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Coexpression cluster:C4149: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004876!3.73e-12!20;UBERON:0003887!1.05e-11!21;UBERON:0000080!6.69e-11!18;UBERON:0002120!6.69e-11!18;UBERON:0004875!6.69e-11!18;UBERON:0005721!6.69e-11!18;UBERON:0005754!6.69e-11!18;UBERON:0007297!6.69e-11!18;UBERON:0002113!2.73e-10!27;UBERON:0003918!2.73e-10!27;UBERON:0005095!2.73e-10!27;UBERON:0007687!2.73e-10!27;UBERON:0006555!4.40e-10!17;UBERON:0005103!4.40e-10!17;UBERON:0000083!4.40e-10!17;UBERON:0009201!4.40e-10!17;UBERON:0004819!4.40e-10!17;UBERON:0006553!4.40e-10!17;UBERON:0003074!4.40e-10!17;UBERON:0003060!4.40e-10!17;UBERON:0003886!5.78e-10!63;UBERON:0002199!6.04e-10!45;UBERON:0002416!6.04e-10!45;UBERON:0000489!6.98e-10!32;UBERON:0004211!2.64e-09!16;UBERON:0001285!2.64e-09!16;UBERON:0007684!2.64e-09!16;UBERON:0003220!2.64e-09!16;UBERON:0004208!2.64e-09!16;UBERON:0003133!7.09e-09!48;UBERON:0002465!1.87e-08!10;UBERON:0002097!2.05e-08!40;UBERON:0009773!4.73e-08!12;UBERON:0001231!4.73e-08!12;UBERON:0004810!4.73e-08!12;UBERON:0001473!4.97e-08!8;UBERON:0004536!4.97e-08!8;UBERON:0006558!4.97e-08!8;UBERON:0000058!7.85e-08!26;UBERON:0003064!8.41e-08!37;UBERON:0002553!1.19e-07!70;UBERON:0005156!2.64e-07!59;UBERON:0000990!2.64e-07!59;UBERON:0001225!2.84e-07!13;UBERON:0008987!2.84e-07!13;UBERON:0001013!4.22e-07!14;UBERON:0001008!4.39e-07!45
|ontology_enrichment_uberon=UBERON:0004876!3.73e-12!20;UBERON:0003887!1.05e-11!21;UBERON:0000080!6.69e-11!18;UBERON:0002120!6.69e-11!18;UBERON:0004875!6.69e-11!18;UBERON:0005721!6.69e-11!18;UBERON:0005754!6.69e-11!18;UBERON:0007297!6.69e-11!18;UBERON:0002113!2.73e-10!27;UBERON:0003918!2.73e-10!27;UBERON:0005095!2.73e-10!27;UBERON:0007687!2.73e-10!27;UBERON:0006555!4.40e-10!17;UBERON:0005103!4.40e-10!17;UBERON:0000083!4.40e-10!17;UBERON:0009201!4.40e-10!17;UBERON:0004819!4.40e-10!17;UBERON:0006553!4.40e-10!17;UBERON:0003074!4.40e-10!17;UBERON:0003060!4.40e-10!17;UBERON:0003886!5.78e-10!63;UBERON:0002199!6.04e-10!45;UBERON:0002416!6.04e-10!45;UBERON:0000489!6.98e-10!32;UBERON:0004211!2.64e-09!16;UBERON:0001285!2.64e-09!16;UBERON:0007684!2.64e-09!16;UBERON:0003220!2.64e-09!16;UBERON:0004208!2.64e-09!16;UBERON:0003133!7.09e-09!48;UBERON:0002465!1.87e-08!10;UBERON:0002097!2.05e-08!40;UBERON:0009773!4.73e-08!12;UBERON:0001231!4.73e-08!12;UBERON:0004810!4.73e-08!12;UBERON:0001473!4.97e-08!8;UBERON:0004536!4.97e-08!8;UBERON:0006558!4.97e-08!8;UBERON:0000058!7.85e-08!26;UBERON:0003064!8.41e-08!37;UBERON:0002553!1.19e-07!70;UBERON:0005156!2.64e-07!59;UBERON:0000990!2.64e-07!59;UBERON:0001225!2.84e-07!13;UBERON:0008987!2.84e-07!13;UBERON:0001013!4.22e-07!14;UBERON:0001008!4.39e-07!45
|tf_chipseq_enrich=ATF3#467;3:22.4631745260087:8.81932387510763e-05:0.00129784608453201!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186935153860179!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223049025798179!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190730352357386!USF2#7392;3:12.9921973850696:0.000455897939342781:0.0042225545305978!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330070069053955
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0221,0.19559,0.000427374,0.188694,2.34779e-09,8.64205e-05,1.3111e-06,8.0582e-09,0.0164446,0.184486,1.56493e-06,0.0876426,0.0952322,0.0112557,0.0268081,0.000222233,0.275244,0.00481323,0.173708,0.0104618,0.00187586,0.0300692,0.00905936,0.0445237,0.052362,0.00179985,0.153187,0.0797897,0.00016623,0.160149,0.000346156,0.0906475,0.00158695,2.5572e-05,3.98752e-10,0.009894,0.0145999,0.00220694,0.211746,0.220538,0.0801488,7.69244e-05,0.000803238,0.193215,0.0549034,8.39064e-05,3.08576e-05,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.348757,0.219556,0.0394698,0.00181534,0.00236266,0.122476,0.108872,0.11002,0.0376172,0.000413007,0.001389,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.0254773,0.190048,0.131088,0.090504,0.237101,0.000416804,0.0761