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Coexpression cluster:C1274: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!3.62e-21!365;UBERON:0004121!1.12e-20!169;UBERON:0000033!7.84e-20!123;UBERON:0000153!3.71e-19!129;UBERON:0007811!3.71e-19!129;UBERON:0000924!6.45e-19!173;UBERON:0006601!6.45e-19!173;UBERON:0001049!7.54e-19!57;UBERON:0005068!7.54e-19!57;UBERON:0006241!7.54e-19!57;UBERON:0007135!7.54e-19!57;UBERON:0002616!8.81e-19!59;UBERON:0007023!9.86e-18!115;UBERON:0000955!2.38e-16!69;UBERON:0006238!2.38e-16!69;UBERON:0003075!3.24e-16!86;UBERON:0007284!3.24e-16!86;UBERON:0005743!2.23e-15!86;UBERON:0001017!2.88e-15!82;UBERON:0000064!1.93e-14!219;UBERON:0000062!3.05e-14!511;UBERON:0002346!4.97e-14!90;UBERON:0003080!6.15e-14!42;UBERON:0002780!1.60e-13!41;UBERON:0001890!1.60e-13!41;UBERON:0006240!1.60e-13!41;UBERON:0000468!1.77e-12!659;UBERON:0000073!2.44e-12!94;UBERON:0001016!2.44e-12!94;UBERON:0000477!3.50e-11!286;UBERON:0001893!4.78e-11!34;UBERON:0002020!5.08e-11!34;UBERON:0003528!5.08e-11!34;UBERON:0000467!7.03e-11!625;UBERON:0000480!8.07e-11!626;UBERON:0003056!1.03e-10!61;UBERON:0002791!1.35e-10!33;UBERON:0000481!3.56e-10!347;UBERON:0001869!4.26e-10!32;UBERON:0003102!5.70e-09!95;UBERON:0000119!2.30e-08!312;UBERON:0000483!3.61e-08!309;UBERON:0005631!6.10e-08!14;UBERON:0000158!6.10e-08!14;UBERON:0004923!6.14e-08!57;UBERON:0002619!6.56e-08!22;UBERON:0004111!9.80e-08!241;UBERON:0001950!6.26e-07!20;UBERON:0000956!6.77e-07!25;UBERON:0000203!6.77e-07!25
|ontology_enrichment_uberon=UBERON:0000475!3.62e-21!365;UBERON:0004121!1.12e-20!169;UBERON:0000033!7.84e-20!123;UBERON:0000153!3.71e-19!129;UBERON:0007811!3.71e-19!129;UBERON:0000924!6.45e-19!173;UBERON:0006601!6.45e-19!173;UBERON:0001049!7.54e-19!57;UBERON:0005068!7.54e-19!57;UBERON:0006241!7.54e-19!57;UBERON:0007135!7.54e-19!57;UBERON:0002616!8.81e-19!59;UBERON:0007023!9.86e-18!115;UBERON:0000955!2.38e-16!69;UBERON:0006238!2.38e-16!69;UBERON:0003075!3.24e-16!86;UBERON:0007284!3.24e-16!86;UBERON:0005743!2.23e-15!86;UBERON:0001017!2.88e-15!82;UBERON:0000064!1.93e-14!219;UBERON:0000062!3.05e-14!511;UBERON:0002346!4.97e-14!90;UBERON:0003080!6.15e-14!42;UBERON:0002780!1.60e-13!41;UBERON:0001890!1.60e-13!41;UBERON:0006240!1.60e-13!41;UBERON:0000468!1.77e-12!659;UBERON:0000073!2.44e-12!94;UBERON:0001016!2.44e-12!94;UBERON:0000477!3.50e-11!286;UBERON:0001893!4.78e-11!34;UBERON:0002020!5.08e-11!34;UBERON:0003528!5.08e-11!34;UBERON:0000467!7.03e-11!625;UBERON:0000480!8.07e-11!626;UBERON:0003056!1.03e-10!61;UBERON:0002791!1.35e-10!33;UBERON:0000481!3.56e-10!347;UBERON:0001869!4.26e-10!32;UBERON:0003102!5.70e-09!95;UBERON:0000119!2.30e-08!312;UBERON:0000483!3.61e-08!309;UBERON:0005631!6.10e-08!14;UBERON:0000158!6.10e-08!14;UBERON:0004923!6.14e-08!57;UBERON:0002619!6.56e-08!22;UBERON:0004111!9.80e-08!241;UBERON:0001950!6.26e-07!20;UBERON:0000956!6.77e-07!25;UBERON:0000203!6.77e-07!25
