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Coexpression cluster:C3784: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002049!1.57e-31!79;UBERON:0007798!1.57e-31!79;UBERON:0004872!3.93e-31!84;UBERON:0003914!1.69e-30!118;UBERON:0000055!1.41e-27!69;UBERON:0001009!3.42e-25!113;UBERON:0001981!5.65e-25!60;UBERON:0007500!5.65e-25!60;UBERON:0004537!5.65e-25!60;UBERON:0006965!5.65e-25!60;UBERON:0004535!1.19e-24!110;UBERON:0000119!4.65e-24!312;UBERON:0000483!9.00e-24!309;UBERON:0005256!1.61e-20!143;UBERON:0000490!2.22e-19!138;UBERON:0000477!1.45e-18!286;UBERON:0000468!2.43e-18!659;UBERON:0001637!2.73e-18!42;UBERON:0003509!2.73e-18!42;UBERON:0004572!2.73e-18!42;UBERON:0004111!1.08e-17!241;UBERON:0002100!1.20e-16!216;UBERON:0000486!2.95e-16!82;UBERON:0000475!1.99e-15!365;UBERON:0000467!7.04e-15!625;UBERON:0000914!8.22e-15!83;UBERON:0002329!8.22e-15!83;UBERON:0003077!8.22e-15!83;UBERON:0003059!8.22e-15!83;UBERON:0007282!8.22e-15!83;UBERON:0009618!8.22e-15!83;UBERON:0007285!8.22e-15!83;UBERON:0000480!1.17e-14!626;UBERON:0000481!2.51e-14!347;UBERON:0002385!8.38e-14!63;UBERON:0001015!8.38e-14!63;UBERON:0000383!8.38e-14!63;UBERON:0001134!9.18e-14!61;UBERON:0002036!9.18e-14!61;UBERON:0003082!9.18e-14!61;UBERON:0004290!1.17e-13!70;UBERON:0004573!1.65e-13!33;UBERON:0004571!1.65e-13!33;UBERON:0000025!4.47e-13!194;UBERON:0003104!7.36e-13!238;UBERON:0009142!7.36e-13!238;UBERON:0003103!7.05e-12!69;UBERON:0001986!3.63e-11!18;UBERON:0004638!3.63e-11!18;UBERON:0004852!3.63e-11!18;UBERON:0000487!2.67e-10!22;UBERON:0000922!3.03e-10!612;UBERON:0002050!1.24e-09!605;UBERON:0005423!1.24e-09!605;UBERON:0000923!1.65e-09!604;UBERON:0005291!1.65e-09!604;UBERON:0006598!1.65e-09!604;UBERON:0002532!1.65e-09!604;UBERON:0006914!1.78e-09!25;UBERON:0007100!2.02e-09!27;UBERON:0000948!4.71e-09!24;UBERON:0005498!4.71e-09!24;UBERON:0004140!4.71e-09!24;UBERON:0009881!4.71e-09!24;UBERON:0004141!4.71e-09!24;UBERON:0003084!4.71e-09!24;UBERON:0007005!4.71e-09!24;UBERON:0004139!4.71e-09!24;UBERON:0004291!4.71e-09!24;UBERON:0000947!1.05e-08!21;UBERON:0010191!1.05e-08!21;UBERON:0003064!1.06e-08!37;UBERON:0004211!3.36e-08!16;UBERON:0001285!3.36e-08!16;UBERON:0007684!3.36e-08!16;UBERON:0003220!3.36e-08!16;UBERON:0004208!3.36e-08!16;UBERON:0000353!3.54e-08!17;UBERON:0004876!5.28e-08!20;UBERON:0001048!5.37e-08!168;UBERON:0006555!5.97e-08!17;UBERON:0005103!5.97e-08!17;UBERON:0000083!5.97e-08!17;UBERON:0009201!5.97e-08!17;UBERON:0004819!5.97e-08!17;UBERON:0006553!5.97e-08!17;UBERON:0003074!5.97e-08!17;UBERON:0003060!5.97e-08!17;UBERON:0009569!8.53e-08!113;UBERON:0000080!9.42e-08!18;UBERON:0002120!9.42e-08!18;UBERON:0004875!9.42e-08!18;UBERON:0005721!9.42e-08!18;UBERON:0005754!9.42e-08!18;UBERON:0007297!9.42e-08!18;UBERON:0006554!2.48e-07!44;UBERON:0001008!2.74e-07!45;UBERON:0000064!3.15e-07!219;UBERON:0003102!3.50e-07!95;UBERON:0003915!4.54e-07!9;UBERON:0004700!4.54e-07!9;UBERON:0001917!4.54e-07!9;UBERON:0000926!4.99e-07!448;UBERON:0004120!4.99e-07!448;UBERON:0006603!4.99e-07!448;UBERON:0001225!6.92e-07!13;UBERON:0008987!6.92e-07!13;UBERON:0003887!8.93e-07!21;UBERON:0000464!9.61e-07!104
