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Coexpression cluster:C3634: Difference between revisions

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|ontology_enrichment_disease=DOID:305!5.82e-12!106;DOID:162!7.51e-12!235;DOID:0050687!1.11e-11!143;DOID:14566!1.64e-11!239
|ontology_enrichment_disease=DOID:305!5.82e-12!106;DOID:162!7.51e-12!235;DOID:0050687!1.11e-11!143;DOID:14566!1.64e-11!239
|ontology_enrichment_uberon=UBERON:0003104!3.34e-15!238;UBERON:0009142!3.34e-15!238;UBERON:0000119!4.42e-14!312;UBERON:0003914!1.63e-13!118;UBERON:0002100!2.14e-13!216;UBERON:0005256!2.94e-13!143;UBERON:0000483!3.32e-13!309;UBERON:0000490!7.35e-13!138;UBERON:0000481!8.49e-12!347;UBERON:0001048!3.03e-10!168;UBERON:0000466!5.58e-10!126;UBERON:0005177!4.14e-09!107;UBERON:0004119!6.67e-09!169;UBERON:0000925!6.67e-09!169;UBERON:0006595!6.67e-09!169;UBERON:0002049!6.84e-09!79;UBERON:0007798!6.84e-09!79;UBERON:0000464!1.11e-08!104;UBERON:0001981!2.15e-08!60;UBERON:0007500!2.15e-08!60;UBERON:0004537!2.15e-08!60;UBERON:0006965!2.15e-08!60;UBERON:0000475!2.46e-08!365;UBERON:0000486!5.19e-08!82;UBERON:0000055!8.04e-08!69;UBERON:0001637!9.40e-08!42;UBERON:0003509!9.40e-08!42;UBERON:0004572!9.40e-08!42;UBERON:0004872!9.68e-08!84;UBERON:0001007!2.83e-07!155;UBERON:0001555!2.83e-07!155;UBERON:0007026!2.83e-07!155;UBERON:0000914!3.12e-07!83;UBERON:0002329!3.12e-07!83;UBERON:0003077!3.12e-07!83;UBERON:0003059!3.12e-07!83;UBERON:0007282!3.12e-07!83;UBERON:0009618!3.12e-07!83;UBERON:0007285!3.12e-07!83;UBERON:0000077!6.82e-07!130
|ontology_enrichment_uberon=UBERON:0003104!3.34e-15!238;UBERON:0009142!3.34e-15!238;UBERON:0000119!4.42e-14!312;UBERON:0003914!1.63e-13!118;UBERON:0002100!2.14e-13!216;UBERON:0005256!2.94e-13!143;UBERON:0000483!3.32e-13!309;UBERON:0000490!7.35e-13!138;UBERON:0000481!8.49e-12!347;UBERON:0001048!3.03e-10!168;UBERON:0000466!5.58e-10!126;UBERON:0005177!4.14e-09!107;UBERON:0004119!6.67e-09!169;UBERON:0000925!6.67e-09!169;UBERON:0006595!6.67e-09!169;UBERON:0002049!6.84e-09!79;UBERON:0007798!6.84e-09!79;UBERON:0000464!1.11e-08!104;UBERON:0001981!2.15e-08!60;UBERON:0007500!2.15e-08!60;UBERON:0004537!2.15e-08!60;UBERON:0006965!2.15e-08!60;UBERON:0000475!2.46e-08!365;UBERON:0000486!5.19e-08!82;UBERON:0000055!8.04e-08!69;UBERON:0001637!9.40e-08!42;UBERON:0003509!9.40e-08!42;UBERON:0004572!9.40e-08!42;UBERON:0004872!9.68e-08!84;UBERON:0001007!2.83e-07!155;UBERON:0001555!2.83e-07!155;UBERON:0007026!2.83e-07!155;UBERON:0000914!3.12e-07!83;UBERON:0002329!3.12e-07!83;UBERON:0003077!3.12e-07!83;UBERON:0003059!3.12e-07!83;UBERON:0007282!3.12e-07!83;UBERON:0009618!3.12e-07!83;UBERON:0007285!3.12e-07!83;UBERON:0000077!6.82e-07!130
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175785,0.0181729,0.015204,0.000120084,0.0046858,0.0112557,0.0268081,0.107043,0.0043762,0.00481323,0.173708,0.141119,0.211595,0.000456679,0.131551,0.0445237,0.052362,0.0235128,0.0123828,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.000803238,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.00102636,0.0791124,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.001389,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.217069,0.190048,0.131088,0.090504,0.0306378,0.286988,0.0761239,0.172491,0.0818785,0.0178107,0.00836526,0.011488,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,1.59254e-06,0.288159,0.0255266,0.0465945,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,6.38787e-