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Coexpression cluster:C3150: Difference between revisions

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|full_id=C3150_mesenchymal_Smooth_Mesenchymal_Fibroblast_Prostate_Anulus_Trabecular
|full_id=C3150_mesenchymal_Smooth_Mesenchymal_Fibroblast_Prostate_Anulus_Trabecular
|id=C3150
|id=C3150
|ontology_enrichment_celltype=CL:0000055!5.76e-37!180;CL:0000057!5.49e-26!75;CL:0000680!1.39e-17!57;CL:0000056!1.39e-17!57;CL:0000355!1.39e-17!57;CL:0000187!2.98e-17!54;CL:0000183!4.38e-17!59;CL:0000393!2.57e-15!60;CL:0000211!2.57e-15!60;CL:0000192!1.11e-13!42;CL:0000514!1.11e-13!42;CL:0002620!1.62e-09!23;CL:0000359!3.37e-09!32;CL:0002334!1.01e-07!12;CL:0002494!1.78e-07!16
|ontology_enrichment_celltype=CL:0000057!2.57e-26!76;CL:0000680!1.47e-16!58;CL:0000056!1.47e-16!58;CL:0000355!1.47e-16!58;CL:0000187!5.36e-16!55;CL:0000183!1.16e-15!59;CL:0000192!3.01e-13!43;CL:0000514!3.01e-13!43;CL:0000393!5.50e-13!61;CL:0000211!5.50e-13!61;CL:0000055!2.12e-10!106;CL:0000359!4.97e-09!32;CL:0002620!1.28e-08!23;CL:0002334!3.09e-08!12;CL:0002494!4.28e-08!16;CL:0002539!9.94e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!5.60e-25!365;UBERON:0000914!4.75e-24!83;UBERON:0002329!4.75e-24!83;UBERON:0003077!4.75e-24!83;UBERON:0003059!4.75e-24!83;UBERON:0007282!4.75e-24!83;UBERON:0009618!4.75e-24!83;UBERON:0007285!4.75e-24!83;UBERON:0004290!3.10e-20!70;UBERON:0000481!9.57e-20!347;UBERON:0000486!2.48e-18!82;UBERON:0002385!1.12e-17!63;UBERON:0001015!1.12e-17!63;UBERON:0000383!1.12e-17!63;UBERON:0001134!1.56e-17!61;UBERON:0002036!1.56e-17!61;UBERON:0003082!1.56e-17!61;UBERON:0000119!1.41e-16!312;UBERON:0000483!1.00e-15!309;UBERON:0000468!8.27e-15!659;UBERON:0005256!9.85e-15!143;UBERON:0000033!2.73e-12!123;UBERON:0003102!3.95e-12!95;UBERON:0000477!5.23e-12!286;UBERON:0000153!8.80e-12!129;UBERON:0007811!8.80e-12!129;UBERON:0000467!7.32e-11!625;UBERON:0000480!1.16e-10!626;UBERON:0004111!3.73e-10!241;UBERON:0002616!6.17e-10!59;UBERON:0003075!7.00e-10!86;UBERON:0007284!7.00e-10!86;UBERON:0004121!2.07e-09!169;UBERON:0007023!3.24e-09!115;UBERON:0002100!3.36e-09!216;UBERON:0002346!4.04e-09!90;UBERON:0001049!4.28e-09!57;UBERON:0005068!4.28e-09!57;UBERON:0006241!4.28e-09!57;UBERON:0007135!4.28e-09!57;UBERON:0007100!5.01e-09!27;UBERON:0000948!5.84e-09!24;UBERON:0005498!5.84e-09!24;UBERON:0004140!5.84e-09!24;UBERON:0009881!5.84e-09!24;UBERON:0004141!5.84e-09!24;UBERON:0003084!5.84e-09!24;UBERON:0007005!5.84e-09!24;UBERON:0004139!5.84e-09!24;UBERON:0004291!5.84e-09!24;UBERON:0000924!6.03e-09!173;UBERON:0006601!6.03e-09!173;UBERON:0000922!8.80e-09!612;UBERON:0002050!4.95e-08!605;UBERON:0005423!4.95e-08!605;UBERON:0000025!5.51e-08!194;UBERON:0000479!6.38e-08!787;UBERON:0000955!7.06e-08!69;UBERON:0006238!7.06e-08!69;UBERON:0000923!8.96e-08!604;UBERON:0005291!8.96e-08!604;UBERON:0006598!8.96e-08!604;UBERON:0002532!8.96e-08!604;UBERON:0004872!1.30e-07!84;UBERON:0001017!1.70e-07!82;UBERON:0005743!2.48e-07!86;UBERON:0000490!2.76e-07!138;UBERON:0000062!3.29e-07!511;UBERON:0003056!3.49e-07!61;UBERON:0002199!4.18e-07!45;UBERON:0002416!4.18e-07!45;UBERON:0001135!6.71e-07!15
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7897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.166024,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.0178982,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.019326,0.131088,0.394069,9.66202e-06,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.288159,0.0255266,0.0465945,0.119215,0.192475,0.0168693,0.547859,0.057571,0.00115086,0.392974,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.145116,0.206454,0.000125718,0.00608582,0.0673484,0.108748,0.0494066,0.00474777,0.0227848,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.00148023,0.00678942,0.0929549,0.172425,0.104948,0.221645,0.057168,0.0298844,0.0759837,0.286863,0.0122477,0.194941,0.0257725,0.101607,0.060512,0.172982,0.0661495,0.151597,0.0626744,0.191335,0.0116284,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.0282663,0.0346616,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.00464715,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.0190329,0.0813902,0.184948,0.156261,0.311847,0.161789,0.0590944,0.247324,0.178389,0.0020701,0.231073,0.407281,0.619906,0.0360851,0.0998546,0.131093,0.0434602,0.00935312,0.418146,0.36927,0.449036,0.0973145,0.231447,0.18653,0.115047,0.37006,0.00255501,0.448797,0.197484,0.0919774,0.0750251,0.00202987,0.0129,0.057779,0.00417723,0.11074,0.0411943,0.390366,0.48809,0.153829,0.443185,0.169835,0.875915,0.871256,0.227104,0.518585,0.617852,0.0867545,0.284625,0.156746,0.04783,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.0642229,0.132529,0.258219,0.119142,0.243383,0.0659137,0.390974,0.382874,0.319063,0.161598,0.751174,0.0868402,0.0323708,0.799185,0.37357,0.0704414,0.477353,0.78384,0.746954,0.771991,9.29919e-05,0.200493,0.0227499,0.300504,0.25656,0.107337,0.349197,0.383291,0.0128729,0.141318,0.00217346,0.0961477,0.055627,0.354789,0.163828,0.0289012,0.120226,0.28424,0.562405,0.0556238,0.0175523,0.0442318,0.000976922,0.616388,0.408413,0.000926901,0.0586066,0.28903,0.33942,0.243065,0.387276,0.0391112,0.802166,0.0433137,0.222037,0.416621,0.416292,0.00379537,0.0457685,0.215157,0.204817,0.452428,0.0101228,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.0628556,0.0120568,0.523625,0.0980968,0.365487,0.534741,0.39088,0.0758087,0.0303438,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.019895,0.305885,0.0317395,0.0795725,0.30666,0.0516603,0.495883,0.0867777,0.159081,0.250964,0.383276,0.00360665,0.156714,0.220231,0.0355483,0.196976,0.191517,0.463751,0.000387553,0.307334,0.0246928,0.283463,0.201728,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.00444763,0.0105648,0.339729,0.197805,0.00278185,0.387069,0.332774,0.173874,0.299887,0.266492,0.205413,0.17639,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,0.0269454,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.000145586,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.0251995,0.158479,0.0262794,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.036274,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.0056723,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.0457063,0.347036,0.141729,0.0381402,0.255956,0.200105,0.0280973,0.29837,0.253509,0.0168099,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.00480369,0.0032012,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0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}}
}}

