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Coexpression cluster:C3843: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!1.97e-17!143;DOID:305!5.98e-16!106;DOID:299!1.36e-07!25;DOID:0050615!2.84e-07!16
|ontology_enrichment_disease=DOID:0050687!1.97e-17!143;DOID:305!5.98e-16!106;DOID:299!1.36e-07!25;DOID:0050615!2.84e-07!16
|ontology_enrichment_uberon=UBERON:0004119!9.00e-15!169;UBERON:0000925!9.00e-15!169;UBERON:0006595!9.00e-15!169;UBERON:0004921!5.81e-13!129;UBERON:0004185!5.81e-13!129;UBERON:0001007!8.77e-13!155;UBERON:0001555!8.77e-13!155;UBERON:0007026!8.77e-13!155;UBERON:0000468!1.18e-11!659;UBERON:0001004!7.09e-11!72;UBERON:0000464!1.08e-10!104;UBERON:0005157!1.89e-10!51;UBERON:0005153!3.23e-10!37;UBERON:0000481!3.71e-10!347;UBERON:0000077!8.00e-10!130;UBERON:0000922!9.32e-10!612;UBERON:0000466!1.11e-09!126;UBERON:0005177!1.29e-09!107;UBERON:0005181!1.84e-09!35;UBERON:0007023!3.64e-09!115;UBERON:0002048!4.13e-09!22;UBERON:0000117!4.13e-09!22;UBERON:0000171!4.13e-09!22;UBERON:0000170!4.13e-09!22;UBERON:0005597!4.13e-09!22;UBERON:0000118!4.13e-09!22;UBERON:0000475!4.54e-09!365;UBERON:0000467!4.72e-09!625;UBERON:0000480!6.74e-09!626;UBERON:0005178!7.26e-09!34;UBERON:0002224!7.26e-09!34;UBERON:0001041!1.28e-08!98;UBERON:0000062!2.25e-08!511;UBERON:0002050!4.55e-08!605;UBERON:0005423!4.55e-08!605;UBERON:0005911!5.05e-08!82;UBERON:0003104!5.16e-08!238;UBERON:0009142!5.16e-08!238;UBERON:0000923!8.07e-08!604;UBERON:0005291!8.07e-08!604;UBERON:0006598!8.07e-08!604;UBERON:0002532!8.07e-08!604;UBERON:0001008!1.11e-07!45;UBERON:0004802!1.32e-07!19;UBERON:0000115!1.32e-07!19;UBERON:0000483!2.88e-07!309;UBERON:0006554!2.97e-07!44;UBERON:0009569!3.37e-07!113;UBERON:0000161!3.61e-07!35;UBERON:0000065!4.02e-07!53;UBERON:0000924!4.98e-07!173;UBERON:0006601!4.98e-07!173;UBERON:0000119!5.37e-07!312
|ontology_enrichment_uberon=UBERON:0004119!9.00e-15!169;UBERON:0000925!9.00e-15!169;UBERON:0006595!9.00e-15!169;UBERON:0004921!5.81e-13!129;UBERON:0004185!5.81e-13!129;UBERON:0001007!8.77e-13!155;UBERON:0001555!8.77e-13!155;UBERON:0007026!8.77e-13!155;UBERON:0000468!1.18e-11!659;UBERON:0001004!7.09e-11!72;UBERON:0000464!1.08e-10!104;UBERON:0005157!1.89e-10!51;UBERON:0005153!3.23e-10!37;UBERON:0000481!3.71e-10!347;UBERON:0000077!8.00e-10!130;UBERON:0000922!9.32e-10!612;UBERON:0000466!1.11e-09!126;UBERON:0005177!1.29e-09!107;UBERON:0005181!1.84e-09!35;UBERON:0007023!3.64e-09!115;UBERON:0002048!4.13e-09!22;UBERON:0000117!4.13e-09!22;UBERON:0000171!4.13e-09!22;UBERON:0000170!4.13e-09!22;UBERON:0005597!4.13e-09!22;UBERON:0000118!4.13e-09!22;UBERON:0000475!4.54e-09!365;UBERON:0000467!4.72e-09!625;UBERON:0000480!6.74e-09!626;UBERON:0005178!7.26e-09!34;UBERON:0002224!7.26e-09!34;UBERON:0001041!1.28e-08!98;UBERON:0000062!2.25e-08!511;UBERON:0002050!4.55e-08!605;UBERON:0005423!4.55e-08!605;UBERON:0005911!5.05e-08!82;UBERON:0003104!5.16e-08!238;UBERON:0009142!5.16e-08!238;UBERON:0000923!8.07e-08!604;UBERON:0005291!8.07e-08!604;UBERON:0006598!8.07e-08!604;UBERON:0002532!8.07e-08!604;UBERON:0001008!1.11e-07!45;UBERON:0004802!1.32e-07!19;UBERON:0000115!1.32e-07!19;UBERON:0000483!2.88e-07!309;UBERON:0006554!2.97e-07!44;UBERON:0009569!3.37e-07!113;UBERON:0000161!3.61e-07!35;UBERON:0000065!4.02e-07!53;UBERON:0000924!4.98e-07!173;UBERON:0006601!4.98e-07!173;UBERON:0000119!5.37e-07!312
