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Coexpression cluster:C4689: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!9.99e-25!365;UBERON:0000468!1.91e-16!659;UBERON:0000481!1.92e-16!347;UBERON:0000153!4.03e-16!129;UBERON:0007811!4.03e-16!129;UBERON:0000033!5.13e-16!123;UBERON:0000062!7.46e-16!511;UBERON:0003075!2.68e-14!86;UBERON:0007284!2.68e-14!86;UBERON:0004121!3.36e-14!169;UBERON:0000064!6.38e-14!219;UBERON:0000924!1.38e-13!173;UBERON:0006601!1.38e-13!173;UBERON:0002346!2.73e-13!90;UBERON:0000467!1.27e-12!625;UBERON:0000480!2.09e-12!626;UBERON:0005743!4.49e-11!86;UBERON:0003056!5.61e-11!61;UBERON:0000073!6.07e-10!94;UBERON:0001016!6.07e-10!94;UBERON:0001049!2.40e-09!57;UBERON:0005068!2.40e-09!57;UBERON:0006241!2.40e-09!57;UBERON:0007135!2.40e-09!57;UBERON:0001017!3.15e-09!82;UBERON:0000922!4.21e-09!612;UBERON:0002616!5.16e-09!59;UBERON:0000955!4.12e-08!69;UBERON:0006238!4.12e-08!69;UBERON:0005631!5.85e-08!14;UBERON:0000158!5.85e-08!14;UBERON:0007023!6.02e-08!115;UBERON:0002050!6.55e-08!605;UBERON:0005423!6.55e-08!605;UBERON:0004923!9.88e-08!57;UBERON:0000923!1.09e-07!604;UBERON:0005291!1.09e-07!604;UBERON:0006598!1.09e-07!604;UBERON:0002532!1.09e-07!604;UBERON:0001444!1.28e-07!48;UBERON:0005256!2.29e-07!143;UBERON:0000483!2.33e-07!309;UBERON:0000119!3.77e-07!312;UBERON:0000970!6.33e-07!20;UBERON:0000020!7.56e-07!23;UBERON:0002104!7.64e-07!21;UBERON:0001456!8.06e-07!21;UBERON:0001032!8.64e-07!24;UBERON:0004456!8.64e-07!24;UBERON:0003102!9.93e-07!95
|ontology_enrichment_uberon=UBERON:0000475!9.99e-25!365;UBERON:0000468!1.91e-16!659;UBERON:0000481!1.92e-16!347;UBERON:0000153!4.03e-16!129;UBERON:0007811!4.03e-16!129;UBERON:0000033!5.13e-16!123;UBERON:0000062!7.46e-16!511;UBERON:0003075!2.68e-14!86;UBERON:0007284!2.68e-14!86;UBERON:0004121!3.36e-14!169;UBERON:0000064!6.38e-14!219;UBERON:0000924!1.38e-13!173;UBERON:0006601!1.38e-13!173;UBERON:0002346!2.73e-13!90;UBERON:0000467!1.27e-12!625;UBERON:0000480!2.09e-12!626;UBERON:0005743!4.49e-11!86;UBERON:0003056!5.61e-11!61;UBERON:0000073!6.07e-10!94;UBERON:0001016!6.07e-10!94;UBERON:0001049!2.40e-09!57;UBERON:0005068!2.40e-09!57;UBERON:0006241!2.40e-09!57;UBERON:0007135!2.40e-09!57;UBERON:0001017!3.15e-09!82;UBERON:0000922!4.21e-09!612;UBERON:0002616!5.16e-09!59;UBERON:0000955!4.12e-08!69;UBERON:0006238!4.12e-08!69;UBERON:0005631!5.85e-08!14;UBERON:0000158!5.85e-08!14;UBERON:0007023!6.02e-08!115;UBERON:0002050!6.55e-08!605;UBERON:0005423!6.55e-08!605;UBERON:0004923!9.88e-08!57;UBERON:0000923!1.09e-07!604;UBERON:0005291!1.09e-07!604;UBERON:0006598!1.09e-07!604;UBERON:0002532!1.09e-07!604;UBERON:0001444!1.28e-07!48;UBERON:0005256!2.29e-07!143;UBERON:0000483!2.33e-07!309;UBERON:0000119!3.77e-07!312;UBERON:0000970!6.33e-07!20;UBERON:0000020!7.56e-07!23;UBERON:0002104!7.64e-07!21;UBERON:0001456!8.06e-07!21;UBERON:0001032!8.64e-07!24;UBERON:0004456!8.64e-07!24;UBERON:0003102!9.93e-07!95
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.016848935935323!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000854867097022211!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.0066860799946758
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8058,0.28262,0.0377931,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.00335855,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.153605,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.0465298,0.057571,0.047591,0.0143259,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.43617,0.0611073,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,4.36088e-05,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.00248603,0.0972686,0.252227,0.0360851,0.0168763,0.131093,0.0434602,0.133616,0.418146,0.36927,0.120614,0.407369,0.231447,0.0455669,0.115047,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.432035,0.0100497,0.390366,0.48809,0.50058,0.443185,0.0391928,0.158867,0.336835,0.227104,0.518585,0.617852,0.38649,0.284625,0.504757,0.55194,0.0108655,0.28907,0.164197,0.128922,0.287881,0.574635,0.478174,0.336276,0.132529,0.258219,0.446557,0.243383,0.0659137,0.390974,0.149257,0.109758,0.161598,0.751174,0.644754,0.496032,0.21803,0.37357,0.0203982,0.477353,0.199161,0.160298,0.0629574,0.20342,0.200493,0.20558,0.0505073,0.25656,0.0189087,0.349197,0.383291,2.87125e-08,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.0175523,0.282286,0.0192486,0.616388,0.408413,0.0374737,0.322213,0.656109,0.33942,0.243065,0.387276,0.0391112,0.802166,0.180745,0.222037,0.416621,0.416292,0.462712,0.0457685,0.579431,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.00623664,0.303709,0.495883,0.386538,0.035296,0.250964,0.383276,0.125961,0.504711,0.220231,0.0355483,0.196976,0.191517,0.463751,0.235208,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,7.28007e-05,0.197805,0.0690807,0.387069,0.332774,0.173874,0.299887,0.634365,0.0227114,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.00135583,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,3.63391e-05,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.0015337,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.0234202,9.45506e-07,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.000123055,0.123917,0.00121059,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.0199603,0.249101,0.000284685,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.00072309,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.0541163,0.280943,0.218161,0.0822373,0.202065,0.000220289,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,2.77084e-05,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.0352561,0.00107794,0.28365,0.264413,0.131761,0.0136582,0.206239,0.19924,0.00501043,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.000113015,0.056548,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.1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}}
}}

