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Coexpression cluster:C2546: Difference between revisions

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|full_id=C2546_neuroectodermal_neuroblastoma_granulosa_peripheral_Cardiac_Fibroblast_aorta
|full_id=C2546_neuroectodermal_neuroblastoma_granulosa_peripheral_Cardiac_Fibroblast_aorta
|id=C2546
|id=C2546
|ontology_enrichment_celltype=CL:0000055!2.11e-22!180;CL:0000057!8.96e-11!75;CL:0002494!3.34e-08!16;CL:0002620!5.59e-07!23;CL:0000187!7.29e-07!54;CL:0000393!7.66e-07!60;CL:0000211!7.66e-07!60
|ontology_enrichment_celltype=CL:0000055!7.49e-10!106;CL:0000057!1.10e-09!76;CL:0002494!2.52e-08!16;CL:0002620!2.97e-07!23;CL:0000187!5.93e-07!55
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!2.20e-15!84;UBERON:0000468!4.45e-14!659;UBERON:0007100!1.87e-12!27;UBERON:0001009!7.01e-12!113;UBERON:0000948!8.67e-12!24;UBERON:0005498!8.67e-12!24;UBERON:0004140!8.67e-12!24;UBERON:0009881!8.67e-12!24;UBERON:0004141!8.67e-12!24;UBERON:0003084!8.67e-12!24;UBERON:0007005!8.67e-12!24;UBERON:0004139!8.67e-12!24;UBERON:0004291!8.67e-12!24;UBERON:0004535!3.36e-11!110;UBERON:0000475!5.30e-11!365;UBERON:0002049!1.93e-09!79;UBERON:0007798!1.93e-09!79;UBERON:0001981!2.55e-09!60;UBERON:0007500!2.55e-09!60;UBERON:0004537!2.55e-09!60;UBERON:0006965!2.55e-09!60;UBERON:0001637!7.72e-09!42;UBERON:0003509!7.72e-09!42;UBERON:0004572!7.72e-09!42;UBERON:0000055!2.50e-08!69;UBERON:0004290!1.32e-07!70;UBERON:0000467!2.09e-07!625;UBERON:0000480!3.06e-07!626;UBERON:0003914!3.33e-07!118;UBERON:0000481!3.35e-07!347;UBERON:0002385!3.61e-07!63;UBERON:0001015!3.61e-07!63;UBERON:0000383!3.61e-07!63;UBERON:0000119!3.72e-07!312;UBERON:0000483!4.45e-07!309;UBERON:0004111!4.57e-07!241;UBERON:0000025!5.91e-07!194;UBERON:0001134!7.12e-07!61;UBERON:0002036!7.12e-07!61;UBERON:0003082!7.12e-07!61;UBERON:0004573!9.63e-07!33;UBERON:0004571!9.63e-07!33
|ontology_enrichment_uberon=UBERON:0004872!2.54e-15!83;UBERON:0007100!3.30e-13!27;UBERON:0000948!2.86e-12!24;UBERON:0005498!2.86e-12!24;UBERON:0004140!2.86e-12!24;UBERON:0009881!2.86e-12!24;UBERON:0004141!2.86e-12!24;UBERON:0003084!2.86e-12!24;UBERON:0007005!2.86e-12!24;UBERON:0004139!2.86e-12!24;UBERON:0004291!2.86e-12!24;UBERON:0001009!5.00e-12!112;UBERON:0004535!3.31e-11!109;UBERON:0000468!1.34e-10!656;UBERON:0001637!1.21e-08!42;UBERON:0003509!1.21e-08!42;UBERON:0004572!1.21e-08!42;UBERON:0007500!1.64e-08!59;UBERON:0001981!1.64e-08!59;UBERON:0004537!1.64e-08!59;UBERON:0006965!1.64e-08!59;UBERON:0002049!5.27e-08!78;UBERON:0007798!5.27e-08!78;UBERON:0002329!3.65e-07!71;UBERON:0003059!3.65e-07!71;UBERON:0007282!3.65e-07!71;UBERON:0004290!3.65e-07!71;UBERON:0009618!3.65e-07!71;UBERON:0002385!4.43e-07!64;UBERON:0001015!4.43e-07!64;UBERON:0000383!4.43e-07!64;UBERON:0007524!4.81e-07!73;UBERON:0000055!6.07e-07!68;UBERON:0003077!7.13e-07!72;UBERON:0007285!7.13e-07!72;UBERON:0001134!8.34e-07!62;UBERON:0002036!8.34e-07!62;UBERON:0003082!8.34e-07!62
|tf_chipseq_enrich=FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353462936496968
|tf_chipseq_enrich=FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353462936496968
|tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.0110447,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.0394878,0.0877018,0.111013,0.204768,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.0111479,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.0412226,0.103044,0.138225,0.0390464,0.194086,0.0106139,0.0999599,0.0720888,0.0667453,0.115055,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.0071179,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.0118782,0.0780785,0.0580589,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.690341,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.00101648,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.0037673,0.0730922,0.0438087,0.0052702,0.0302521,0.0146861,0.262198,0.202388,0.701894,0.0913381,0.00877859,0.00636631,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.0473319,0.124982,0.000666124,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.0300065,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.00794845,0.0687034,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.0144563,0.180711,0.112956,0.0797807,0.0790532,0.309911,0.137848,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.0123368,0.206234,0.238926,0.239646,0.128521,0.00864814,0.207017,0.14037,0.259646,0.0916845,0.112868,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.00590953,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.0458938,0.113754,0.0504034,0.169684,0.690367,0.495926,0.869559,0.73998,0.3024,0.901171,0.644298,0.420045,0.381628,0.0627015,0.545329,0.464128,0.0881702,0.594055,0.414547,0.146105,0.413223,0.639461,0.364388,0.34505,0.369161,0.153719,0.0311814,0.323639,0.341822,0.241524,0.0232022,0.234628,0.520726,0.0108883,0.41477,0.279946,0.0395226,0.467825,0.563725,0.404903,0.632838,0.624969,0.460819,0.511459,0.586668,0.322903,0.0703732,0.0838963,0.0590382,0.398372,0.286293,0.606558,0.708425,0.359128,0.395864,0.683133,0.368633,0.547291,0.682118,0.162437,0.0116693,0.578349,0.181193,0.464342,0.683088,0.714007,0.0301914,0.804772,0.199727,0.548076,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.730486,0.606382,0.617741,0.0774588,0.316925,0.356561,0.210197,0.211506,0.0883859,0.0962508,0.238465,0.341199,0.853221,0.323783,0.508325,0.187096,0.651927,0.656755,0.54723,0.280307,0.0144019,0.794849,0.0596868,0.0984075,0.293026,0.16661,0.694744,0.605423,0.372182,0.429205,0.578951,0.365653,0.41035,0.784024,0.35234,0.644643,0.525923,0.291917,0.421082,0.25441,0.202782,0.307342,0.166182,0.0124357,0.517001,0.0746589,0.73448,0.419676,0.188259,0.0191441,0.138387,0.46699,0.546448,0.0505495,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.283924,0.0117791,0.360161,0.109421,0.386216,0.385297,0.706685,0.239407,0.259338,0.360203,0.0631823,0.447838,0.289666,0.153861,0.0365674,0.122807,0.565545,0.556975,0.265037,0.261923,0.754776,0.53531,0.341771,0.424526,0.657528,0.0727712,0.184395,0.55524,0.624689,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.629381,0.729876,0.433821,0.0211186,0.436806,0.21267,0.499072,0.744662,0.149061,0.397546,0.0919254,0.00277343,0.248103,0.102621,0.00296492,0.187642,0.286156,0.261868,0.541583,0.540322,0.247151,0.146385,0.0769978,0.0576261,0.0847761,0.164977,0.175633,0.139918,0.34669,0.0828344,0.4729,0.0238089,0.383126,0.354433,0.48311,0.0614918,0.219485,0.149782,0.136923,0.000301188,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.0334797,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.0397278,0.0212281,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.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}}
}}