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825,0.19886,0.125399,0.000155637,0.00803236,0.291561,0.0337354,0.146629,0.426032,0.440859,0.177111,0.167984,0.337564,0.00176382,0.123448,0.17256,0.126216,0.0947479,0.0787488,0.0883646,0.496336,6.54437e-06,0.407665,0.11039,0.361507,0.660283,0.0754745,0.632378,0.439214,0.0896836,0.133679,0.718626,0.262768,0.235824,4.45413e-07,0.506939,0.0654706,0.0408918,0.305348,0.0883079,0.192275,0.123717,2.32969e-06,0.494788,0.435034,0.388488,0.27954,0.689314,0.468189,3.56419e-12,0.168686,0.35711,0.180717,0.375467,6.11858e-09,0.00655126,0.299453,0.347601,0.297851,0.195385,0.578705,1.91119e-05,0.106912,0.207535,2.39074e-07,0.283013,0.17144,0.236468,0.274647,0.280244,0.000519824,0.000596365,0.1168,0.00012214,0.112879,0.138362,0.1674,0.205022,0.304414,0.0775871,3.77643e-05,0.00753056,0.0152373,1.1888e-05,0.435374,0.00138741,0.25636,0.392755,0.00126726,0.843094,0.12921,0.107541,0.688004,0.136306,0.362226,0.565792,0.158567,0.446426,0.551931,0.0810658,0.268889,0.361819,0.209733,1.36574e-05,0.417001,0.0206565,0.234633,0.150144,0.235575,0.111506,0.209512,0.101765,0.167545,0.1033,0.238509,0.156356,0.450242,0.322099,0.0857464,1.40003e-06,0.101873,0.121306,0.0332472,0.203595,0.356991,0.227948,0.00306437,0.128341,0.025439,4.66236e-08,0.545636,0.320047,0.397073,0.437057,0.221207,0.0146911,0.358,0.00326035,0.318595,0.140173,0.390753,0.312917,0.0258881,0.326484,0.15977,0.201434,0.134947,0.304849,0.316782,0.212636,0.00755937,0.353123,1.0321e-06,0.291345,0.453507,0.491263,0.547467,0.00345812,0.184894,0.609179,0.244347,0.243363,0.382464,7.68278e-06,0.207462,0.51104,0.487422,0.29768,0.217499,0.000761068,0.225368,0.244195,0.0586175,0.348776,0.198885,0.0186296,0.347052,0.00160212,0.1797,0.00147932,0.327304,0.058337,0.0892444,0.132491,0.143033,0.367752,0.436987,0.0244296,0.704893,0.00850809,0.0821811,0.0373253,0.279549,0.0984834,0.284421,0.71736,0.00495141,0.751141,0.344864,0.458949,0.547863,0.741039,2.06828e-06,0.000396659,0.750889,0.401507,0.692805,0.648881,0.0351248,0.673541,0.147712,0.910041,0.732853,0.0329228,0.684866,0.790371,0.00640162,0.0499894,0.00204455,0.361096,0.346053,0.451787,0.818359,0.894024,0.680172,0.184591,0.805952,0.0124119,1.8987e-05,0.0468619,0.341975,0.765292,0.188404,0.0163678,0.780774,0.615729,0.000839504,0.501908,0.74852,0.478352,1.90228e-07,0.685599,0.00465855,0.000476818,0.337191,0.00195,0.0365749,0.797881,4.70274e-07,0.664234,2.61628e-07,0.779967,5.4519e-06,5.53271e-08,0.0614674,0.411785,0.40673,0.415502,0.565657,0.499305,8.87211e-06,0.632958,0.676266,0.327011