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Coexpression cluster:C4429: Difference between revisions

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|full_id=C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal
|full_id=C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal
|id=C4429
|id=C4429
|ontology_enrichment_celltype=CL:0000055!3.87e-15!180;CL:0000222!1.46e-14!119;CL:0000680!6.92e-13!57;CL:0000056!6.92e-13!57;CL:0000355!6.92e-13!57;CL:0000187!3.90e-12!54;CL:0000359!7.98e-12!32;CL:0000393!9.71e-12!60;CL:0000211!9.71e-12!60;CL:0000723!1.48e-11!436;CL:0000048!2.74e-11!430;CL:0000192!3.23e-11!42;CL:0000514!3.23e-11!42;CL:0000183!5.85e-11!59;CL:0000034!7.89e-11!444;CL:0000057!2.82e-09!75;CL:0002371!1.92e-08!591;CL:0000136!1.75e-07!15;CL:0002139!3.92e-07!24;CL:0000144!4.23e-07!625
|ontology_enrichment_celltype=CL:0000222!9.50e-15!121;CL:0000680!7.52e-13!58;CL:0000056!7.52e-13!58;CL:0000355!7.52e-13!58;CL:0000187!3.86e-12!55;CL:0000393!1.14e-11!61;CL:0000211!1.14e-11!61;CL:0000359!1.64e-11!32;CL:0000192!3.49e-11!43;CL:0000514!3.49e-11!43;CL:0000183!3.91e-11!59;CL:0000723!1.50e-10!433;CL:0000048!3.83e-10!427;CL:0000034!8.68e-10!441;CL:0000057!1.74e-09!76;CL:0002371!2.62e-08!588;CL:0002139!5.95e-08!24;CL:0000136!1.12e-07!15;CL:0000055!7.02e-07!106;CL:0002321!7.32e-07!250;CL:0000071!7.48e-07!18;CL:0002546!7.48e-07!18
|ontology_enrichment_disease=DOID:2394!1.39e-07!14
|ontology_enrichment_disease=DOID:2394!1.77e-07!14
|ontology_enrichment_uberon=UBERON:0004872!1.63e-21!84;UBERON:0001981!2.46e-19!60;UBERON:0007500!2.46e-19!60;UBERON:0004537!2.46e-19!60;UBERON:0006965!2.46e-19!60;UBERON:0002049!1.67e-18!79;UBERON:0007798!1.67e-18!79;UBERON:0000055!3.21e-18!69;UBERON:0001637!5.60e-16!42;UBERON:0003509!5.60e-16!42;UBERON:0004572!5.60e-16!42;UBERON:0004535!8.09e-16!110;UBERON:0001009!1.02e-15!113;UBERON:0003914!6.91e-15!118;UBERON:0002385!1.49e-13!63;UBERON:0001015!1.49e-13!63;UBERON:0000383!1.49e-13!63;UBERON:0002204!3.95e-13!167;UBERON:0000486!6.45e-13!82;UBERON:0004573!7.21e-13!33;UBERON:0004571!7.21e-13!33;UBERON:0000490!7.69e-13!138;UBERON:0000914!7.77e-13!83;UBERON:0002329!7.77e-13!83;UBERON:0003077!7.77e-13!83;UBERON:0003059!7.77e-13!83;UBERON:0007282!7.77e-13!83;UBERON:0009618!7.77e-13!83;UBERON:0007285!7.77e-13!83;UBERON:0001134!8.19e-13!61;UBERON:0002036!8.19e-13!61;UBERON:0003082!8.19e-13!61;UBERON:0000468!1.43e-12!659;UBERON:0004290!1.69e-12!70;UBERON:0000467!2.59e-12!625;UBERON:0000480!5.58e-12!626;UBERON:0003081!1.58e-11!216;UBERON:0005256!5.50e-11!143;UBERON:0000926!2.49e-09!448;UBERON:0004120!2.49e-09!448;UBERON:0006603!2.49e-09!448;UBERON:0000947!2.21e-08!21;UBERON:0010191!2.21e-08!21;UBERON:0002050!2.83e-08!605;UBERON:0005423!2.83e-08!605;UBERON:0000923!4.60e-08!604;UBERON:0005291!4.60e-08!604;UBERON:0006598!4.60e-08!604;UBERON:0002532!4.60e-08!604;UBERON:0000922!8.72e-08!612;UBERON:0000479!6.46e-07!787;UBERON:0002100!9.26e-07!216
|ontology_enrichment_uberon=UBERON:0000926!3.21e-22!315;UBERON:0004120!3.21e-22!315;UBERON:0006603!3.21e-22!315;UBERON:0004872!3.61e-20!83;UBERON:0002049!2.92e-18!78;UBERON:0007798!2.92e-18!78;UBERON:0007500!3.02e-18!59;UBERON:0001981!3.02e-18!59;UBERON:0004537!3.02e-18!59;UBERON:0006965!3.02e-18!59;UBERON:0000055!4.97e-18!68;UBERON:0000468!3.87e-16!656;UBERON:0004535!1.36e-15!109;UBERON:0001009!1.42e-15!112;UBERON:0001637!1.58e-15!42;UBERON:0003509!1.58e-15!42;UBERON:0004572!1.58e-15!42;UBERON:0000467!4.47e-15!624;UBERON:0003914!8.14e-15!117;UBERON:0000480!9.96e-15!625;UBERON:0002050!1.43e-13!564;UBERON:0000490!2.25e-13!148;UBERON:0002385!3.16e-13!64;UBERON:0001015!3.16e-13!64;UBERON:0000383!3.16e-13!64;UBERON:0002204!6.13e-13!167;UBERON:0000923!6.46e-13!560;UBERON:0010316!6.46e-13!560;UBERON:0005291!6.46e-13!560;UBERON:0006598!6.46e-13!560;UBERON:0010317!6.46e-13!560;UBERON:0002532!6.46e-13!560;UBERON:0004573!8.77e-13!33;UBERON:0004571!8.77e-13!33;UBERON:0001134!1.45e-12!62;UBERON:0002036!1.45e-12!62;UBERON:0003082!1.45e-12!62;UBERON:0000486!1.53e-12!83;UBERON:0003081!2.05e-12!203;UBERON:0007524!3.04e-12!73;UBERON:0002329!3.57e-12!71;UBERON:0003059!3.57e-12!71;UBERON:0007282!3.57e-12!71;UBERON:0004290!3.57e-12!71;UBERON:0009618!3.57e-12!71;UBERON:0003077!5.27e-12!72;UBERON:0007285!5.27e-12!72;UBERON:0005423!1.75e-11!581;UBERON:0005256!2.49e-11!122;UBERON:0007503!2.70e-11!78;UBERON:0000922!2.67e-10!592;UBERON:0000947!1.92e-08!21;UBERON:0010191!1.92e-08!21;UBERON:0000479!4.00e-08!773;UBERON:0003104!1.07e-07!160;UBERON:0009142!1.07e-07!160;UBERON:0004638!7.48e-07!18;UBERON:0001986!7.48e-07!18;UBERON:0004852!7.48e-07!18