Revision as of 14:09, 19 October 2012


Full id: C2546_neuroectodermal_neuroblastoma_granulosa_peripheral_Cardiac_Fibroblast_aorta



Phase1 CAGE Peaks

Hg19::chr1:185703496..185703509,+p2@HMCN1
Hg19::chr1:185703513..185703544,+p1@HMCN1
Hg19::chr1:185880819..185880830,+p@chr1:185880819..185880830
+
Hg19::chr1:186159161..186159177,+p@chr1:186159161..186159177
+


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>

Cell Type
Ontology termp-valuen
non-terminally differentiated cell7.49e-10106
fibroblast1.10e-0976
cardiocyte2.52e-0816
skin fibroblast2.97e-0723
muscle cell5.93e-0755
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm2.54e-1583
primary circulatory organ3.30e-1327
heart2.86e-1224
primitive heart tube2.86e-1224
primary heart field2.86e-1224
anterior lateral plate mesoderm2.86e-1224
heart tube2.86e-1224
heart primordium2.86e-1224
cardiac mesoderm2.86e-1224
cardiogenic plate2.86e-1224
heart rudiment2.86e-1224
circulatory system5.00e-12112
cardiovascular system3.31e-11109
multi-cellular organism1.34e-10656
artery1.21e-0842
arterial blood vessel1.21e-0842
arterial system1.21e-0842
epithelial tube open at both ends1.64e-0859
blood vessel1.64e-0859
blood vasculature1.64e-0859
vascular cord1.64e-0859
vasculature5.27e-0878
vascular system5.27e-0878
somite3.65e-0771
presomitic mesoderm3.65e-0771
presumptive segmental plate3.65e-0771
dermomyotome3.65e-0771
trunk paraxial mesoderm3.65e-0771
muscle tissue4.43e-0764
musculature4.43e-0764
musculature of body4.43e-0764
dense mesenchyme tissue4.81e-0773
vessel6.07e-0768
paraxial mesoderm7.13e-0772
presumptive paraxial mesoderm7.13e-0772
skeletal muscle tissue8.34e-0762
striated muscle tissue8.34e-0762
myotome8.34e-0762


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
FOXA2#3170212.31523187633260.009361916285467240.0353462936496968



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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