Revision as of 14:14, 5 September 2012


Full id: C4689_Retinal_renal_Osteoblast_retina_Ciliary_Hepatocyte_glioblastoma



Phase1 CAGE Peaks

Hg19::chr7:47576906..47576950,-p@chr7:47576906..47576950
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Hg19::chr7:47576976..47577001,-p@chr7:47576976..47577001
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Hg19::chr7:47577036..47577094,-p@chr7:47577036..47577094
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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 cell4.06e-11180
fibroblast1.66e-0875
skin fibroblast5.78e-0823
Uber Anatomy
Ontology termp-valuen
organism subdivision9.99e-25365
multi-cellular organism1.91e-16659
multi-tissue structure1.92e-16347
anterior region of body4.03e-16129
craniocervical region4.03e-16129
head5.13e-16123
organ7.46e-16511
neural plate2.68e-1486
presumptive neural plate2.68e-1486
ectoderm-derived structure3.36e-14169
organ part6.38e-14219
ectoderm1.38e-13173
presumptive ectoderm1.38e-13173
neurectoderm2.73e-1390
anatomical system1.27e-12625
anatomical group2.09e-12626
pre-chordal neural plate5.61e-1161
regional part of nervous system6.07e-1094
nervous system6.07e-1094
neural tube2.40e-0957
neural rod2.40e-0957
future spinal cord2.40e-0957
neural keel2.40e-0957
central nervous system3.15e-0982
embryo4.21e-09612
regional part of brain5.16e-0959
brain4.12e-0869
future brain4.12e-0869
extraembryonic membrane5.85e-0814
membranous layer5.85e-0814
adult organism6.02e-08115
embryonic structure6.55e-08605
developing anatomical structure6.55e-08605
organ component layer9.88e-0857
germ layer1.09e-07604
embryonic tissue1.09e-07604
presumptive structure1.09e-07604
epiblast (generic)1.09e-07604
subdivision of head1.28e-0748
trunk mesenchyme2.29e-07143
epithelium2.33e-07309
cell layer3.77e-07312
eye6.33e-0720
sense organ7.56e-0723
visual system7.64e-0721
face8.06e-0721
sensory system8.64e-0724
entire sense organ system8.64e-0724
surface structure9.93e-0795


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
EP300#203336.77394172622320.003216880500103790.016848935935323
GATA3#2625327.2365163572064.94721007899563e-050.000854867097022211
RAD21#5885310.35503389545630.0009004912073565420.0066860799946758



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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