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141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,9.0044e-05,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,8.35469e-08,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.0199999,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.0791124,0.0330727,0.348757,6.34879e-06,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.00370214,0.0286025,2.02725e-05,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.00012295,0.00133367,0.00899422,0.090504,0.0027004,0.286988,0.0761239,0.000982125,0.0818785,0.182701,0.000835367,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.00502301,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.00681584,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.00452901,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,1.40366e-05,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.226002,6.6291e-06,0.00173453,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,1.64204e-07,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.0122477,0.194941,0.218271,0.000189228,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.0126914,0.170295,0.193653,0.000479913,0.228144,0.0346616,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.00020131,0.113069,0.025556,1.50087e-06,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0062542,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0161946,0.619906,0.0360851,0.412187,0.00899487,1.41419e-05,0.133616,0.418146,0.0785808,0.449036,0.407369,0.231447,0.0455669,0.43956,0.37006,0.10748,0.448797,0.197484,0.396996,0.0107863,0.406019,0.0129,0.057779,0.0210246,5.53622e-10,0.00207232,0.390366,6.6846e-06,0.0334527,0.443185,0.522904,0.3468,0.0184337,0.227104,0.00667974,0.617852,0.38649,0.284625,0.000799065,0.55194,0.729153,0.28907,0.164197,0.128922,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.442897,0.390974,0.73485,0.029557,0.000800088,0.751174,0.277094,0.0323708,0.799185,0.37357,0.454657,0.0282154,0.199161,0.746954,0.000852086,0.20342,0.200493,0.20558,0.300504,7.31928e-07,0.425963,0.349197,0.383291,0.156104,0.0104921,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.00475227,0.0674279,7.55159e-06,0.408413,0.165147,0.322213,0.656109,0.0655189,0.243065,0.387276,0.522605,7.95705e-06,0.537348,0.222037,0.416621,0.416292,0.462712,0.734551,0.579431,0.204817,0.452428,0.138871,0.00105709,0.166905,0.19783,0.0833851,0.056391,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.0768488,0.534741,0.000165487,0.363192,0.236011,0.203486,0.273398,0.0123025,0.119167,0.351067,0.275347,0.019895,0.00618487,0.241132,0.00133934,4.05192e-05,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.457886,0.504711,0.00213139,0.159791,0.196976,0.00136659,0.463751,0.0663581,0.307334,0.459728,0.283463,0.0517073,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.138622,0.0105648,0.339729,0.197805,0.0690807,0.387069,0.332774,0.52832,0.299887,0.634365,9.6965e-05,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.0140817,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.0232009,0.447185,0.179412,0.0200828,0.220904,0.222977,0.000913176,0.310674,0.21801,2.88804e-12,2.67737e-09,0.000344402,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,6.58743e-10,0.131118,0.20837,0.00310436,0.00219731,0.0673329,0.00178902,0.266544,0.0066506,0.145701,0.229428,0.162145,3.43584e-07,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.0370716,4.14805e-05,5.59615e-05,0.159884,0.257294,0.0119784,0.0254879,0.123917,0.184317,0.0183464,0.0723291,0.0367308,0.261744,0.0223377,0.00193951,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.00149718,0.240478,0.156465,0.13108,0.256963,0.000137586,0.0157468,0.176789,0.00485777,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.00717361,0.261724,0.211332,0.187731,0.0025753,0.0192232,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.000785583,0.206239,0.021315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}}
}}

