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Coexpression cluster:C3412: Difference between revisions

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|full_id=C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast
|full_id=C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast
|id=C3412
|id=C3412
|ontology_enrichment_celltype=CL:0000055!2.45e-27!180;CL:0002371!4.18e-25!591;CL:0000144!1.29e-23!625;CL:0000222!7.84e-23!119;CL:0000183!3.19e-19!59;CL:0000680!4.69e-19!57;CL:0000056!4.69e-19!57;CL:0000355!4.69e-19!57;CL:0000220!2.14e-18!246;CL:0000192!2.33e-18!42;CL:0000514!2.33e-18!42;CL:0000187!3.34e-18!54;CL:0002321!6.66e-18!248;CL:0000359!2.99e-16!32;CL:0000393!1.63e-15!60;CL:0000211!1.63e-15!60;CL:0000548!2.74e-14!679;CL:0000004!2.74e-14!679;CL:0000255!2.74e-14!679;CL:0000012!1.67e-13!682;CL:0000048!2.25e-09!430;CL:0000723!4.30e-09!436;CL:0000057!7.84e-09!75;CL:0000115!3.09e-08!35;CL:0000034!4.43e-08!444;CL:0002078!8.10e-08!44;CL:0002539!2.93e-07!10;CL:0000213!7.11e-07!57;CL:0000215!7.11e-07!57
|ontology_enrichment_celltype=CL:0002371!2.02e-26!588;CL:0000222!7.80e-24!121;CL:0000183!2.16e-19!59;CL:0000680!3.71e-19!58;CL:0000056!3.71e-19!58;CL:0000355!3.71e-19!58;CL:0000192!8.61e-19!43;CL:0000514!8.61e-19!43;CL:0000187!2.12e-18!55;CL:0000055!9.16e-18!106;CL:0002321!1.83e-17!250;CL:0000359!2.53e-16!32;CL:0000393!1.16e-15!61;CL:0000211!1.16e-15!61;CL:0000548!5.49e-14!679;CL:0000255!5.49e-14!679;CL:0000048!9.08e-11!427;CL:0000723!1.82e-10!433;CL:0000034!2.11e-09!441;CL:0000057!4.47e-09!76;CL:0000115!8.65e-09!36;CL:0002078!3.01e-08!45;CL:0000213!1.67e-07!58;CL:0000215!1.67e-07!58;CL:0002539!2.99e-07!10;CL:0000071!9.95e-07!18;CL:0002546!9.95e-07!18
|ontology_enrichment_disease=DOID:2394!1.56e-07!14
|ontology_enrichment_disease=DOID:2394!1.99e-07!14
|ontology_enrichment_uberon=UBERON:0001637!2.15e-22!42;UBERON:0003509!2.15e-22!42;UBERON:0004572!2.15e-22!42;UBERON:0004872!4.52e-22!84;UBERON:0001981!1.31e-21!60;UBERON:0007500!1.31e-21!60;UBERON:0004537!1.31e-21!60;UBERON:0006965!1.31e-21!60;UBERON:0002049!2.04e-21!79;UBERON:0007798!2.04e-21!79;UBERON:0000486!2.63e-21!82;UBERON:0000055!2.02e-20!69;UBERON:0000914!9.36e-20!83;UBERON:0002329!9.36e-20!83;UBERON:0003077!9.36e-20!83;UBERON:0003059!9.36e-20!83;UBERON:0007282!9.36e-20!83;UBERON:0009618!9.36e-20!83;UBERON:0007285!9.36e-20!83;UBERON:0004290!4.95e-19!70;UBERON:0003914!1.05e-18!118;UBERON:0001134!3.35e-18!61;UBERON:0002036!3.35e-18!61;UBERON:0003082!3.35e-18!61;UBERON:0004573!4.90e-18!33;UBERON:0004571!4.90e-18!33;UBERON:0002385!1.15e-17!63;UBERON:0001015!1.15e-17!63;UBERON:0000383!1.15e-17!63;UBERON:0002204!8.29e-17!167;UBERON:0005256!2.73e-16!143;UBERON:0000926!6.33e-16!448;UBERON:0004120!6.33e-16!448;UBERON:0006603!6.33e-16!448;UBERON:0000468!1.17e-15!659;UBERON:0000490!3.45e-15!138;UBERON:0004535!6.03e-15!110;UBERON:0001009!2.91e-14!113;UBERON:0000467!7.01e-14!625;UBERON:0003081!1.11e-13!216;UBERON:0000480!1.42e-13!626;UBERON:0000947!1.41e-11!21;UBERON:0010191!1.41e-11!21;UBERON:0002100!1.44e-11!216;UBERON:0002050!1.44e-11!605;UBERON:0005423!1.44e-11!605;UBERON:0000923!2.08e-11!604;UBERON:0005291!2.08e-11!604;UBERON:0006598!2.08e-11!604;UBERON:0002532!2.08e-11!604;UBERON:0000922!3.73e-11!612;UBERON:0000119!7.32e-09!312;UBERON:0000483!7.83e-09!309;UBERON:0004237!2.93e-07!10;UBERON:0004695!2.93e-07!10;UBERON:0002111!2.93e-07!10;UBERON:0004178!2.93e-07!10;UBERON:0001135!5.77e-07!15
