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Coexpression cluster:C3678: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0004111!9.21e-29!241;UBERON:0000477!1.55e-28!286;UBERON:0000483!8.67e-23!309;UBERON:0000480!1.77e-22!626;UBERON:0000467!2.24e-22!625;UBERON:0000025!4.58e-22!194;UBERON:0000119!5.92e-22!312;UBERON:0000468!9.21e-21!659;UBERON:0002050!2.44e-20!605;UBERON:0005423!2.44e-20!605;UBERON:0000923!5.02e-20!604;UBERON:0005291!5.02e-20!604;UBERON:0006598!5.02e-20!604;UBERON:0002532!5.02e-20!604;UBERON:0000922!8.78e-20!612;UBERON:0000481!2.04e-19!347;UBERON:0007023!4.16e-15!115;UBERON:0000064!8.72e-14!219;UBERON:0000062!2.90e-13!511;UBERON:0000475!5.49e-13!365;UBERON:0005743!1.63e-12!86;UBERON:0004121!1.71e-11!169;UBERON:0001017!2.02e-11!82;UBERON:0003914!6.76e-11!118;UBERON:0001049!8.49e-11!57;UBERON:0005068!8.49e-11!57;UBERON:0006241!8.49e-11!57;UBERON:0007135!8.49e-11!57;UBERON:0003075!9.29e-11!86;UBERON:0007284!9.29e-11!86;UBERON:0001986!1.58e-10!18;UBERON:0004638!1.58e-10!18;UBERON:0004852!1.58e-10!18;UBERON:0000924!3.63e-10!173;UBERON:0006601!3.63e-10!173;UBERON:0000073!4.16e-10!94;UBERON:0001016!4.16e-10!94;UBERON:0000033!8.03e-10!123;UBERON:0003103!1.08e-09!69;UBERON:0000955!2.33e-09!69;UBERON:0006238!2.33e-09!69;UBERON:0004119!2.58e-09!169;UBERON:0000925!2.58e-09!169;UBERON:0006595!2.58e-09!169;UBERON:0000153!2.62e-09!129;UBERON:0007811!2.62e-09!129;UBERON:0006914!2.64e-09!25;UBERON:0002346!5.69e-09!90;UBERON:0005177!7.89e-09!107;UBERON:0000487!8.03e-09!22;UBERON:0002616!1.93e-08!59;UBERON:0003104!4.45e-08!238;UBERON:0009142!4.45e-08!238;UBERON:0003080!6.19e-08!42;UBERON:0001007!1.90e-07!155;UBERON:0001555!1.90e-07!155;UBERON:0007026!1.90e-07!155;UBERON:0002780!1.92e-07!41;UBERON:0001890!1.92e-07!41;UBERON:0006240!1.92e-07!41;UBERON:0002020!2.18e-07!34;UBERON:0003528!2.18e-07!34;UBERON:0000055!3.43e-07!69;UBERON:0001893!4.52e-07!34;UBERON:0002791!4.85e-07!33;UBERON:0004921!9.10e-07!129;UBERON:0004185!9.10e-07!129;UBERON:0004872!9.51e-07!84
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8866,0.153187,0.0797897,0.0974211,0.160149,0.00796449,0.0906475,0.0558058,0.28262,0.00662343,0.137332,0.0145999,0.0656973,0.211746,0.026334,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.0355977,0.170307,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,1.65628e-05,0.0286025,0.190156,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.000242011,0.217069,0.190048,0.131088,1.43218e-05,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.00315933,0.132886,0.0774373,0.109194,0.128564,0.131452,0.323837,3.73213e-05,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.00447267,0.00264443,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.000216899,0.000581378,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.00474777,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.00921075,0.0450031,0.0539144,0.000271748,0.0929549,0.0158019,0.104948,0.221645,0.057168,0.234298,0.0759837,0.00500888,0.152372,0.00144552,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.0116284,0.0058211,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,1.59953e-06,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.01625,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.220462,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.000874248,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0020598,0.000500398,0.0360851,0.000227331,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.0162067,0.231447,0.00858901,0.0210947,0.37006,0.10748,0.448797,0.197484,0.0148336,0.36145,0.406019,0.000142346,0.580441,1.48564e-07,0.0198622,0.366326,0.390366,0.48809,0.50058,0.0217093,0.00696618,0.0608227,2.72893e-07,0.227104,0.0380245,0.617852,0.38649,0.284625,0.156746,0.192225,0.729153,0.28907,0.164197,0.462688,0.0461094,3.14651e-05,5.54529e-06,0.00846715,0.468444,0.258219,0.446557,0.243383,2.80434e-05,0.0140783,0.149257,0.319063,0.161598,0.164332,0.277094,8.02175e-05,0.00136122,0.0805771,3.35117e-05,0.477353,0.0201095,0.399222,0.0629574,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.000180531,0.616388,0.408413,0.000926901,0.322213,0.28903,0.33942,0.0156581,0.387276,0.0391112,0.00143411,0.537348,0.222037,0.416621,0.416292,0.128937,0.734551,0.0019893,0.204817,0.452428,0.138871,2.27405e-05,0.0147755,0.19783,0.0833851,0.056391,6.28651e-05,0.175199,0.332919,0.373557,0.523625,0.0980968,0.0111982,9.47497e-09,0.0889149,0.363192,0.236011,0.203486,0.000336234,0.375787,0.4466,0.351067,0.275347,0.00388821,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.0867777,0.508064,0.00324315,0.383276,0.457886,0.0344603,0.220231,0.509064,0.196976,0.191517,0.463751,0.235208,0.307334,0.00367772,0.283463,0.000222968,0.135386,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.00088965,0.197805,0.0153645,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.00343724,0.20753,3.63391e-05,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.00206345,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.00803363,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.00394192,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.00145205,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.0223377,0.21382,0.00176424,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.00347819,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.0297055,0.189559,0.0812887,0.000169901,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.0457063,0.0687209,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.0257187,0.223831,0.11528,0.194982,0.190993,0.281727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}}
}}

