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Coexpression cluster:C4506: Difference between revisions

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|full_id=C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous
|full_id=C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous
|id=C4506
|id=C4506
|ontology_enrichment_celltype=CL:0000222!1.74e-33!119;CL:0002139!1.20e-21!24;CL:0000359!1.56e-19!32;CL:0000680!2.44e-18!57;CL:0000056!2.44e-18!57;CL:0000355!2.44e-18!57;CL:0000115!1.41e-17!35;CL:0000055!2.85e-17!180;CL:0000071!6.89e-17!18;CL:0002546!6.89e-17!18;CL:0000187!9.78e-17!54;CL:0000213!2.18e-16!57;CL:0000215!2.18e-16!57;CL:0000183!2.63e-16!59;CL:0000192!7.31e-15!42;CL:0000514!7.31e-15!42;CL:0000393!9.17e-14!60;CL:0000211!9.17e-14!60;CL:0002078!9.08e-13!44;CL:0000220!1.41e-12!246;CL:0002321!2.95e-12!248;CL:0002539!2.51e-10!10;CL:1000413!2.25e-09!9;CL:0000076!6.09e-07!62;CL:0002595!6.19e-07!5;CL:0000057!6.43e-07!75;CL:0002494!8.82e-07!16
|ontology_enrichment_celltype=CL:0000222!9.49e-34!121;CL:0002139!2.84e-30!24;CL:0000115!1.37e-25!36;CL:0000071!1.50e-23!18;CL:0002546!1.50e-23!18;CL:0000359!2.83e-20!32;CL:0000213!8.29e-20!58;CL:0000215!8.29e-20!58;CL:0002078!1.31e-18!45;CL:0000187!4.80e-16!55;CL:0000192!5.90e-16!43;CL:0000514!5.90e-16!43;CL:0000680!6.01e-16!58;CL:0000056!6.01e-16!58;CL:0000355!6.01e-16!58;CL:0000183!2.49e-14!59;CL:0002321!3.31e-14!250;CL:0000393!1.46e-13!61;CL:0000211!1.46e-13!61;CL:1000413!5.51e-13!9;CL:0002539!1.14e-11!10;CL:0002544!4.86e-09!6;CL:0002595!5.95e-09!5;CL:0002543!1.43e-08!6;CL:0000055!1.65e-08!106;CL:0000076!2.38e-08!63;CL:0005020!2.90e-08!6;CL:0002138!2.90e-08!6;CL:0005022!2.90e-08!6;CL:0000548!5.74e-07!679;CL:0000255!5.74e-07!679
|ontology_enrichment_disease=DOID:2394!8.64e-08!14
|ontology_enrichment_disease=DOID:2394!8.03e-11!14
|ontology_enrichment_uberon=UBERON:0000055!2.84e-37!69;UBERON:0001637!1.89e-35!42;UBERON:0003509!1.89e-35!42;UBERON:0004572!1.89e-35!42;UBERON:0001981!8.95e-34!60;UBERON:0007500!8.95e-34!60;UBERON:0004537!8.95e-34!60;UBERON:0006965!8.95e-34!60;UBERON:0004872!6.71e-30!84;UBERON:0004573!1.15e-28!33;UBERON:0004571!1.15e-28!33;UBERON:0002049!1.20e-28!79;UBERON:0007798!1.20e-28!79;UBERON:0003914!6.75e-25!118;UBERON:0004535!1.44e-24!110;UBERON:0001009!2.80e-23!113;UBERON:0000490!7.78e-19!138;UBERON:0000947!5.61e-17!21;UBERON:0010191!5.61e-17!21;UBERON:0001986!6.89e-17!18;UBERON:0004638!6.89e-17!18;UBERON:0004852!6.89e-17!18;UBERON:0001134!3.34e-16!61;UBERON:0002036!3.34e-16!61;UBERON:0003082!3.34e-16!61;UBERON:0002385!3.01e-15!63;UBERON:0001015!3.01e-15!63;UBERON:0000383!3.01e-15!63;UBERON:0004290!4.95e-15!70;UBERON:0000487!1.79e-14!22;UBERON:0000486!2.58e-14!82;UBERON:0006914!4.83e-13!25;UBERON:0004111!1.10e-12!241;UBERON:0000914!1.38e-12!83;UBERON:0002329!1.38e-12!83;UBERON:0003077!1.38e-12!83;UBERON:0003059!1.38e-12!83;UBERON:0007282!1.38e-12!83;UBERON:0009618!1.38e-12!83;UBERON:0007285!1.38e-12!83;UBERON:0000119!1.63e-12!312;UBERON:0000025!1.63e-12!194;UBERON:0000483!1.67e-11!309;UBERON:0004237!2.51e-10!10;UBERON:0004695!2.51e-10!10;UBERON:0002111!2.51e-10!10;UBERON:0004178!2.51e-10!10;UBERON:0000477!6.51e-10!286;UBERON:0003915!2.25e-09!9;UBERON:0004700!2.25e-09!9;UBERON:0001917!2.25e-09!9;UBERON:0005256!8.22e-09!143;UBERON:0002100!6.74e-08!216;UBERON:0003834!6.19e-07!5;UBERON:0001533!6.19e-07!5