,0.299176,4.61144e-05,0.210121,0.585578,0.640275,0.341296,4.31653e-05,0.258349,0.541728,0.854621,3.79549e-05,0.373172,0.538803,7.56305e-09,0.893074,0.706206,0.816529,0.000358728,0.917146,0.0744189,0.000100499,0.00117491,0.00203502,0.977195,0.0103387,0.00308622,0.715629,8.6542e-07,0.765316,2.21918e-05,0.32901,0.41419,0.7547,0.0054598,0.0499027,0.346938,0.40211,0.183851,0.588416,0.783193,0.362009,0.070405,2.27712e-06,0.250792,0.126341,0.0919405,0.0100024,0.685486,0.00011416,0.466416,1.48405e-06,0.525367,0.667,0.00299173,8.79399e-05,0.00734144,0.0108269,0.573415,0.474724,0.000135669,0.574524,0.570287,0.00132736,0.315643,2.85297e-09,0.490466,0.105241,0.000699752,0.805909,0.440345,3.24736e-10,0.400622,0.391073,0.766374,0.0225605,0.575489,0.762263,0.540565,0.855535,3.96555e-06,0.695855,0.525188,0.0938213,0.52794,0.67786,0.00469564,0.087524,0.620377,0.402066,1.8702e-05,0.108221,5.84094e-05,0.523153,0.564763,0.0894143,0.415214,0.364157,1.46162e-09,0.53064,0.415017,0.0769041,0.0136926,0.502902,0.385339,0.159832,0.000878985,0.0086964,0.390233,0.339879,0.114722,0.41967,0.197678,0.208523,0.34551,0.4924,0.026431,0.497662,0.418843,0.0518311,0.369586,0.00177803,0.441472,0.444932,0.00052264,0.580249,0.020606,0.403472,0.0130952,0.264429,0.404954,0.0744027,0.204325,0.0389664,0.00132321,0.451398,0.0421649,0.188364,0.279598,0.420279,0.485091,0.443868,0.150111,0.420451,0.0370381,0.244241,0.307495,0.455626,0.3382,0.000414682,0.350305,0.0875262,0.147486,0.117583,0.103076,0.518238,0.40865,0.634608,0.324846,0.25829,0.215261,0.0300732,0.133496,0.433115,0.331422,0.440492,0.00183854,0.266168,0.504119,0.57634,0.371725,0.334024,0.500457,0.316975,0.435107,0.26559,0.378345,0.0836911,0.160696,0.0338793,0.507413,0.412407,0.00265168,0.418893,0.300222,0.0144202,0.487504,0.249956,0.447581,0.482721,0.35808,0.406625,0.296254,0.400859,0.473667,0.327684,0.279523,0.153383,0.118008,9.62151e-05,0.364875,0.211724,0.0165104,0.0575627,0.536787,0.436872,0.181464,0.40945,0.231548,0.120636,0.121001,0.317719,0.172653,0.0924531,0.0076245,0.0627928,0.507382,0.0188111,0.0132872,0.462521,8.8266e-07,0.00111326,0.214126,0.143317,0.261663,0.14273,0.227254,0.147968,0.168955,0.274981,0.236422,0.0999117,0.149301,0.196723,0.0836477,0.0458204,0.413461,0.558766,0.545381,0.630108,0.299959,0.509613,0.498355,0.406059,0.452427,0.56256,3.24139e-09,0.366448,0.183454,0.511559,0.280842,0.335456,0.102233,0.404559,1.90021e-05,0.467154,5.53867e-06,1.28306e-05,0.43669,0.446356,0.248584,1.08511e-06,0.390152,0.537963,0.540199,0.0307221,0.342785,0.447064,0.20487,0.603936,0.449548,0.41929,0.209566,0.189123,0.588995,9.49364e-05,0.00812209,0.0389799,0.158122,0.521096,0.220023,0.444217,0.363335,0.329186,0.432735,0.493369,0.416144,0.648861
}}
}}