239,0.0158143,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.28711,1.82894e-05,0.094881,0.445524,0.132886,0.0774373,0.109194,0.128564,0.000419898,0.323837,0.00327218,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.000585365,7.20365e-05,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.0088427,0.057571,0.00115086,0.392974,0.0608699,0.175319,0.300597,6.38787e-05,0.223874,0.00525614,0.0355833,3.24692e-07,0.175094,0.911304,0.00217769,0.206454,0.218192,0.00608582,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.000243212,0.070276,0.226171,0.0124298,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.00217546,0.057168,0.00259914,0.0759837,1.55357e-06,0.152372,0.194941,0.00207136,0.101607,0.00771936,0.000990951,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.0128248,0.0718905,0.000138924,0.0602373,0.144304,0.000642001,0.000166026,0.000702525,0.0154015,0.0200941,0.137219,0.0282663,0.251466,0.000423995,0.11903,0.0838874,0.331451,0.113145,0.000260208,0.186638,0.01625,0.0948451,0.264079,0.249049,1.94222e-05,0.000178916,3.18233e-08,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,4.0114e-05,0.0190329,0.00340589,0.184948,0.0128995,0.311847,0.000874248,0.0590944,0.0334734,0.0169521,0.000125811,0.231073,0.0161946,0.619906,0.0360851,0.412187,0.000416337,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.0455669,0.43956,0.37006,0.42622,3.73344e-05,0.197484,0.396996,0.36145,0.0160226,0.381071,0.580441,1.28363e-05,0.0198622,0.0411943,0.390366,0.145312,0.0334527,0.443185,0.522904,0.875915,0.00127936,0.227104,0.518585,0.250246,0.0867545,0.284625,0.0344717,0.55194,0.0108655,2.90252e-05,0.164197,0.462688,0.287881,0.00187974,0.478174,0.336276,0.468444,0.0366482,0.446557,0.032364,0.191695,0.0889613,0.382874,0.683217,0.161598,0.751174,1.30828e-05,7.75114e-06,0.21803,0.37357,0.200632,0.138234,0.199161,0.160298,0.0175763,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.0104921,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.0192486,0.00305733,0.408413,0.516511,0.322213,0.000830547,0.33942,0.0700181,0.0871388,0.522605,0.221908,0.00120002,0.222037,0.416621,0.416292,0.462712,0.000454034,0.0019893,0.204817,0.0233392,0.138871,0.00583733,0.000885521,0.19783,0.0833851,0.316453,0.140384,0.175199,0.332919,0.373557,1.17642e-06,1.87226e-05,8.3468e-06,0.178743,0.0889149,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.00388821,0.305885,0.241132,0.371414,0.0527347,0.0516603,0.0323359,0.386538,0.508064,0.250964,0.383276,0.457886,0.0344603,0.220231,0.0355483,0.196976,0.191517,0.0254647,0.601877,0.00628197,0.459728,0.044623,0.000222968,0.472935,0.399569,0.273281,0.368095,0.275089,0.0133102,0.47795,0.359231,0.339729,0.197805,0.000423937,0.387069,0.332774,0.173874,0.299887,0.0814305,0.205413,0.00105378,0.0779009,1.22165e-06,0.205298,0.0337138,0.18966,0.258854,0.0189519,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.000872573,0.252184,0.000136473,0.00343724,1.80271e-07,0.447185,0.179412,0.193601,0.220904,0.222977,7.52509e-05,1.4148e-07,0.21801,0.0015337,0.186804,0.123324,0.199468,0.0325925,0.00449563,0.12405,0.00112112,0.0023439,0.27872,0.0855609,4.06602e-07,0.00178627,0.00310436,0.222339,0.0673329,0.000103317,0.266544,0.0066506,0.0111711,0.229428,0.162145,0.228955,0.0151141,0.0384949,0.00223436,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.000773769,0.257294,0.150733,0.217112,0.123917,0.184317,0.0183464,0.0723291,0.258496,0.261744,4.23749e-06,0.21382,0.207559,0.141867,0.193031,2.44694e-08,0.115972,0.0273485,0.246105,0.173026,0.200432,0.000508432,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.00206803,0.00347819,9.03667e-05,0.106739,0.0536053,0.0537737,0.000648679,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,9.53285e-05,0.0981146,0.064145,0.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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C4149_neuroblastoma_kidney_Endothelial_uterus_Renal_smallcell_bronchogenic