|ontology_enrichment_uberon=UBERON:0000055!1.48e-46!68;UBERON:0007500!1.13e-42!59;UBERON:0001981!1.13e-42!59;UBERON:0004537!1.13e-42!59;UBERON:0006965!1.13e-42!59;UBERON:0001637!7.15e-41!42;UBERON:0003509!7.15e-41!42;UBERON:0004572!7.15e-41!42;UBERON:0002049!2.80e-38!78;UBERON:0007798!2.80e-38!78;UBERON:0004573!2.14e-35!33;UBERON:0004571!2.14e-35!33;UBERON:0004872!1.51e-32!83;UBERON:0004535!4.36e-28!109;UBERON:0001009!7.58e-27!112;UBERON:0003914!2.34e-26!117;UBERON:0004638!1.50e-23!18;UBERON:0001986!1.50e-23!18;UBERON:0004852!1.50e-23!18;UBERON:0000947!1.04e-21!21;UBERON:0010191!1.04e-21!21;UBERON:0000490!2.26e-21!148;UBERON:0000487!1.05e-20!22;UBERON:0006914!1.79e-17!25;UBERON:0007503!1.64e-15!78;UBERON:0001134!2.65e-14!62;UBERON:0002036!2.65e-14!62;UBERON:0003082!2.65e-14!62;UBERON:0002385!1.45e-13!64;UBERON:0001015!1.45e-13!64;UBERON:0000383!1.45e-13!64;UBERON:0002329!3.21e-13!71;UBERON:0003059!3.21e-13!71;UBERON:0007282!3.21e-13!71;UBERON:0004290!3.21e-13!71;UBERON:0009618!3.21e-13!71;UBERON:0004111!3.30e-13!240;UBERON:0003915!5.51e-13!9;UBERON:0004700!5.51e-13!9;UBERON:0001917!5.51e-13!9;UBERON:0003077!6.69e-13!72;UBERON:0007285!6.69e-13!72;UBERON:0007524!1.36e-12!73;UBERON:0000486!3.17e-12!83;UBERON:0004237!1.14e-11!10;UBERON:0004695!1.14e-11!10;UBERON:0002111!1.14e-11!10;UBERON:0004178!1.14e-11!10;UBERON:0000025!1.45e-11!192;UBERON:0000119!4.22e-11!309;UBERON:0000926!1.30e-10!315;UBERON:0004120!1.30e-10!315;UBERON:0006603!1.30e-10!315;UBERON:0000483!2.24e-10!306;UBERON:0005256!3.13e-10!122;UBERON:0003834!5.95e-09!5;UBERON:0001533!5.95e-09!5;UBERON:0003081!8.75e-08!203;UBERON:0002100!1.04e-07!199;UBERON:0003104!1.74e-07!160;UBERON:0009142!1.74e-07!160;UBERON:0002118!4.71e-07!5;UBERON:0001135!4.97e-07!15
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090095821189172!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438562771852617!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445900619163672!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015745037635736!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064489277007336
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.0090095821189172!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438562771852617!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445900619163672!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015745037635736!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064489277007336
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5244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.00294748,0.161801,0.193215,0.0549034,8.39064e-05,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,4.88543e-05,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.00615421,0.11002,0.26144,0.0286025,0.549354,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.000982125,0.0818785,0.182701,0.335058,0.147698,0.000527702,0.167267,0.140622,0.00012571,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.00307881,0.109194,0.128564,0.131452,0.0306206,0.448776,0.051838,0.000176849,0.0500365,0.061829,0.0755121,0.00452901,0.144075,0.0340203,0.0741807,0.0425274,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.000364559,0.0163112,0.911304,0.936279,1.74258e-07,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.00293103,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.000980