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Coexpression cluster:C4144: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0002049!6.76e-29!79;UBERON:0007798!6.76e-29!79;UBERON:0000055!8.24e-25!69;UBERON:0004872!4.89e-24!84;UBERON:0001981!6.31e-21!60;UBERON:0007500!6.31e-21!60;UBERON:0004537!6.31e-21!60;UBERON:0006965!6.31e-21!60;UBERON:0003914!2.37e-20!118;UBERON:0004535!3.07e-20!110;UBERON:0001009!6.60e-20!113;UBERON:0000914!1.14e-17!83;UBERON:0002329!1.14e-17!83;UBERON:0003077!1.14e-17!83;UBERON:0003059!1.14e-17!83;UBERON:0007282!1.14e-17!83;UBERON:0009618!1.14e-17!83;UBERON:0007285!1.14e-17!83;UBERON:0005256!1.77e-17!143;UBERON:0001134!2.15e-17!61;UBERON:0002036!2.15e-17!61;UBERON:0003082!2.15e-17!61;UBERON:0002385!4.84e-17!63;UBERON:0001015!4.84e-17!63;UBERON:0000383!4.84e-17!63;UBERON:0004290!2.24e-16!70;UBERON:0000486!6.93e-16!82;UBERON:0000490!3.33e-15!138;UBERON:0001637!3.45e-15!42;UBERON:0003509!3.45e-15!42;UBERON:0004572!3.45e-15!42;UBERON:0000119!6.03e-15!312;UBERON:0000477!1.35e-14!286;UBERON:0000483!1.55e-14!309;UBERON:0000475!7.05e-14!365;UBERON:0004573!2.15e-12!33;UBERON:0004571!2.15e-12!33;UBERON:0002100!2.64e-12!216;UBERON:0000468!3.83e-11!659;UBERON:0004111!4.12e-11!241;UBERON:0000481!4.03e-10!347;UBERON:0003104!2.77e-08!238;UBERON:0009142!2.77e-08!238;UBERON:0000947!3.42e-08!21;UBERON:0010191!3.42e-08!21;UBERON:0000025!3.66e-08!194;UBERON:0000353!8.61e-08!17;UBERON:0001986!1.81e-07!18;UBERON:0004638!1.81e-07!18;UBERON:0004852!1.81e-07!18;UBERON:0004211!2.89e-07!16;UBERON:0001285!2.89e-07!16;UBERON:0007684!2.89e-07!16;UBERON:0003220!2.89e-07!16;UBERON:0004208!2.89e-07!16;UBERON:0003103!5.80e-07!69;UBERON:0006555!8.51e-07!17;UBERON:0005103!8.51e-07!17;UBERON:0000083!8.51e-07!17;UBERON:0009201!8.51e-07!17;UBERON:0004819!8.51e-07!17;UBERON:0006553!8.51e-07!17;UBERON:0003074!8.51e-07!17;UBERON:0003060!8.51e-07!17;UBERON:0006914!8.82e-07!25;UBERON:0000480!9.81e-07!626
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37332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.0694567,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.00370214,0.0286025,0.00896808,0.0109933,0.038848,0.0874516,0.0550279,0.144067,0.000242011,0.217069,0.190048,0.131088,0.0144628,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.0637246,0.147698,0.141463,0.167267,0.140622,0.0889592,4.27652e-05,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.120459,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.000356768,0.047822,0.655293,0.21727,0.0465945,0.119215,0.192475,0.177967,0.188967,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.0121461,3.18684e-05,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.0457643,0.152372,0.194941,0.00207136,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.0998546,0.131093,0.0434602,0.133616,0.418146,0.00130397,0.449036,0.000211816,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.580441,0.276075,0.432035,0.366326,0.390366,0.48809,0.50058,0.443185,0.522904,0.0199034,0.00516504,0.227104,0.518585,0.250246,0.38649,0.284625,0.504757,0.192225,0.729153,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.191695,0.390974,0.73485,0.683217,0.161598,0.164332,0.277094,0.496032,0.0239796,0.37357,0.0704414,0.477353,0.00492096,0.160298,0.185744,0.20342,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,2.64048e-05,0.562405,0.314429,0.181415,0.282286,0.78,0.616388,0.408413,0.000926901,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,4.99296e-05,0.180745,0.222037,0.416621,0.416292,0.128937,0.0457685,0.215157,0.204817,0.452428,0.138871,0.103502,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.0830022,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.00164832,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.00358475,0.188263,0.0719199,0.00386277,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.0224033,0.179412,0.193601,0.220904,2.88613e-07,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.00376943,0.131118,0.20837,0.0335483,0.0267847,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.00160819,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.0246892,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.00899301,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.0404514,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205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}}
}}

