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Coexpression cluster:C4529: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!4.77e-14!312;UBERON:0000483!1.19e-12!309;UBERON:0000475!8.83e-12!365;UBERON:0002200!2.06e-10!11;UBERON:0006876!2.06e-10!11;UBERON:0000490!1.47e-09!138;UBERON:0002049!2.35e-09!79;UBERON:0007798!2.35e-09!79;UBERON:0004535!3.95e-09!110;UBERON:0000477!8.08e-09!286;UBERON:0007625!1.31e-08!11;UBERON:0001009!1.72e-08!113;UBERON:0000914!8.76e-08!83;UBERON:0002329!8.76e-08!83;UBERON:0003077!8.76e-08!83;UBERON:0003059!8.76e-08!83;UBERON:0007282!8.76e-08!83;UBERON:0009618!8.76e-08!83;UBERON:0007285!8.76e-08!83;UBERON:0005256!2.35e-07!143
|ontology_enrichment_uberon=UBERON:0000119!4.77e-14!312;UBERON:0000483!1.19e-12!309;UBERON:0000475!8.83e-12!365;UBERON:0002200!2.06e-10!11;UBERON:0006876!2.06e-10!11;UBERON:0000490!1.47e-09!138;UBERON:0002049!2.35e-09!79;UBERON:0007798!2.35e-09!79;UBERON:0004535!3.95e-09!110;UBERON:0000477!8.08e-09!286;UBERON:0007625!1.31e-08!11;UBERON:0001009!1.72e-08!113;UBERON:0000914!8.76e-08!83;UBERON:0002329!8.76e-08!83;UBERON:0003077!8.76e-08!83;UBERON:0003059!8.76e-08!83;UBERON:0007282!8.76e-08!83;UBERON:0009618!8.76e-08!83;UBERON:0007285!8.76e-08!83;UBERON:0005256!2.35e-07!143
|tf_chipseq_enrich=FOS#2353;3:8.9979553088944:0.00137249927241713:0.00901071482976946!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438639050271932!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00446012560741705
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52322,0.0112557,0.222432,0.107043,2.20551e-05,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.0235128,0.153187,0.00327141,0.0974211,0.160149,0.00796449,0.0906475,0.0558058,0.00477066,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.013859,0.193215,2.87669e-05,0.0779715,0.0561838,0.0008845,0.0345419,0.0388736,0.000246135,0.0154037,0.201033,2.02233e-05,0.174921,0.370421,0.0330727,0.348757,0.00211059,1.05605e-05,0.0596469,0.419264,0.00782667,0.00615421,0.000241884,0.26144,3.98541e-06,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,6.78956e-07,0.00203513,0.190048,0.131088,0.394069,0.237101,0.00501606,0.0761239,0.000982125,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.00465073,0.445524,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,2.41547e-05,0.0993999,0.00127324,0.061829,1.48718e-06,0.000147224,0.144075,0.0340203,7.20365e-05,0.277091,0.739716,0.288159,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.00103374,0.300597,0.0713214,0.0271723,3.58916e-09,0.0355833,0.00824114,0.175094,0.911304,0.936279,0.206454,0.00206897,0.108277,1.29569e-08,0.108748,0.0494066,0.0958493,0.0227848,0.0755808,0.045654,5.30526e-11,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.00020908,3.0857e-10,0.057168,0.234298,0.0759837,0.286863,0.152372,0.00144552,0.218271,0.101607,0.327067,0.172982,0.00886538,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,6.54495e-05,0.0919008,0.0602373,0.144304,0.000642001,0.0973823,0.0126914,0.0154015,0.193653,0.137219,0.0282663,0.0346616,2.84797e-05,0.11903,0.0838874,0.0622625,0.00665699,0.112651,0.0186145,0.174776,0.000153071,0.264079,0.0339656,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,4.41518e-08,0.188651,0.0813902,0.0182671,0.156261,0.0065917,0.511859,0.0590944,0.247324,0.178389,0.218229,0.0290303,0.407281,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.0227305,0.407369,0.231447,0.544776,0.0210947,0.37006,0.00255501,0.448797,0.197484,0.000181515,0.36145,1.77931e-05,0.381071,0.580441,0.0863135,0.432035,0.138468,0.0140037,0.48809,0.50058,2.81064e-06,0.522904,0.875915,0.871256,0.227104,0.0380245,0.0167433,1.24485e-05,0.00488219,0.156746,0.0091887,0.729153,0.000430404,0.164197,0.462688,0.287881,0.21103,6.0419e-05,0.336276,0.468444,0.258219,0.0222932,0.00293755,0.777351,0.00170027,0.73485,0.683217,0.161598,0.164332,0.644754,7.75114e-06,0.476802,0.000126599,0.78509,0.477353,0.78384,0.746954,0.771991,0.20342,0.200493,0.00171127,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.0104921,0.411941,0.0961477,0.055627,0.354789,0.163828,0.00246909,0.000318278,0.0448825,0.562405,0.00677385,0.181415,0.00475227,0.78,0.0165273,0.0978616,1.01409e-06,0.0586066,0.0931134,7.2419e-05,0.61031,0.387276,0.0391112,0.802166,0.00800402,0.222037,0.0175112,0.10205,0.0252635,0.382478,0.579431,0.0225745,0.122646,0.138871,0.308032,0.166905,0.0210039,0.0833851,0.00691922,0.0289164,0.175199,0.332919,0.373557,0.170369,0.000216517,0.000111345,0.00780726,0.0889149,0.363192,0.236011,0.203486,0.273398,0.0816179,0.4466,0.00977892,0.0419637,0.0830022,0.305885,0.241132,0.000122364,0.30666,0.303709,8.00304e-05,0.0135408,0.508064,0.00324315,0.383276,0.457886,0.504711,0.220231,9.85308e-06,0.196976,0.191517,0.129584,0.235208,0.307334,0.459728,0.283463,0.0102434,0.0272975,0.0932845,0.0413011,0.368095,0.275089,0.0133102,0.47795,0.359231,0.0656472,0.197805,0.608187,0.0870376,0.332774,0.0406989,0.00579439,8.64162e-05,0.00170684,0.17639,0.0779009,0.00446098,0.00170381,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.00135583,0.000822975,0.219428,0.00177656,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.00343724,0.00176345,0.000373385,0.179412,0.0200828,0.220904,0.000138062,1.59747e-08,0.00651011,1.53733e-18,0.0015337,3.26444e-14,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.00310436,0.00219731,0.0673329,0.20847,0.0391817,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,1.17735e-08,0.0521984,0.0455518,0.268741,0.0218443,0.00102523,0.154941,0.00753169,0.0986735,0.00610703,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.00361981,0.30793,0.180606,0.159884,0.00351525,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,1.80437e-07,0.010576,0.193031,0.249101,0.115972,0.0022686,0.000211932,0.173026,0.200432,0.0102599,0.0208458,0.240478,0.0129343,0.13108,0.256963,0.222798,0.0157468,0.176789,0.00485777,0.00162178,0.310405,0.00467879,0.00206803,0.0822373,0.202065,0.000220289,0.00146315,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.0012829,0.233626,6.87647e-05,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.000206969,5.11722e-05,0.0762523,0.128736,0.109171,0.04411,0.066952,0.00414049,0.0367455,0.13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}}
}}