951,0.104948,0.221645,0.057168,9.05232e-06,0.0759837,0.286863,0.152372,0.194941,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.00200641,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.0154015,0.00141547,0.00987736,0.0282663,0.00326415,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.0103728,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,2.75081e-06,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.36927,3.74842e-05,0.407369,0.00249898,0.544776,0.43956,0.37006,0.10748,0.448797,0.197484,1.51104e-05,0.36145,0.406019,0.0129,0.057779,0.643768,0.00272579,0.366326,0.0886602,0.48809,0.153829,0.443185,0.522904,0.875915,0.871256,0.0279976,0.518585,0.250246,0.38649,0.0450114,0.504757,0.192225,0.000415039,0.28907,0.00084117,0.128922,0.287881,0.574635,0.138768,0.0642229,0.468444,0.258219,0.000370166,1.11545e-05,0.777351,0.0889613,0.149257,0.319063,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.78509,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.0227499,0.000511639,0.25656,0.000277336,0.349197,0.383291,0.156104,0.000526011,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.0448825,0.562405,0.314429,0.181415,0.0442318,0.78,0.616388,0.0978616,0.165147,0.0073454,0.28903,0.33942,0.0156581,0.0136291,0.00694606,0.802166,0.180745,0.222037,0.102227,0.416292,0.0252635,0.382478,0.579431,0.204817,0.122646,0.138871,0.673493,0.166905,0.19783,0.0833851,0.056391,0.48065,0.00103152,0.332919,0.373557,0.170369,0.0164118,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.00319628,0.00977892,0.275347,0.637444,0.305885,0.0317395,0.0795725,0.30666,0.303709,0.000713369,0.00161207,0.508064,0.0345164,0.000147288,0.457886,0.156714,0.0262575,0.509064,0.196976,0.191517,0.463751,0.235208,0.0529819,0.127092,0.044623,0.563586,0.0272975,0.399569,0.00427533,0.368095,0.00436817,0.384593,0.47795,0.0740334,0.0656472,0.197805,0.608187,0.0870376,0.332774,0.173874,0.0502872,1.07042e-05,0.205413,0.17639,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.036838,0.188263,0.0719199,0.0386691,0.00081525,0.19104,0.000822975,0.219428,0.208013,0.00418416,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.119514,0.179412,7.52457e-05,0.220904,0.222977,0.341681,0.310674,0.0257082,0.198614,0.186804,0.123324,8.54934e-05,0.0325925,0.0933115,0.12405,0.00112112,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.0267847,0.0673329,0.20847,4.16332e-08,0.113092,0.145701,0.229428,0.162145,0.00241368,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,4.44211e-08,0.201602,0.0701861,0.0126763,1.01156e-05,0.000172898,0.108462,0.0595618,0.000120193,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,1.51586e-05,0.150733,0.217112,0.00801612,6.10196e-05,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.0232077,0.000532415,0.0199603,0.00316602,0.115972,0.224568,0.246105,0.173026,0.00157872,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.000591588,0.280943,0.218161,0.0822373,9.03667e-05,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.0240944,0.187731,0.233626,0.189559,0.00339727,0.0981146,0.064145,0.121913,0.00208455,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,4.30677e-06,0.295769,0.0457063,0.0687209,0.141729,0.0037817,0.255956,0.00157056,0.0280973,0.00569858,0.253509,2.02815e-06,0.28365,0.264413,0.131761,0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}}
}}