Revision as of 12:43, 5 September 2012


Full id: C1274_Preadipocyte_Olfactory_Adipocyte_amniotic_serous_spindle_mesodermal



Phase1 CAGE Peaks

Hg19::chr5:125759038..125759049,+p7@GRAMD3
Hg19::chr5:125759064..125759131,+p1@GRAMD3
Hg19::chr5:125759140..125759175,+p2@GRAMD3
Hg19::chr5:125759213..125759224,+p5@GRAMD3
Hg19::chr5:125759230..125759241,+p6@GRAMD3
Hg19::chr5:125759251..125759262,+p13@GRAMD3
Hg19::chr5:125759280..125759291,+p12@GRAMD3


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
fibroblast3.63e-0775
Uber Anatomy
Ontology termp-valuen
organism subdivision3.62e-21365
ectoderm-derived structure1.12e-20169
head7.84e-20123
anterior region of body3.71e-19129
craniocervical region3.71e-19129
ectoderm6.45e-19173
presumptive ectoderm6.45e-19173
neural tube7.54e-1957
neural rod7.54e-1957
future spinal cord7.54e-1957
neural keel7.54e-1957
regional part of brain8.81e-1959
adult organism9.86e-18115
brain2.38e-1669
future brain2.38e-1669
neural plate3.24e-1686
presumptive neural plate3.24e-1686
central nervous system2.88e-1582
organ part1.93e-14219
organ3.05e-14511
neurectoderm4.97e-1490
anterior neural tube6.15e-1442
regional part of forebrain1.60e-1341
forebrain1.60e-1341
future forebrain1.60e-1341
multi-cellular organism1.77e-12659
regional part of nervous system2.44e-1294
nervous system2.44e-1294
anatomical cluster3.50e-11286
telencephalon4.78e-1134
gray matter5.08e-1134
brain grey matter5.08e-1134
anatomical system7.03e-11625
anatomical group8.07e-11626
pre-chordal neural plate1.03e-1061
regional part of telencephalon1.35e-1033
multi-tissue structure3.56e-10347
cerebral hemisphere4.26e-1032
surface structure5.70e-0995
cell layer2.30e-08312
epithelium3.61e-08309
extraembryonic membrane6.10e-0814
membranous layer6.10e-0814
organ component layer6.14e-0857
regional part of cerebral cortex6.56e-0822
anatomical conduit9.80e-08241
neocortex6.26e-0720
cerebral cortex6.77e-0725
pallium6.77e-0725


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
E2F1#186974.907389214879321.45832274679793e-050.000346937971190954
ELK4#2005716.2356816584683.35702334142222e-092.76938515604103e-07
GABPB1#255344.038676477818380.00980113494696150.0368513782167157
HDAC2#3066713.41562023662631.27676792256388e-089.45034479551018e-07
MYC#460975.22228187160949.4355989882785e-060.000251068668213202
NFKB1#479075.488063424193846.66568321176054e-060.000194947434599008
PBX3#5090721.91451268674414.11002992557057e-104.03428021989347e-08
POLR2A#543072.147453176558070.004747636447610280.022356210963162
RFX5#5993712.04791082719512.7106444306642e-081.86125571133556e-06
SMARCB1#6598615.64518495527781.8015574550748e-079.86126095652814e-06
SP1#666775.69838137814095.12280185510121e-060.000157312644206091
TAF1#687273.343046285745290.0002142336319622450.002468212497353
TBP#690873.706770687096390.0001039672097505110.00145221765669836
TCF12#6938710.63446490218646.49404108872792e-083.973234664708e-06
ZNF263#1012778.221841637010683.93423095812578e-071.90932689142982e-05



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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