Revision as of 12:32, 5 September 2012


Full id: C3678_Mast_Mesenchymal_Renal_breast_Synoviocyte_myeloma_CD14



Phase1 CAGE Peaks

Hg19::chr17:73874625..73874640,-p3@TRIM47
Hg19::chr17:73874641..73874653,-p5@TRIM47
Hg19::chr17:73874654..73874675,-p1@TRIM47


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
anatomical conduit9.21e-29241
anatomical cluster1.55e-28286
epithelium8.67e-23309
anatomical group1.77e-22626
anatomical system2.24e-22625
tube4.58e-22194
cell layer5.92e-22312
multi-cellular organism9.21e-21659
embryonic structure2.44e-20605
developing anatomical structure2.44e-20605
germ layer5.02e-20604
embryonic tissue5.02e-20604
presumptive structure5.02e-20604
epiblast (generic)5.02e-20604
embryo8.78e-20612
multi-tissue structure2.04e-19347
adult organism4.16e-15115
organ part8.72e-14219
organ2.90e-13511
organism subdivision5.49e-13365
ectoderm-derived structure1.71e-11169
central nervous system2.02e-1182
epithelial tube6.76e-11118
neural tube8.49e-1157
neural rod8.49e-1157
future spinal cord8.49e-1157
neural keel8.49e-1157
neural plate9.29e-1186
presumptive neural plate9.29e-1186
endothelium1.58e-1018
blood vessel endothelium1.58e-1018
cardiovascular system endothelium1.58e-1018
ectoderm3.63e-10173
presumptive ectoderm3.63e-10173
regional part of nervous system4.16e-1094
nervous system4.16e-1094
head8.03e-10123
compound organ1.08e-0969
brain2.33e-0969
future brain2.33e-0969
endoderm-derived structure2.58e-09169
endoderm2.58e-09169
presumptive endoderm2.58e-09169
anterior region of body2.62e-09129
craniocervical region2.62e-09129
squamous epithelium2.64e-0925
neurectoderm5.69e-0990
trunk region element7.89e-09107
simple squamous epithelium8.03e-0922
regional part of brain1.93e-0859
mesenchyme4.45e-08238
entire embryonic mesenchyme4.45e-08238
anterior neural tube6.19e-0842
digestive system1.90e-07155
digestive tract1.90e-07155
primitive gut1.90e-07155
regional part of forebrain1.92e-0741
forebrain1.92e-0741
future forebrain1.92e-0741
gray matter2.18e-0734
brain grey matter2.18e-0734
vessel3.43e-0769
telencephalon4.52e-0734
regional part of telencephalon4.85e-0733
subdivision of digestive tract9.10e-07129
endodermal part of digestive tract9.10e-07129
splanchnic layer of lateral plate mesoderm9.51e-0784


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
CHD2#1106310.34402283411690.0009033701102746880.00660046669560502
CTCF#1066435.360256373075030.0064925092527670.0279213989643703
E2F1#186934.907389214879320.008460985347239390.0324993324266397
E2F6#187635.017155731697390.00791769806886330.032180746754904
EGR1#195834.988179094810140.008056488137383440.0320342482517395
MAFF#23764356.31535648994525.59409009993116e-060.000169002365040992
MXI1#460139.96157162875930.001011470541259020.00719744987794175
MYC#460935.22228187160940.007020843755740150.0294253341227877
ZBTB7A#5134137.35190930787590.002516255860282270.0140037965358638



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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