|ontology_enrichment_uberon=UBERON:0002049!1.57e-31!79;UBERON:0007798!1.57e-31!79;UBERON:0004872!3.93e-31!84;UBERON:0003914!1.69e-30!118;UBERON:0000055!1.41e-27!69;UBERON:0001009!3.42e-25!113;UBERON:0001981!5.65e-25!60;UBERON:0007500!5.65e-25!60;UBERON:0004537!5.65e-25!60;UBERON:0006965!5.65e-25!60;UBERON:0004535!1.19e-24!110;UBERON:0000119!4.65e-24!312;UBERON:0000483!9.00e-24!309;UBERON:0005256!1.61e-20!143;UBERON:0000490!2.22e-19!138;UBERON:0000477!1.45e-18!286;UBERON:0000468!2.43e-18!659;UBERON:0001637!2.73e-18!42;UBERON:0003509!2.73e-18!42;UBERON:0004572!2.73e-18!42;UBERON:0004111!1.08e-17!241;UBERON:0002100!1.20e-16!216;UBERON:0000486!2.95e-16!82;UBERON:0000475!1.99e-15!365;UBERON:0000467!7.04e-15!625;UBERON:0000914!8.22e-15!83;UBERON:0002329!8.22e-15!83;UBERON:0003077!8.22e-15!83;UBERON:0003059!8.22e-15!83;UBERON:0007282!8.22e-15!83;UBERON:0009618!8.22e-15!83;UBERON:0007285!8.22e-15!83;UBERON:0000480!1.17e-14!626;UBERON:0000481!2.51e-14!347;UBERON:0002385!8.38e-14!63;UBERON:0001015!8.38e-14!63;UBERON:0000383!8.38e-14!63;UBERON:0001134!9.18e-14!61;UBERON:0002036!9.18e-14!61;UBERON:0003082!9.18e-14!61;UBERON:0004290!1.17e-13!70;UBERON:0004573!1.65e-13!33;UBERON:0004571!1.65e-13!33;UBERON:0000025!4.47e-13!194;UBERON:0003104!7.36e-13!238;UBERON:0009142!7.36e-13!238;UBERON:0003103!7.05e-12!69;UBERON:0001986!3.63e-11!18;UBERON:0004638!3.63e-11!18;UBERON:0004852!3.63e-11!18;UBERON:0000487!2.67e-10!22;UBERON:0000922!3.03e-10!612;UBERON:0002050!1.24e-09!605;UBERON:0005423!1.24e-09!605;UBERON:0000923!1.65e-09!604;UBERON:0005291!1.65e-09!604;UBERON:0006598!1.65e-09!604;UBERON:0002532!1.65e-09!604;UBERON:0006914!1.78e-09!25;UBERON:0007100!2.02e-09!27;UBERON:0000948!4.71e-09!24;UBERON:0005498!4.71e-09!24;UBERON:0004140!4.71e-09!24;UBERON:0009881!4.71e-09!24;UBERON:0004141!4.71e-09!24;UBERON:0003084!4.71e-09!24;UBERON:0007005!4.71e-09!24;UBERON:0004139!4.71e-09!24;UBERON:0004291!4.71e-09!24;UBERON:0000947!1.05e-08!21;UBERON:0010191!1.05e-08!21;UBERON:0003064!1.06e-08!37;UBERON:0004211!3.36e-08!16;UBERON:0001285!3.36e-08!16;UBERON:0007684!3.36e-08!16;UBERON:0003220!3.36e-08!16;UBERON:0004208!3.36e-08!16;UBERON:0000353!3.54e-08!17;UBERON:0004876!5.28e-08!20;UBERON:0001048!5.37e-08!168;UBERON:0006555!5.97e-08!17;UBERON:0005103!5.97e-08!17;UBERON:0000083!5.97e-08