|ontology_enrichment_uberon=UBERON:0000926!1.43e-25!315;UBERON:0004120!1.43e-25!315;UBERON:0006603!1.43e-25!315;UBERON:0001637!1.75e-22!42;UBERON:0003509!1.75e-22!42;UBERON:0004572!1.75e-22!42;UBERON:0004872!3.00e-22!83;UBERON:0007500!8.40e-22!59;UBERON:0001981!8.40e-22!59;UBERON:0004537!8.40e-22!59;UBERON:0006965!8.40e-22!59;UBERON:0002049!1.81e-21!78;UBERON:0007798!1.81e-21!78;UBERON:0000486!3.34e-21!83;UBERON:0000055!1.88e-20!68;UBERON:0007503!1.28e-19!78;UBERON:0002204!3.26e-19!167;UBERON:0002329!5.92e-19!71;UBERON:0003059!5.92e-19!71;UBERON:0007282!5.92e-19!71;UBERON:0004290!5.92e-19!71;UBERON:0009618!5.92e-19!71;UBERON:0007524!1.46e-18!73;UBERON:0003077!1.87e-18!72;UBERON:0007285!1.87e-18!72;UBERON:0004573!2.95e-18!33;UBERON:0004571!2.95e-18!33;UBERON:0001134!4.53e-18!62;UBERON:0002036!4.53e-18!62;UBERON:0003082!4.53e-18!62;UBERON:0003914!6.91e-18!117;UBERON:0002385!1.45e-17!64;UBERON:0001015!1.45e-17!64;UBERON:0000383!1.45e-17!64;UBERON:0000490!4.62e-16!148;UBERON:0000468!7.08e-16!656;UBERON:0004535!6.58e-15!109;UBERON:0003081!7.23e-15!203;UBERON:0001009!3.21e-14!112;UBERON:0000467!4.17e-14!624;UBERON:0000480!8.41e-14!625;UBERON:0005256!8.77e-14!122;UBERON:0003104!4.77e-12!160;UBERON:0009142!4.77e-12!160;UBERON:0000947!1.29e-11!21;UBERON:0010191!1.29e-11!21;UBERON:0002050!3.33e-11!564;UBERON:0005423!9.40e-11!581;UBERON:0000923!3.11e-10!560;UBERON:0010316!3.11e-10!560;UBERON:0005291!3.11e-10!560;UBERON:0006598!3.11e-10!560;UBERON:0010317!3.11e-10!560;UBERON:0002532!3.11e-10!560;UBERON:0000475!5.02e-10!264;UBERON:0000922!5.84e-10!592;UBERON:0002100!1.22e-09!199;UBERON:0000119!2.16e-08!309;UBERON:0000483!2.32e-08!306;UBERON:0004237!2.99e-07!10;UBERON:0004695!2.99e-07!10;UBERON:0002111!2.99e-07!10;UBERON:0004178!2.99e-07!10;UBERON:0001135!5.63e-07!15;UBERON:0004638!9.95e-07!18;UBERON:0001986!9.95e-07!18;UBERON:0004852!9.95e-07!18
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129258286201031!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278800696455628!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000856866558084417!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066276533618823
|tf_chipseq_enrich=CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000129258286201031!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278800696455628!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000856866558084417!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066276533618823
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76426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,2.87669e-05,0.0779715,0.0561838,0.0417636,0.00060356,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.000789388,0.0596469,0.419264,0.122476,0.108872,0.11002,0.0376172,0.000413007,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.0353101,0.217069,0.190048,0.131088,0.090504,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.0178107,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.00315933,0.132886,0.0774373,0.000236316,0.128564