196533174786410.0434886821790561
PBX3#5090316.43588451505810.0003669431395554610.00365783855607834
POU2F2#545236.829593043306890.004860473775203740.022758261403654
POU5F1#54602167.7196007259535.30170476996226e-050.000899455400373763
REST#597849.650028716128020.0001152825614219170.00156954705153743
RXRA#6256315.055962854350.0004758307997303580.00433830579598768
SETDB1#9869220.16001308900520.00356908685407640.018083338764512
STAT3#677437.889598747865680.003190760481680130.0167415138882789
TAF7#687938.574802053692940.00250055433515240.0140308061144889
TBP#690843.706770687096390.005296377814784350.0244064773472583
TCF12#693837.975848676639820.003090920396013070.0162773615993954
THAP1#55145215.68457230142570.005840469678357920.0262478081130007
USF1#739134.771124457905970.01370465887188020.0483009100637901
YY1#752844.911170749853860.00171871838055440.0106801468999061
ZBTB33#10009323.74854377248590.0001229451908818380.00165531426975742
ZEB1#6935312.66632401315790.000793336075912850.00613197353702355
ZNF263#1012736.166381227758010.006539814347975980.0279716467642011



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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