!17;UBERON:0009201!5.97e-08!17;UBERON:0004819!5.97e-08!17;UBERON:0006553!5.97e-08!17;UBERON:0003074!5.97e-08!17;UBERON:0003060!5.97e-08!17;UBERON:0009569!8.53e-08!113;UBERON:0000080!9.42e-08!18;UBERON:0002120!9.42e-08!18;UBERON:0004875!9.42e-08!18;UBERON:0005721!9.42e-08!18;UBERON:0005754!9.42e-08!18;UBERON:0007297!9.42e-08!18;UBERON:0006554!2.48e-07!44;UBERON:0001008!2.74e-07!45;UBERON:0000064!3.15e-07!219;UBERON:0003102!3.50e-07!95;UBERON:0003915!4.54e-07!9;UBERON:0004700!4.54e-07!9;UBERON:0001917!4.54e-07!9;UBERON:0000926!4.99e-07!448;UBERON:0004120!4.99e-07!448;UBERON:0006603!4.99e-07!448;UBERON:0001225!6.92e-07!13;UBERON:0008987!6.92e-07!13;UBERON:0003887!8.93e-07!21;UBERON:0000464!9.61e-07!104
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58058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.0458068,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.0458479,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.000207829,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,1.59254e-06,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.00174134,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.0163112,9.26534e-06,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.00446076,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.0195983,0.148574,9.16892e-05,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.0182671,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.00318326,0.0360851,0.000227331,0.131093,0.0434602,0.133616,0.103051,0.36927,0.449036,0.407369,0.231447,0.18653,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.580441,0.643768,0.432035,0.138468,0.390366,0.145312,0.50058,0.443185,0.522904,1.22574e-05,3.95207e-08,0.227104,0.518585,0.617852,0.38649,0.284625,0.156746,0.55194,0.375373,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.000933637,0.390974,7.41696e-05,0.00650842,0.161598,0.00310283,0.021206,0.496032,0.00136122,0.37357,3.35117e-05,0.138234,0.069689,0.0132585,0.0175763,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.00465874,0.616388,0.408413,0.516511,0.322213,0.656109,0.0655189,0.61031,0.387276,0.522605,0.00640674,0.180745,0.222037,0.416621,0.416292,0.462712,0.0115406,0.579431,0.204817,0.452428,0.138871,0.00583733,0.166905,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.0303438,0.0222706,0.273398,0.375787,0.4466,0.351067,0.275347,0.019895,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.159081,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.201728,0.472935,0.399569,0.273281,0.0780405,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.173874,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.0151141,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
}}
}}