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280763187383435!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764281260476262!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109011565114893!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329356908552315!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010984527830586
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280763187383435!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00764281260476262!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109011565114893!TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329356908552315!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010984527830586
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6475,0.0558058,0.0443426,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,2.25098e-05,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,6.05949e-07,0.167267,0.140622,0.0889592,0.00643528,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.000821167,0.21727,0.00514993,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.392974,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.0163112,0.696435,0.00739585,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.00020908,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.0119616,0.0973823,0.15503,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.00806892,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.00109188,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.00935312,0.418146,0.36927,0.449036,0.407369,0.231447,0.00858901,0.43956,0.37006,0.42622,0.120472,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.0863135,0.432035,0.138468,0.390366,0.48809,0.153829,0.443185,0.522904,0.0608227,0.336835,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.04783,0.144318,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.442897,0.390974,0.73485,0.109758,0.161598,0.751174,0.644754,0.496032,0.799185,0.37357,0.78509,0.138234,0.78384,0.746954,0.771991,1.45055e-10,0.200493,0.20558,0.00583368,0.25656,0.425963,0.00960524,0.0851996,0.156104,0.141318,0.000226517,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.0674279,0.24884,0.408413,0.516511,0.322213,0.28903,0.00873429,0.61031,0.0871388,0.522605,0.802166,0.180745,0.222037,0.102227,0.416292,0.0252635,0.148994,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.178743,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.0223007,0.351067,0.275347,0.269604,0.0524515,0.241132,0.371414,0.30666,0.303709,0.495883,0.0135408,9.6746e-06,0.250964,0.383276,0.000432158,0.504711,0.220231,0.159791,0.196976,0.191517,0.463751,0.0663581,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.0114705,0.0418805,0.384593,0.138622,0.359231,0.339729,0.197805,0.0690807,0.387069,0.332774,0.0406989,0.0502872,0.634365,0.205413,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.0211771,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.0279371,0.27872,0.0855609,0.131118,0.20837,0.0335483,0.222339,0.00231953,0.20847,0.266544,0.0066506,0.0111711,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.00632223,0.180606,0.159884,0.00351525,0.150733,0.0254879,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.0022686,0.246105,0.173026,0.200432,0.0102599,0.0208458,0.240478,0.0129343,0.13108,0.00350063,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.00345643,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.0607319,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.04045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}}
}}