Phase1 CAGE Peaks

Hg19::chr2:176987441..176987454,+p1@HOXD9
Hg19::chr2:176987463..176987479,+p2@HOXD9
Hg19::chr2:176987485..176987496,+p3@HOXD9


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
urogenital ridge3.73e-1220
intraembryonic coelom1.05e-1121
mesonephros6.69e-1118
pronephros6.69e-1118
nephrogenic cord6.69e-1118
pronephric mesoderm6.69e-1118
rostral part of nephrogenic cord6.69e-1118
presumptive pronephric mesoderm6.69e-1118
kidney2.73e-1027
kidney mesenchyme2.73e-1027
kidney rudiment2.73e-1027
kidney field2.73e-1027
excretory tube4.40e-1017
mesonephric epithelium4.40e-1017
mesonephric tubule4.40e-1017
nephric duct4.40e-1017
kidney epithelium4.40e-1017
renal duct4.40e-1017
mesonephric duct4.40e-1017
pronephric duct4.40e-1017
body cavity precursor5.78e-1063
integument6.04e-1045
integumental system6.04e-1045
cavitated compound organ6.98e-1032
nephron epithelium2.64e-0916
nephron2.64e-0916
uriniferous tubule2.64e-0916
metanephric mesenchyme2.64e-0916
nephrogenic mesenchyme2.64e-0916
reproductive organ7.09e-0948
lymphoid system1.87e-0810
skin of body2.05e-0840
renal tubule4.73e-0812
nephron tubule4.73e-0812
nephron tubule epithelium4.73e-0812
lymphatic vessel4.97e-088
lymph vasculature4.97e-088
lymphatic part of lymphoid system4.97e-088
duct7.85e-0826
intermediate mesoderm8.41e-0837
anatomical cavity1.19e-0770
reproductive structure2.64e-0759
reproductive system2.64e-0759
cortex of kidney2.84e-0713
renal parenchyma2.84e-0713
adipose tissue4.22e-0714
renal system4.39e-0745


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
ATF3#467322.46317452600878.81932387510763e-050.00129784608453201
MAX#414936.452555509007120.003721913834265510.0186935153860179
SUZ12#23512350.11578091106297.93834897779404e-060.000223049025798179
USF1#739136.361499277207960.00388404057290560.0190730352357386
USF2#7392312.99219738506960.0004558979393427810.0042225545305978
YY1#752834.911170749853860.008441455341808260.0330070069053955



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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