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Coexpression cluster:C3024: Difference between revisions

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|full_id=C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart
|full_id=C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart
|id=C3024
|id=C3024
|ontology_enrichment_celltype=CL:0000055!7.41e-26!180;CL:0000057!1.31e-16!75;CL:0000680!2.42e-15!57;CL:0000056!2.42e-15!57;CL:0000355!2.42e-15!57;CL:0000187!1.18e-14!54;CL:0000393!3.29e-13!60;CL:0000211!3.29e-13!60;CL:0000183!6.11e-13!59;CL:0000192!1.26e-10!42;CL:0000514!1.26e-10!42;CL:0002334!1.51e-08!12;CL:0000359!3.73e-08!32;CL:0002494!4.80e-08!16;CL:0000136!1.99e-07!15
|ontology_enrichment_celltype=CL:0000057!7.51e-16!76;CL:0000680!5.39e-14!58;CL:0000056!5.39e-14!58;CL:0000355!5.39e-14!58;CL:0000187!3.97e-13!55;CL:0000183!2.06e-12!59;CL:0000393!7.36e-11!61;CL:0000211!7.36e-11!61;CL:0002334!3.38e-09!12;CL:0000192!9.68e-09!43;CL:0000514!9.68e-09!43;CL:0000055!1.99e-07!106;CL:0002494!6.03e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:2394!7.39e-07!14
|ontology_enrichment_uberon=UBERON:0002385!4.90e-18!63;UBERON:0001015!4.90e-18!63;UBERON:0000383!4.90e-18!63;UBERON:0001134!1.53e-17!61;UBERON:0002036!1.53e-17!61;UBERON:0003082!1.53e-17!61;UBERON:0004290!2.27e-17!70;UBERON:0007023!2.66e-16!115;UBERON:0000475!9.72e-16!365;UBERON:0000914!1.41e-15!83;UBERON:0002329!1.41e-15!83;UBERON:0003077!1.41e-15!83;UBERON:0003059!1.41e-15!83;UBERON:0007282!1.41e-15!83;UBERON:0009618!1.41e-15!83;UBERON:0007285!1.41e-15!83;UBERON:0007100!2.05e-14!27;UBERON:0000486!9.21e-13!82;UBERON:0000948!1.12e-12!24;UBERON:0005498!1.12e-12!24;UBERON:0004140!1.12e-12!24;UBERON:0009881!1.12e-12!24;UBERON:0004141!1.12e-12!24;UBERON:0003084!1.12e-12!24;UBERON:0007005!1.12e-12!24;UBERON:0004139!1.12e-12!24;UBERON:0004291!1.12e-12!24;UBERON:0000481!1.35e-12!347;UBERON:0004872!3.25e-12!84;UBERON:0000483!2.35e-11!309;UBERON:0000119!5.76e-11!312;UBERON:0005256!2.92e-10!143;UBERON:0000468!3.05e-10!659;UBERON:0002100!1.64e-09!216;UBERON:0000025!5.35e-09!194;UBERON:0004111!1.50e-08!241;UBERON:0000477!3.04e-08!286;UBERON:0000490!3.92e-08!138;UBERON:0001009!1.48e-07!113;UBERON:0003103!4.26e-07!69;UBERON:0000467!6.09e-07!625;UBERON:0001637!6.32e-07!42;UBERON:0003509!6.32e-07!42;UBERON:0004572!6.32e-07!42;UBERON:0003914!6.56e-07!118;UBERON:0001981!8.07e-07!60;UBERON:0007500!8.07e-07!60;UBERON:0004537!8.07e-07!60;UBERON:0006965!8.07e-07!60;UBERON:0000480!8.29e-07!626
|ontology_enrichment_uberon=UBERON:0007023!6.53e-17!114;UBERON:0002385!7.27e-17!64;UBERON:0001015!7.27e-17!64;UBERON:0000383!7.27e-17!64;UBERON:0001134!2.69e-16!62;UBERON:0002036!2.69e-16!62;UBERON:0003082!2.69e-16!62;UBERON:0003077!2.46e-15!72;UBERON:0007285!2.46e-15!72;UBERON:0002329!3.01e-15!71;UBERON:0003059!3.01e-15!71;UBERON:0007282!3.01e-15!71;UBERON:0004290!3.01e-15!71;UBERON:0009618!3.01e-15!71;UBERON:0007524!7.46e-15!73;UBERON:0007100!6.10e-14!27;UBERON:0007503!3.59e-12!78;UBERON:0000948!5.44e-12!24;UBERON:0005498!5.44e-12!24;UBERON:0004140!5.44e-12!24;UBERON:0009881!5.44e-12!24;UBERON:0004141!5.44e-12!24;UBERON:0003084!5.44e-12!24;UBERON:0007005!5.44e-12!24;UBERON:0004139!5.44e-12!24;UBERON:0004291!5.44e-12!24;UBERON:0000486!1.92e-11!83;UBERON:0005256!1.29e-10!122;UBERON:0000481!3.68e-10!342;UBERON:0004872!9.06e-10!83;UBERON:0003104!3.41e-09!160;UBERON:0009142!3.41e-09!160;UBERON:0000483!1.01e-08!306;UBERON:0000468!1.50e-08!656;UBERON:0000119!1.64e-08!309;UBERON:0002100!3.12e-08!199;UBERON:0010314!5.03e-08!132;UBERON:0003103!1.32e-07!68;UBERON:0000475!1.36e-07!264;UBERON:0004797!2.53e-07!7;UBERON:0000490!4.01e-07!148
|tf_chipseq_enrich=USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189429958622251
|tf_chipseq_enrich=USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189429958622251
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481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.00330134,0.0757897,0.161801,0.193215,0.00153556,0.0779715,0.00160873,0.0417636,0.00060356,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.000789388,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.000413007,0.549354,0.144567,0.038848,0.0874516,0.0550279,2.15531e-05,0.253693,0.217069,0.190048,0.131088,0.394069,0.0306378,0.00501606,0.00297388,0.0158143,0.0818785,0.0178107,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,1.82894e-05,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,7.20365e-05,0.277091,0.389379,0.00475792,0.21727,0.289306,0.119215,0.192475,0.0168693,0.547859,0.057571,0.047591,0.0899568,0.0608699,0.175319,3.61858e-05,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0121461,0.0225581,0.206454,0.218192,0.000230242,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.000615006,0.0058211,0.155821,0.0718905,0.00435853,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.0346616,0.0461822,0.11903,0.0838874,0.331451,0.113145,0.112651,0.0186145,0.174776,0.000153071,0.264079,0.249049,0.140533,0.0997756,0.257598,0.00020131,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.0190329,0.00340589,0.184948,0.156261,0.311847,0.0062542,0.0590944,0.247324,0.178389,0.0020701,0.231073,0.000211542,0.00318326,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0973145,0.231447,0.544776,0.43956,0.0116789,0.0189483,0.120472,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.0863135,0.432035,0.0411943,0.0886602,0.145312,0.000757632,0.117158,0.0391928,0.00142909,0.871256,0.227104,0.518585,0.0734371,0.0867545,0.284625,0.504757,0.00143312,0.00228337,0.28907,0.164197,0.128922,0.287881,0.21103,0.478174,0.336276,0.468444,0.0366482,3.5958e-05,0.032364,6.92931e-08,0.390974,0.00247135,0.00650842,0.161598,0.00310283,0.277094,0.496032,0.000266268,0.37357,6.9989e-07,5.96264e-05,0.199161,0.0508568,0.771991,0.20342,0.00158025,0.20558,0.300504,0.25656,0.107337,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,4.44343e-06,0.00305733,0.408413,0.516511,0.0073454,0.656109,0.33942,0.00285083,0.387276,0.00100024,0.221908,0.537348,0.222037,0.416621,0.416292,0.462712,7.37404e-05,0.579431,0.204817,0.122646,0.138871,0.673493,0.166905,0.19783,0.0833851,0.00691922,0.0289164,0.175199,0.332919,0.0120568,0.523625,0.0980968,0.365487,0.178743,0.0889149,0.363192,0.236011,0.203486,0.273398,0.0123025,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.371414,0.0527347,0.303709,0.495883,0.386538,0.00602464,0.250964,0.383276,0.000432158,0.0344603,0.220231,6.7973e-08,0.00149391,0.191517,0.463751,5.75625e-07,0.307334,0.459728,0.283463,0.201728,0.000528727,0.0151656,0.273281,0.0114705,0.275089,0.384593,0.0283414,0.359231,0.0656472,0.197805,6.43499e-06,0.387069,0.332774,0.173874,0.299887,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.00210664,0.208013,0.0900729,0.00469907,0.166124,0.252184,0.0828367,0.0358457,0.20753,0.447185,0.179412,0.0200828,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,5.35812e-05,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.0398662,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.0223377,0.21382,0.0232077,0.141867,0.00140109,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.000220289,0.00146315,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,5.26612e-05,0.089609,0.000683539,4.73315e-07,9.49159e-05,0.295769,0.286691,0.347036,0.0105548,0.0381402,0.255956,0.0215087,0.227491,0.29837,0.253509,0.0168099,0.28365,0.264413,1.48336e-05,0.160658,0.206239,0.0213159,0.0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}}
}}