,0.131452,0.000207829,0.000381649,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,7.20365e-05,0.277091,0.153605,0.000821167,0.21727,0.00514993,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.00103374,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.00102956,0.00352878,0.145116,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.0227848,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.0457643,0.0122477,0.194941,0.218271,0.101607,0.00771936,0.172982,0.0661495,0.151597,0.0626744,7.15556e-05,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.0186145,0.174776,0.000153071,0.264079,0.00316392,0.140533,0.0997756,0.0364628,0.103667,0.113069,0.025556,0.16791,0.09066,3.989e-07,0.0147868,0.188651,0.0813902,0.184948,0.000720136,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.412187,0.00899487,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.0291288,0.544776,0.43956,0.0116789,0.10748,0.022688,0.197484,0.0919774,0.36145,0.406019,0.0841307,0.057779,0.276075,0.432035,0.722159,0.390366,0.48809,0.50058,0.00308025,0.522904,0.00567172,0.0184337,0.0279976,0.518585,0.00310917,0.0135352,0.0450114,0.156746,0.55194,0.144318,0.28907,0.164197,0.462688,0.287881,0.21103,0.478174,0.000849258,0.468444,0.000261508,0.000370166,1.11545e-05,0.0659137,0.390974,0.0458848,0.00120937,0.000800088,0.0527155,0.00422412,0.496032,0.21803,0.0013757,0.0203982,0.477353,0.00492096,0.0508568,0.0629574,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.0696455,0.383291,0.156104,0.141318,0.00217346,0.0961477,0.00677445,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0192486,0.616388,1.85733e-05,0.165147,0.322213,0.28903,1.50013e-08,0.0156581,0.387276,0.0391112,0.481611,0.0433137,0.222037,2.14873e-05,0.416292,0.0252635,0.0115406,0.0118519,0.00169113,0.0233392,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.00818864,0.0120568,1.28312e-05,0.408861,0.365487,0.178743,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.0419637,0.637444,0.305885,0.241132,0.371414,0.30666,0.303709,0.0323359,0.386538,0.035296,0.0345164,0.383276,4.34235e-05,0.504711,0.00213139,0.0355483,0.196976,0.191517,0.463751,0.00258603,0.0529819,0.127092,0.283463,0.0517073,0.00422311,0.0151656,0.273281,0.0114705,0.00436817,0.0133102,0.00444763,0.0105648,0.00088965,0.197805,0.0690807,0.387069,0.0627969,0.00734059,3.57051e-05,0.0814305,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.00265057,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,4.24523e-08,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.00893033,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.000145586,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.00178902,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.0126763,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.00632223,0.180606,0.159884,0.257294,0.150733,0.217112,0.00801612,0.184317,0.0183464,0.0723291,0.258496,0.00371613,0.00166408,0.21382,0.0232077,0.141867,0.193031,0.249101,0.115972,0.0022686,0.0030448,0.173026,0.0215816,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.000975743,0.176789,8.43561e-08,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.00236454,0.2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}}
}}