05,0.223874,1.71711e-06,0.0355833,0.125606,0.175094,1.70007e-06,6.6291e-06,0.206454,0.00206897,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.00102818,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.00217546,0.057168,0.00259914,0.0759837,0.286863,0.152372,0.0203723,0.218271,0.101607,0.060512,0.172982,0.0661495,0.151597,0.0626744,0.0195983,0.148574,0.000797393,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.000642001,0.0973823,2.93332e-05,0.000943322,0.193653,1.75758e-05,0.228144,0.251466,0.288096,0.11903,0.0838874,0.000795326,0.113145,0.112651,0.186638,0.174776,0.0948451,0.00382477,0.0339656,0.140533,0.00515192,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.0190329,0.00340589,0.184948,0.156261,0.0546539,0.0362615,0.0590944,0.0334734,0.178389,0.218229,0.231073,0.407281,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.0115948,0.00328135,0.407369,0.231447,0.00858901,0.43956,0.0116789,0.10748,0.00038176,0.197484,0.396996,0.36145,0.00202987,0.381071,0.057779,0.643768,0.432035,8.1243e-06,0.0140037,0.0305485,0.0334527,0.117158,0.522904,3.32586e-07,9.2035e-12,0.227104,0.00667974,0.0167433,0.0135352,0.284625,0.000799065,0.00143312,1.54927e-08,0.28907,0.164197,0.0252589,0.287881,3.14651e-05,0.000566617,0.336276,0.468444,0.00355636,0.0031948,0.243383,2.80434e-05,0.390974,1.86828e-09,0.00120937,0.161598,2.12518e-06,0.00422412,7.75114e-06,1.05823e-06,0.37357,3.35117e-05,0.477353,0.452741,0.000558506,0.0175763,0.00165472,0.200493,0.20558,0.300504,0.00348292,0.107337,0.349197,0.383291,0.156104,0.000526011,0.0168417,0.0961477,0.314438,0.0720718,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.282286,0.00465874,0.0727621,0.408413,0.0374737,0.0073454,0.28903,0.33942,0.61031,0.0136291,0.522605,0.0816402,1.63987e-05,0.222037,0.0175112,0.416292,0.0252635,1.84971e-09,0.215157,0.204817,3.96668e-05,0.138871,0.103502,0.166905,0.19783,0.0833851,4.84518e-05,0.140384,0.175199,0.332919,0.0805711,0.170369,0.0164118,0.00124345,0.000145338,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.0223007,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.00623664,0.303709,0.0323359,0.000154868,0.035296,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.129584,5.75625e-07,0.307334,0.00367772,0.283463,0.201728,0.472935,0.0932845,0.273281,0.368095,0.275089,0.0133102,0.138622,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.52832,0.299887,0.00375452,0.205413,0.17639,0.0779009,0.276869,0.00170381,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.000822975,0.219428,0.208013,0.0900729,0.0953646,0.000872573,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.0200828,0.220904,0.0269454,7.52509e-05,0.310674,0.21801,0.0211771,0.00126297,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.00178902,0.00394192,0.113092,0.0111711,0.229428,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.0701861,0.154941,0.120196,0.0986735,0.108462,0.00181011,0.21593,0.158479,0.220319,0.195218,0.000352159,0.00361981,0.30793,0.0173907,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.000211932,0.173026,0.200432,0.0102599,0.197112,0.240478,0.156465,0.13108,0.00350063,0.0269005,0.0157468,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,8.4053e-05,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0025753,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.00618871,0.04411,0.00229305,0.089609,0.0367455,0.1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}}
}}