Revision as of 14:43, 19 October 2012


Full id: C3024_Fibroblast_lung_Wilms_Adipocyte_Cardiac_aorta_heart



Phase1 CAGE Peaks

Hg19::chr10:52750837..52750889,+p4@PRKG1
Hg19::chr10:52750899..52750917,+p6@PRKG1
Hg19::chr10:52750930..52750950,+p5@PRKG1


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>

Uber Anatomy
Ontology termp-valuen
adult organism6.53e-17114
muscle tissue7.27e-1764
musculature7.27e-1764
musculature of body7.27e-1764
skeletal muscle tissue2.69e-1662
striated muscle tissue2.69e-1662
myotome2.69e-1662
paraxial mesoderm2.46e-1572
presumptive paraxial mesoderm2.46e-1572
somite3.01e-1571
presomitic mesoderm3.01e-1571
presumptive segmental plate3.01e-1571
dermomyotome3.01e-1571
trunk paraxial mesoderm3.01e-1571
dense mesenchyme tissue7.46e-1573
primary circulatory organ6.10e-1427
epithelial vesicle3.59e-1278
heart5.44e-1224
primitive heart tube5.44e-1224
primary heart field5.44e-1224
anterior lateral plate mesoderm5.44e-1224
heart tube5.44e-1224
heart primordium5.44e-1224
cardiac mesoderm5.44e-1224
cardiogenic plate5.44e-1224
heart rudiment5.44e-1224
multilaminar epithelium1.92e-1183
trunk mesenchyme1.29e-10122
multi-tissue structure3.68e-10342
splanchnic layer of lateral plate mesoderm9.06e-1083
mesenchyme3.41e-09160
entire embryonic mesenchyme3.41e-09160
epithelium1.01e-08306
multi-cellular organism1.50e-08656
cell layer1.64e-08309
trunk3.12e-08199
structure with developmental contribution from neural crest5.03e-08132
compound organ1.32e-0768
organism subdivision1.36e-07264
blood vessel layer2.53e-077
unilaminar epithelium4.01e-07148
Disease
Ontology termp-valuen
ovarian cancer7.39e-0714


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
USF1#739136.361499277207960.00388404057290560.0189429958622251



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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