Revision as of 15:05, 19 October 2012


Full id: C3412_Smooth_Aortic_mesenchymal_CD14_Endothelial_Fibroblast_Osteoblast



Phase1 CAGE Peaks

Hg19::chr14:23305848..23305863,+p3@MMP14
Hg19::chr14:23305868..23305889,+p4@MMP14
Hg19::chr14:23305909..23305918,+p5@MMP14


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
somatic cell2.02e-26588
mesodermal cell7.80e-24121
contractile cell2.16e-1959
muscle precursor cell3.71e-1958
myoblast3.71e-1958
multi-potent skeletal muscle stem cell3.71e-1958
smooth muscle cell8.61e-1943
smooth muscle myoblast8.61e-1943
muscle cell2.12e-1855
non-terminally differentiated cell9.16e-18106
embryonic cell1.83e-17250
vascular associated smooth muscle cell2.53e-1632
electrically responsive cell1.16e-1561
electrically active cell1.16e-1561
animal cell5.49e-14679
eukaryotic cell5.49e-14679
multi fate stem cell9.08e-11427
somatic stem cell1.82e-10433
stem cell2.11e-09441
fibroblast4.47e-0976
endothelial cell8.65e-0936
meso-epithelial cell3.01e-0845
lining cell1.67e-0758
barrier cell1.67e-0758
aortic smooth muscle cell2.99e-0710
blood vessel endothelial cell9.95e-0718
embryonic blood vessel endothelial progenitor cell9.95e-0718
Uber Anatomy
Ontology termp-valuen
mesoderm1.43e-25315
mesoderm-derived structure1.43e-25315
presumptive mesoderm1.43e-25315
artery1.75e-2242
arterial blood vessel1.75e-2242
arterial system1.75e-2242
splanchnic layer of lateral plate mesoderm3.00e-2283
epithelial tube open at both ends8.40e-2259
blood vessel8.40e-2259
blood vasculature8.40e-2259
vascular cord8.40e-2259
vasculature1.81e-2178
vascular system1.81e-2178
multilaminar epithelium3.34e-2183
vessel1.88e-2068
epithelial vesicle1.28e-1978
musculoskeletal system3.26e-19167
somite5.92e-1971
presomitic mesoderm5.92e-1971
presumptive segmental plate5.92e-1971
dermomyotome5.92e-1971
trunk paraxial mesoderm5.92e-1971
dense mesenchyme tissue1.46e-1873
paraxial mesoderm1.87e-1872
presumptive paraxial mesoderm1.87e-1872
systemic artery2.95e-1833
systemic arterial system2.95e-1833
skeletal muscle tissue4.53e-1862
striated muscle tissue4.53e-1862
myotome4.53e-1862
epithelial tube6.91e-18117
muscle tissue1.45e-1764
musculature1.45e-1764
musculature of body1.45e-1764
unilaminar epithelium4.62e-16148
multi-cellular organism7.08e-16656
cardiovascular system6.58e-15109
lateral plate mesoderm7.23e-15203
circulatory system3.21e-14112
anatomical system4.17e-14624
anatomical group8.41e-14625
trunk mesenchyme8.77e-14122
mesenchyme4.77e-12160
entire embryonic mesenchyme4.77e-12160
aorta1.29e-1121
aortic system1.29e-1121
embryonic structure3.33e-11564
developing anatomical structure9.40e-11581
germ layer3.11e-10560
germ layer / neural crest3.11e-10560
embryonic tissue3.11e-10560
presumptive structure3.11e-10560
germ layer / neural crest derived structure3.11e-10560
epiblast (generic)3.11e-10560
organism subdivision5.02e-10264
embryo5.84e-10592
trunk1.22e-09199
cell layer2.16e-08309
epithelium2.32e-08306
blood vessel smooth muscle2.99e-0710
arterial system smooth muscle2.99e-0710
artery smooth muscle tissue2.99e-0710
aorta smooth muscle tissue2.99e-0710
smooth muscle tissue5.63e-0715
blood vessel endothelium9.95e-0718
endothelium9.95e-0718
cardiovascular system endothelium9.95e-0718
Disease
Ontology termp-valuen
ovarian cancer1.99e-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
CTBP2#1488362.71700033932814.049570681927e-060.000129258286201031
CTCF#1066435.360256373075030.0064925092527670.0278800696455628
MAFK#7975327.10073313782995.02195559325033e-050.000856866558084417
RAD21#5885310.35503389545630.0009004912073565420.0066276533618823



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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