Revision as of 11:53, 5 September 2012


Full id: C3843_merkel_pineal_small_heart_maxillary_skeletal_salivary



Phase1 CAGE Peaks

Hg19::chr1:10856639..10856662,-p2@CASZ1
Hg19::chr1:10856665..10856683,-p4@CASZ1
Hg19::chr1:10856694..10856715,-p3@CASZ1


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
epithelial cell4.20e-21254
endo-epithelial cell2.01e-1343
endodermal cell8.63e-1159
epithelial cell of lung1.32e-0719
epithelial cell of alimentary canal5.24e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.00e-15169
endoderm9.00e-15169
presumptive endoderm9.00e-15169
subdivision of digestive tract5.81e-13129
endodermal part of digestive tract5.81e-13129
digestive system8.77e-13155
digestive tract8.77e-13155
primitive gut8.77e-13155
multi-cellular organism1.18e-11659
respiratory system7.09e-1172
anatomical space1.08e-10104
epithelial fold1.89e-1051
epithelial bud3.23e-1037
multi-tissue structure3.71e-10347
mixed endoderm/mesoderm-derived structure8.00e-10130
embryo9.32e-10612
immaterial anatomical entity1.11e-09126
trunk region element1.29e-09107
thoracic segment organ1.84e-0935
adult organism3.64e-09115
lung4.13e-0922
respiratory tube4.13e-0922
respiration organ4.13e-0922
pair of lungs4.13e-0922
lung primordium4.13e-0922
lung bud4.13e-0922
organism subdivision4.54e-09365
anatomical system4.72e-09625
anatomical group6.74e-09626
thoracic cavity element7.26e-0934
thoracic cavity7.26e-0934
foregut1.28e-0898
organ2.25e-08511
embryonic structure4.55e-08605
developing anatomical structure4.55e-08605
endo-epithelium5.05e-0882
mesenchyme5.16e-08238
entire embryonic mesenchyme5.16e-08238
germ layer8.07e-08604
embryonic tissue8.07e-08604
presumptive structure8.07e-08604
epiblast (generic)8.07e-08604
renal system1.11e-0745
respiratory tract epithelium1.32e-0719
lung epithelium1.32e-0719
epithelium2.88e-07309
urinary system structure2.97e-0744
subdivision of trunk3.37e-07113
orifice3.61e-0735
respiratory tract4.02e-0753
ectoderm4.98e-07173
presumptive ectoderm4.98e-07173
cell layer5.37e-07312
Disease
Ontology termp-valuen
cell type cancer1.97e-17143
carcinoma5.98e-16106
adenocarcinoma1.36e-0725
respiratory system cancer2.84e-0716


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-060.00012973408357355
EGR1#195834.988179094810140.008056488137383440.0320672115774301
EP300#203336.77394172622320.003216880500103790.0167456403603818
GABPB1#255337.067683836182170.002832212825417420.0154131350775765
GATA3#2625327.2365163572064.94721007899563e-050.00085106518438515
JUND#372736.994663941871030.002921845042734990.0156787018660124
NRF1#4899312.21027944771090.0005492172401020010.00471204299178616
RAD21#5885310.35503389545630.0009004912073565420.00664122598722617
RFX5#5993312.04791082719510.0005717246050312580.00484543909963966
SP1#666735.69838137814090.005403962701712170.0246531455293809
TCF7L2#6934310.77017656313730.0008003181298398380.00613824081386083
YY1#752834.911170749853860.008441455341808260.0329441035253956



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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