Revision as of 14:50, 19 October 2012


Full id: C3150_mesenchymal_Smooth_Mesenchymal_Fibroblast_Prostate_Anulus_Trabecular



Phase1 CAGE Peaks

Hg19::chr11:35547154..35547191,-p1@PAMR1
Hg19::chr11:35547277..35547288,-p2@PAMR1
Hg19::chr11:35547572..35547588,-p3@PAMR1


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>

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest2.47e-17132
dense mesenchyme tissue6.26e-1773
paraxial mesoderm6.45e-1772
presumptive paraxial mesoderm6.45e-1772
somite1.30e-1671
presomitic mesoderm1.30e-1671
presumptive segmental plate1.30e-1671
dermomyotome1.30e-1671
trunk paraxial mesoderm1.30e-1671
muscle tissue6.84e-1664
musculature6.84e-1664
musculature of body6.84e-1664
skeletal muscle tissue9.17e-1662
striated muscle tissue9.17e-1662
myotome9.17e-1662
multi-tissue structure1.49e-15342
multilaminar epithelium1.51e-1383
epithelial vesicle1.53e-1378
cell layer2.31e-13309
epithelium8.53e-13306
trunk mesenchyme2.52e-11122
multi-cellular organism4.09e-11656
surface structure6.31e-1199
adult organism8.42e-11114
neural tube2.22e-1056
neural rod2.22e-1056
future spinal cord2.22e-1056
neural keel2.22e-1056
neural plate2.42e-1082
presumptive neural plate2.42e-1082
anatomical conduit4.19e-10240
neurectoderm9.65e-1086
anatomical cluster1.70e-09373
mesenchyme2.94e-09160
entire embryonic mesenchyme2.94e-09160
regional part of nervous system3.57e-0953
regional part of brain3.57e-0953
heart3.69e-0924
primitive heart tube3.69e-0924
primary heart field3.69e-0924
anterior lateral plate mesoderm3.69e-0924
heart tube3.69e-0924
heart primordium3.69e-0924
cardiac mesoderm3.69e-0924
cardiogenic plate3.69e-0924
heart rudiment3.69e-0924
anatomical system8.10e-09624
tissue8.99e-09773
primary circulatory organ1.06e-0827
anatomical group1.12e-08625
ecto-epithelium1.45e-08104
brain2.43e-0868
future brain2.43e-0868
ectoderm-derived structure6.46e-08171
ectoderm6.46e-08171
presumptive ectoderm6.46e-08171
smooth muscle tissue7.26e-0815
tube7.64e-08192
regional part of forebrain2.22e-0741
forebrain2.22e-0741
anterior neural tube2.22e-0741
future forebrain2.22e-0741
embryonic structure2.24e-07564
systemic artery3.18e-0733
systemic arterial system3.18e-0733
organism subdivision3.70e-07264
central nervous system4.40e-0781
splanchnic layer of lateral plate mesoderm4.47e-0783
germ layer5.21e-07560
germ layer / neural crest5.21e-07560
embryonic tissue5.21e-07560
presumptive structure5.21e-07560
germ layer / neural crest derived structure5.21e-07560
epiblast (generic)5.21e-07560
brain grey matter6.74e-0734
gray matter6.74e-0734
unilaminar epithelium7.57e-07148
telencephalon8.44e-0734
blood vessel smooth muscle9.94e-0710
arterial system smooth muscle9.94e-0710
artery smooth muscle tissue9.94e-0710
aorta smooth muscle tissue9.94e-0710


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

No analysis results for this cluster

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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