Revision as of 15:57, 19 October 2012


Full id: C4429_Adipocyte_Preadipocyte_neuroblastoma_Smooth_Fibroblast_Mesenchymal_mesenchymal



Phase1 CAGE Peaks

Hg19::chr4:80993800..80993850,-p5@ANTXR2
Hg19::chr4:80993855..80993906,-p3@ANTXR2
Hg19::chr4:80993925..80993962,-p4@ANTXR2


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
mesoderm3.21e-22315
mesoderm-derived structure3.21e-22315
presumptive mesoderm3.21e-22315
splanchnic layer of lateral plate mesoderm3.61e-2083
vasculature2.92e-1878
vascular system2.92e-1878
epithelial tube open at both ends3.02e-1859
blood vessel3.02e-1859
blood vasculature3.02e-1859
vascular cord3.02e-1859
vessel4.97e-1868
multi-cellular organism3.87e-16656
cardiovascular system1.36e-15109
circulatory system1.42e-15112
artery1.58e-1542
arterial blood vessel1.58e-1542
arterial system1.58e-1542
anatomical system4.47e-15624
epithelial tube8.14e-15117
anatomical group9.96e-15625
embryonic structure1.43e-13564
unilaminar epithelium2.25e-13148
muscle tissue3.16e-1364
musculature3.16e-1364
musculature of body3.16e-1364
musculoskeletal system6.13e-13167
germ layer6.46e-13560
germ layer / neural crest6.46e-13560
embryonic tissue6.46e-13560
presumptive structure6.46e-13560
germ layer / neural crest derived structure6.46e-13560
epiblast (generic)6.46e-13560
systemic artery8.77e-1333
systemic arterial system8.77e-1333
skeletal muscle tissue1.45e-1262
striated muscle tissue1.45e-1262
myotome1.45e-1262
multilaminar epithelium1.53e-1283
lateral plate mesoderm2.05e-12203
dense mesenchyme tissue3.04e-1273
somite3.57e-1271
presomitic mesoderm3.57e-1271
presumptive segmental plate3.57e-1271
dermomyotome3.57e-1271
trunk paraxial mesoderm3.57e-1271
paraxial mesoderm5.27e-1272
presumptive paraxial mesoderm5.27e-1272
developing anatomical structure1.75e-11581
trunk mesenchyme2.49e-11122
epithelial vesicle2.70e-1178
embryo2.67e-10592
aorta1.92e-0821
aortic system1.92e-0821
tissue4.00e-08773
mesenchyme1.07e-07160
entire embryonic mesenchyme1.07e-07160
blood vessel endothelium7.48e-0718
endothelium7.48e-0718
cardiovascular system endothelium7.48e-0718
Disease
Ontology termp-valuen
ovarian cancer1.77e-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
CTCF#1066435.360256373075030.0064925092527670.0280763187383435
ETS1#211339.728760922202340.001085840092584840.00764281260476262
HMGN3#932438.178547723350590.001827766942164210.0109011565114893
TRIM28#10155212.39368336350830.008368344129438470.0329356908552315
ZNF263#1012738.221841637010680.001799043925565870.010984527830586



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4429&oldid=2250759"