Revision as of 16:00, 19 October 2012


Full id: C4506_mesothelioma_schwannoma_Smooth_thyroid_leiomyoma_osteosarcoma_fibrous



Phase1 CAGE Peaks

Hg19::chr5:54281586..54281597,-p5@ESM1
Hg19::chr5:54281688..54281697,-p6@ESM1
Hg19::chr5:54281739..54281753,-p3@ESM1


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
mesodermal cell9.49e-34121
endothelial cell of vascular tree2.84e-3024
endothelial cell1.37e-2536
blood vessel endothelial cell1.50e-2318
embryonic blood vessel endothelial progenitor cell1.50e-2318
vascular associated smooth muscle cell2.83e-2032
lining cell8.29e-2058
barrier cell8.29e-2058
meso-epithelial cell1.31e-1845
muscle cell4.80e-1655
smooth muscle cell5.90e-1643
smooth muscle myoblast5.90e-1643
muscle precursor cell6.01e-1658
myoblast6.01e-1658
multi-potent skeletal muscle stem cell6.01e-1658
contractile cell2.49e-1459
embryonic cell3.31e-14250
electrically responsive cell1.46e-1361
electrically active cell1.46e-1361
endothelial cell of artery5.51e-139
aortic smooth muscle cell1.14e-1110
aortic endothelial cell4.86e-096
smooth muscle cell of the subclavian artery5.95e-095
vein endothelial cell1.43e-086
non-terminally differentiated cell1.65e-08106
squamous epithelial cell2.38e-0863
lymphangioblast2.90e-086
endothelial cell of lymphatic vessel2.90e-086
vascular lymphangioblast2.90e-086
animal cell5.74e-07679
eukaryotic cell5.74e-07679
Uber Anatomy
Ontology termp-valuen
vessel1.48e-4668
epithelial tube open at both ends1.13e-4259
blood vessel1.13e-4259
blood vasculature1.13e-4259
vascular cord1.13e-4259
artery7.15e-4142
arterial blood vessel7.15e-4142
arterial system7.15e-4142
vasculature2.80e-3878
vascular system2.80e-3878
systemic artery2.14e-3533
systemic arterial system2.14e-3533
splanchnic layer of lateral plate mesoderm1.51e-3283
cardiovascular system4.36e-28109
circulatory system7.58e-27112
epithelial tube2.34e-26117
blood vessel endothelium1.50e-2318
endothelium1.50e-2318
cardiovascular system endothelium1.50e-2318
aorta1.04e-2121
aortic system1.04e-2121
unilaminar epithelium2.26e-21148
simple squamous epithelium1.05e-2022
squamous epithelium1.79e-1725
epithelial vesicle1.64e-1578
skeletal muscle tissue2.65e-1462
striated muscle tissue2.65e-1462
myotome2.65e-1462
muscle tissue1.45e-1364
musculature1.45e-1364
musculature of body1.45e-1364
somite3.21e-1371
presomitic mesoderm3.21e-1371
presumptive segmental plate3.21e-1371
dermomyotome3.21e-1371
trunk paraxial mesoderm3.21e-1371
anatomical conduit3.30e-13240
endothelial tube5.51e-139
arterial system endothelium5.51e-139
endothelium of artery5.51e-139
paraxial mesoderm6.69e-1372
presumptive paraxial mesoderm6.69e-1372
dense mesenchyme tissue1.36e-1273
multilaminar epithelium3.17e-1283
blood vessel smooth muscle1.14e-1110
arterial system smooth muscle1.14e-1110
artery smooth muscle tissue1.14e-1110
aorta smooth muscle tissue1.14e-1110
tube1.45e-11192
cell layer4.22e-11309
mesoderm1.30e-10315
mesoderm-derived structure1.30e-10315
presumptive mesoderm1.30e-10315
epithelium2.24e-10306
trunk mesenchyme3.13e-10122
thoracic segment blood vessel5.95e-095
subclavian artery5.95e-095
lateral plate mesoderm8.75e-08203
trunk1.04e-07199
mesenchyme1.74e-07160
entire embryonic mesenchyme1.74e-07160
right ovary4.71e-075
smooth muscle tissue4.97e-0715
Disease
Ontology termp-valuen
ovarian cancer8.03e-1114


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
FOS#235338.99795530889440.001372499272417130.0090095821189172
GATA2#2624312.7449317335540.0004829527704283790.00438562771852617
JUN#3725312.51282919233630.0005103313992726250.00445900619163672
JUND#372736.994663941871030.002921845042734990.015745037635736
STAT3#6774310.51946499715420.0008589184530415310.0064489277007336



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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