Revision as of 12:07, 5 September 2012


Full id: C3784_Endothelial_Alveolar_Renal_Sebocyte_Fibroblast_Mesothelial_Prostate



Phase1 CAGE Peaks

Hg19::chr19:3971050..3971128,-p1@DAPK3
Hg19::chr1:16085244..16085253,+p3@FBLIM1
Hg19::chr1:16085263..16085314,+p1@FBLIM1


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
embryonic cell5.81e-37248
mesodermal cell4.24e-32119
non-terminally differentiated cell8.47e-22180
contractile cell1.43e-1759
epithelial cell2.34e-16254
meso-epithelial cell2.33e-1544
muscle cell5.03e-1554
lining cell6.35e-1557
barrier cell6.35e-1557
muscle precursor cell7.05e-1557
myoblast7.05e-1557
multi-potent skeletal muscle stem cell7.05e-1557
smooth muscle cell1.22e-1442
smooth muscle myoblast1.22e-1442
endothelial cell3.75e-1435
electrically responsive cell8.53e-1460
electrically active cell8.53e-1460
endothelial cell of vascular tree1.64e-1324
vascular associated smooth muscle cell1.61e-1232
squamous epithelial cell1.65e-1162
blood vessel endothelial cell3.63e-1118
embryonic blood vessel endothelial progenitor cell3.63e-1118
animal cell4.53e-09679
eukaryotic cell4.53e-09679
fibroblast1.92e-0875
epithelial cell of nephron3.36e-0816
somatic cell6.23e-08591
cardiocyte1.01e-0716
endothelial cell of artery4.54e-079
kidney cortical cell6.92e-0713
renal cortical epithelial cell6.92e-0713
Uber Anatomy
Ontology termp-valuen
vasculature1.57e-3179
vascular system1.57e-3179
splanchnic layer of lateral plate mesoderm3.93e-3184
epithelial tube1.69e-30118
vessel1.41e-2769
circulatory system3.42e-25113
blood vessel5.65e-2560
epithelial tube open at both ends5.65e-2560
blood vasculature5.65e-2560
vascular cord5.65e-2560
cardiovascular system1.19e-24110
cell layer4.65e-24312
epithelium9.00e-24309
trunk mesenchyme1.61e-20143
unilaminar epithelium2.22e-19138
anatomical cluster1.45e-18286
multi-cellular organism2.43e-18659
artery2.73e-1842
arterial blood vessel2.73e-1842
arterial system2.73e-1842
anatomical conduit1.08e-17241
trunk1.20e-16216
multilaminar epithelium2.95e-1682
organism subdivision1.99e-15365
anatomical system7.04e-15625
somite8.22e-1583
paraxial mesoderm8.22e-1583
presomitic mesoderm8.22e-1583
presumptive segmental plate8.22e-1583
trunk paraxial mesoderm8.22e-1583
presumptive paraxial mesoderm8.22e-1583
anatomical group1.17e-14626
multi-tissue structure2.51e-14347
muscle tissue8.38e-1463
musculature8.38e-1463
musculature of body8.38e-1463
skeletal muscle tissue9.18e-1461
striated muscle tissue9.18e-1461
myotome9.18e-1461
dermomyotome1.17e-1370
systemic artery1.65e-1333
systemic arterial system1.65e-1333
tube4.47e-13194
mesenchyme7.36e-13238
entire embryonic mesenchyme7.36e-13238
compound organ7.05e-1269
endothelium3.63e-1118
blood vessel endothelium3.63e-1118
cardiovascular system endothelium3.63e-1118
simple squamous epithelium2.67e-1022
embryo3.03e-10612
embryonic structure1.24e-09605
developing anatomical structure1.24e-09605
germ layer1.65e-09604
embryonic tissue1.65e-09604
presumptive structure1.65e-09604
epiblast (generic)1.65e-09604
squamous epithelium1.78e-0925
primary circulatory organ2.02e-0927
heart4.71e-0924
primitive heart tube4.71e-0924
primary heart field4.71e-0924
anterior lateral plate mesoderm4.71e-0924
heart tube4.71e-0924


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
SRF#6722313.79717826216780.0003806615025800190.00375020344004854



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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