Revision as of 13:01, 5 September 2012


Full id: C4529_alveolar_papillary_Meningeal_mesenchymal_Lens_Ciliary_bone



Phase1 CAGE Peaks

Hg19::chr5:92498140..92498169,-p@chr5:92498140..92498169
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Hg19::chr5:92498181..92498202,-p@chr5:92498181..92498202
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Hg19::chr5:92498209..92498218,-p@chr5:92498209..92498218
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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 cell5.71e-16180
mesodermal cell1.29e-12119
fibroblast2.04e-1175
embryonic cell1.02e-08248
animal cell1.22e-07679
eukaryotic cell1.22e-07679
somatic cell1.47e-07591
endothelial cell of vascular tree3.24e-0724
lining cell3.32e-0757
barrier cell3.32e-0757
endothelial cell4.67e-0735
Uber Anatomy
Ontology termp-valuen
cell layer4.77e-14312
epithelium1.19e-12309
organism subdivision8.83e-12365
vasculature of head2.06e-1011
vasculature of organ2.06e-1011
unilaminar epithelium1.47e-09138
vasculature2.35e-0979
vascular system2.35e-0979
cardiovascular system3.95e-09110
anatomical cluster8.08e-09286
pigment epithelium of eye1.31e-0811
circulatory system1.72e-08113
somite8.76e-0883
paraxial mesoderm8.76e-0883
presomitic mesoderm8.76e-0883
presumptive segmental plate8.76e-0883
trunk paraxial mesoderm8.76e-0883
presumptive paraxial mesoderm8.76e-0883
trunk mesenchyme2.35e-07143


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
FOS#235338.99795530889440.001372499272417130.00901071482976946
GATA2#2624312.7449317335540.0004829527704283790.00438639050271932
JUN#3725312.51282919233630.0005103313992726250.00446012560741705



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.