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Coexpression cluster:C4793: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281649501079848
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281649501079848
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897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.000234172,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.0254773,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.120459,0.051838,0.0993999,0.0500365,4.13072e-05,7.60655e-05,0.0936516,0.144075,0.0340203,7.20365e-05,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,4.93279e-05,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0987169,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.114242,0.0929549,0.000980951,0.104948,0.221645,0.00166615,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.101607,0.327067,0.172982,0.0661495,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,8.52865e-08,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.0227305,0.407369,0.231447,0.00858901,0.115047,5.96881e-07,0.42622,0.448797,0.00150618,0.396996,0.36145,0.406019,0.381071,0.580441,0.643768,0.432035,0.722159,0.0886602,0.48809,0.50058,0.0217093,0.522904,0.3468,0.871256,3.8272e-10,0.0380245,0.0167433,0.38649,0.284625,0.156746,0.192225,0.0108655,0.0465139,0.164197,0.462688,0.00506733,0.574635,0.478174,0.0642229,0.0263888,0.258219,0.446557,0.00293755,0.00448654,0.390974,0.0458848,0.00650842,0.161598,0.0527155,0.644754,0.496032,0.0239796,0.37357,0.00500957,0.477353,0.199161,0.0132585,0.0629574,0.00165472,0.200493,1.69499e-07,0.0505073,0.25656,0.425963,0.0696455,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.000835245,3.60015e-07,0.120226,0.000399377,0.562405,0.314429,0.181415,0.00475227,0.194707,0.616388,0.0978616,0.516511,0.0586066,0.656109,0.00873429,0.61031,0.0136291,0.522605,0.802166,0.00120002,0.222037,0.102227,1.08601e-07,0.462712,0.148994,0.579431,0.204817,0.452428,0.138871,0.103502,0.166905,8.25294e-05,0.0833851,0.316453,0.140384,0.175199,0.0628556,0.373557,0.523625,0.408861,0.365487,0.0425451,0.39088,0.363192,0.0303438,0.203486,0.273398,0.0816179,0.4466,0.00977892,0.275347,0.637444,0.305885,0.241132,0.371414,0.0527347,0.303709,0.0323359,0.0135408,0.508064,0.250964,0.383276,0.457886,0.504711,0.00213139,0.509064,0.196976,0.191517,0.463751,0.0145214,0.307334,0.459728,0.283463,0.201728,0.00422311,0.0151656,0.273281,0.368095,0.275089,0.0858306,0.47795,0.0740334,0.0656472,0.197805,0.24107,0.0136044,4.31449e-06,0.52832,0.00579439,8.64162e-05,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.036838,0.188263,0.0719199,0.00386277,0.0139948,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.0348699,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.00899848,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,9.78978e-06,0.0660995,0.0521984,1.63098e-05,0.00404853,0.201602,0.350452,0.0126763,0.120196,0.0986735,0.00610703,0.0595618,0.21593,0.0132793,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.0119784,0.217112,0.00801612,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.00316602,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.00106131,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.00497886,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.00866687,0.109171,0.04411,0.066952,0.089609,8.50334e-06,0.13497,0.204393,0.295769,0.286691,0.347036,0.0105548,0.0381402,0.255956,0.0215087,0.00236454,0.29837,0.253509,0.177664,0.00482769,0.0385243,0.131761,0.160658,0.00172878,0.19924,0.28689,0.236464,0.325148,0.00698179,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,0.641468,0.853988,0.937929,1.23863,0.491742,0.221898,0.820209,2.25583,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.461452,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,2.71743,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,1.68795,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.553386,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232
}}
}}

Revision as of 16:58, 26 November 2012


Full id: C4793_Fibroblast_Hair_Skeletal_mesodermal_Preadipocyte_neuroectodermal_Pancreatic



Phase1 CAGE Peaks

Hg19::chr9:118358874..118358932,+p@chr9:118358874..118358932
+
Hg19::chr9:118358945..118358954,+p@chr9:118358945..118358954
+
Hg19::chr9:118358956..118358970,+p@chr9:118358956..118358970
+


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
somite4.58e-2671
presomitic mesoderm4.58e-2671
presumptive segmental plate4.58e-2671
dermomyotome4.58e-2671
trunk paraxial mesoderm4.58e-2671
paraxial mesoderm2.02e-2572
presumptive paraxial mesoderm2.02e-2572
dense mesenchyme tissue8.52e-2573
epithelial vesicle8.58e-2378
multilaminar epithelium1.98e-2183
skeletal muscle tissue2.15e-2162
striated muscle tissue2.15e-2162
myotome2.15e-2162
muscle tissue3.40e-2064
musculature3.40e-2064
musculature of body3.40e-2064
skin of body3.31e-1441
integument1.77e-1346
integumental system1.77e-1346
artery1.70e-1242
arterial blood vessel1.70e-1242
arterial system1.70e-1242
trunk mesenchyme1.18e-11122
systemic artery1.43e-1033
systemic arterial system1.43e-1033
cardiovascular system6.37e-10109
splanchnic layer of lateral plate mesoderm1.32e-0983
unilaminar epithelium2.06e-09148
vasculature2.32e-0978
vascular system2.32e-0978
circulatory system2.99e-09112
mesenchyme3.25e-08160
entire embryonic mesenchyme3.25e-08160
heart8.84e-0824
primitive heart tube8.84e-0824
primary heart field8.84e-0824
anterior lateral plate mesoderm8.84e-0824
heart tube8.84e-0824
heart primordium8.84e-0824
cardiac mesoderm8.84e-0824
cardiogenic plate8.84e-0824
heart rudiment8.84e-0824
surface structure9.08e-0899
blood vessel smooth muscle1.11e-0710
arterial system smooth muscle1.11e-0710
artery smooth muscle tissue1.11e-0710
aorta smooth muscle tissue1.11e-0710
epithelial tube open at both ends2.22e-0759
blood vessel2.22e-0759
blood vasculature2.22e-0759
vascular cord2.22e-0759
organism subdivision6.11e-07264
smooth muscle tissue6.91e-0715
trunk9.62e-07199
Disease
Ontology termp-valuen
ovarian cancer3.73e-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#1066435.360256373075030.0064925092527670.0281649501079848



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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