Revision as of 12:52, 5 September 2012


Full id: C4144_Mesenchymal_Smooth_Renal_hepatic_Lens_epithelioid_Endothelial



Phase1 CAGE Peaks

Hg19::chr2:1748276..1748295,-p1@PXDN
Hg19::chr2:1748302..1748326,-p2@PXDN
Hg19::chr2:1748343..1748352,-p3@PXDN


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
vasculature6.76e-2979
vascular system6.76e-2979
vessel8.24e-2569
splanchnic layer of lateral plate mesoderm4.89e-2484
blood vessel6.31e-2160
epithelial tube open at both ends6.31e-2160
blood vasculature6.31e-2160
vascular cord6.31e-2160
epithelial tube2.37e-20118
cardiovascular system3.07e-20110
circulatory system6.60e-20113
somite1.14e-1783
paraxial mesoderm1.14e-1783
presomitic mesoderm1.14e-1783
presumptive segmental plate1.14e-1783
trunk paraxial mesoderm1.14e-1783
presumptive paraxial mesoderm1.14e-1783
trunk mesenchyme1.77e-17143
skeletal muscle tissue2.15e-1761
striated muscle tissue2.15e-1761
myotome2.15e-1761
muscle tissue4.84e-1763
musculature4.84e-1763
musculature of body4.84e-1763
dermomyotome2.24e-1670
multilaminar epithelium6.93e-1682
unilaminar epithelium3.33e-15138
artery3.45e-1542
arterial blood vessel3.45e-1542
arterial system3.45e-1542
cell layer6.03e-15312
anatomical cluster1.35e-14286
epithelium1.55e-14309
organism subdivision7.05e-14365
systemic artery2.15e-1233
systemic arterial system2.15e-1233
trunk2.64e-12216
multi-cellular organism3.83e-11659
anatomical conduit4.12e-11241
multi-tissue structure4.03e-10347
mesenchyme2.77e-08238
entire embryonic mesenchyme2.77e-08238
aorta3.42e-0821
aortic system3.42e-0821
tube3.66e-08194
parenchyma8.61e-0817
endothelium1.81e-0718
blood vessel endothelium1.81e-0718
cardiovascular system endothelium1.81e-0718
nephron epithelium2.89e-0716
nephron2.89e-0716
uriniferous tubule2.89e-0716
metanephric mesenchyme2.89e-0716
nephrogenic mesenchyme2.89e-0716
compound organ5.80e-0769
excretory tube8.51e-0717
mesonephric epithelium8.51e-0717
mesonephric tubule8.51e-0717
nephric duct8.51e-0717
kidney epithelium8.51e-0717
renal duct8.51e-0717
mesonephric duct8.51e-0717
pronephric duct8.51e-0717
squamous epithelium8.82e-0725
anatomical group9.81e-07626


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
E2F1#186934.907389214879320.008460985347239390.0326168923918623
NRF1#4899312.21027944771090.0005492172401020010.00471902092464113
ZNF263#1012738.221841637010680.001799043925565870.0109633766216696



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4144&oldid=2131662"