Revision as of 12:39, 5 September 2012


Full id: C3634_testicular_Trabecular_osteosarcoma_gastric_Fibroblast_teratocarcinoma_lung



Phase1 CAGE Peaks

Hg19::chr17:41622982..41623001,-p11@ETV4
Hg19::chr17:41623009..41623053,-p4@ETV4
Hg19::chr17:41623075..41623101,-p9@ETV4


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
epithelial cell3.60e-32254
embryonic cell8.27e-24248
animal cell5.83e-21679
eukaryotic cell5.83e-21679
non-terminally differentiated cell3.79e-11180
mesodermal cell3.92e-10119
native cell5.44e-10722
squamous epithelial cell6.71e-0962
endodermal cell1.41e-0759
contractile cell2.44e-0759
somatic cell3.54e-07591
electrically responsive cell5.74e-0760
electrically active cell5.74e-0760
Uber Anatomy
Ontology termp-valuen
mesenchyme3.34e-15238
entire embryonic mesenchyme3.34e-15238
cell layer4.42e-14312
epithelial tube1.63e-13118
trunk2.14e-13216
trunk mesenchyme2.94e-13143
epithelium3.32e-13309
unilaminar epithelium7.35e-13138
multi-tissue structure8.49e-12347
primordium3.03e-10168
immaterial anatomical entity5.58e-10126
trunk region element4.14e-09107
endoderm-derived structure6.67e-09169
endoderm6.67e-09169
presumptive endoderm6.67e-09169
vasculature6.84e-0979
vascular system6.84e-0979
anatomical space1.11e-08104
blood vessel2.15e-0860
epithelial tube open at both ends2.15e-0860
blood vasculature2.15e-0860
vascular cord2.15e-0860
organism subdivision2.46e-08365
multilaminar epithelium5.19e-0882
vessel8.04e-0869
artery9.40e-0842
arterial blood vessel9.40e-0842
arterial system9.40e-0842
splanchnic layer of lateral plate mesoderm9.68e-0884
digestive system2.83e-07155
digestive tract2.83e-07155
primitive gut2.83e-07155
somite3.12e-0783
paraxial mesoderm3.12e-0783
presomitic mesoderm3.12e-0783
presumptive segmental plate3.12e-0783
trunk paraxial mesoderm3.12e-0783
presumptive paraxial mesoderm3.12e-0783
mixed endoderm/mesoderm-derived structure6.82e-07130
Disease
Ontology termp-valuen
carcinoma5.82e-12106
cancer7.51e-12235
cell type cancer1.11e-11143
disease of cellular proliferation1.64e-11239


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000284375772087996
CCNT2#90536.336201576962630.003930750035764890.018982872606365
CHD2#1106310.34402283411690.0009033701102746880.00659954329511599
CTCF#1066435.360256373075030.0064925092527670.0279145022374432
E2F1#186934.907389214879320.008460985347239390.0324897730965635
E2F6#187635.017155731697390.00791769806886330.0321694794247817
EGR1#195834.988179094810140.008056488137383440.0320220568039347
EP300#203336.77394172622320.003216880500103790.0167322965561203
FOSL2#2355316.93020060456170.0002060162053171620.00242763471365441
FOXA1#3169311.08141974938550.000734755275698670.00580769743727339
GABPB1#255337.067683836182170.002832212825417420.0153946848794509
HDAC2#3066313.41562023662630.0004140761399857210.00390868564569493
HNF4A#3172323.13229036295378.07584663437677e-050.00122734771048847
HNF4G#3174328.75342252644684.20470658818262e-050.000756347487707897
RXRA#6256320.07461713913330.0001235730348432220.0016516309426659
SIN3A#2594235.408884726815140.006318961977991520.0276324611656599
SP1#666735.69838137814090.005403962701712170.024620881237365
TCF7L2#6934310.77017656313730.0008003181298398380.00612923848077604
YY1#752834.911170749853860.008441455341808260.0328937077249128
ZBTB7A#5134137.35190930787590.002516255860282270.013999320572769



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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