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Coexpression cluster:C351: Difference between revisions

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|ontology_enrichment_disease=DOID:2394!7.08e-07!14
|ontology_enrichment_disease=DOID:2394!7.08e-07!14
|ontology_enrichment_uberon=UBERON:0000914!7.14e-21!83;UBERON:0002329!7.14e-21!83;UBERON:0003077!7.14e-21!83;UBERON:0003059!7.14e-21!83;UBERON:0007282!7.14e-21!83;UBERON:0009618!7.14e-21!83;UBERON:0007285!7.14e-21!83;UBERON:0000486!3.62e-20!82;UBERON:0004290!7.96e-20!70;UBERON:0004872!2.98e-19!84;UBERON:0002385!1.13e-18!63;UBERON:0001015!1.13e-18!63;UBERON:0000383!1.13e-18!63;UBERON:0001134!1.27e-18!61;UBERON:0002036!1.27e-18!61;UBERON:0003082!1.27e-18!61;UBERON:0001981!5.02e-16!60;UBERON:0007500!5.02e-16!60;UBERON:0004537!5.02e-16!60;UBERON:0006965!5.02e-16!60;UBERON:0005256!5.17e-16!143;UBERON:0002049!5.21e-16!79;UBERON:0007798!5.21e-16!79;UBERON:0001637!4.16e-15!42;UBERON:0003509!4.16e-15!42;UBERON:0004572!4.16e-15!42;UBERON:0000055!3.77e-14!69;UBERON:0004573!5.13e-13!33;UBERON:0004571!5.13e-13!33;UBERON:0003914!7.62e-13!118;UBERON:0000475!1.31e-12!365;UBERON:0000468!1.46e-12!659;UBERON:0000490!1.95e-12!138;UBERON:0002100!9.09e-12!216;UBERON:0001009!3.42e-11!113;UBERON:0004535!5.21e-11!110;UBERON:0003102!6.69e-10!95;UBERON:0000119!1.81e-09!312;UBERON:0000483!2.12e-09!309;UBERON:0002199!2.90e-09!45;UBERON:0002416!2.90e-09!45;UBERON:0000947!3.73e-09!21;UBERON:0010191!3.73e-09!21;UBERON:0000467!5.01e-09!625;UBERON:0000480!8.88e-09!626;UBERON:0000948!2.63e-07!24;UBERON:0005498!2.63e-07!24;UBERON:0004140!2.63e-07!24;UBERON:0009881!2.63e-07!24;UBERON:0004141!2.63e-07!24;UBERON:0003084!2.63e-07!24;UBERON:0007005!2.63e-07!24;UBERON:0004139!2.63e-07!24;UBERON:0004291!2.63e-07!24;UBERON:0007100!2.80e-07!27;UBERON:0002097!3.15e-07!40;UBERON:0001135!3.38e-07!15
|ontology_enrichment_uberon=UBERON:0000914!7.14e-21!83;UBERON:0002329!7.14e-21!83;UBERON:0003077!7.14e-21!83;UBERON:0003059!7.14e-21!83;UBERON:0007282!7.14e-21!83;UBERON:0009618!7.14e-21!83;UBERON:0007285!7.14e-21!83;UBERON:0000486!3.62e-20!82;UBERON:0004290!7.96e-20!70;UBERON:0004872!2.98e-19!84;UBERON:0002385!1.13e-18!63;UBERON:0001015!1.13e-18!63;UBERON:0000383!1.13e-18!63;UBERON:0001134!1.27e-18!61;UBERON:0002036!1.27e-18!61;UBERON:0003082!1.27e-18!61;UBERON:0001981!5.02e-16!60;UBERON:0007500!5.02e-16!60;UBERON:0004537!5.02e-16!60;UBERON:0006965!5.02e-16!60;UBERON:0005256!5.17e-16!143;UBERON:0002049!5.21e-16!79;UBERON:0007798!5.21e-16!79;UBERON:0001637!4.16e-15!42;UBERON:0003509!4.16e-15!42;UBERON:0004572!4.16e-15!42;UBERON:0000055!3.77e-14!69;UBERON:0004573!5.13e-13!33;UBERON:0004571!5.13e-13!33;UBERON:0003914!7.62e-13!118;UBERON:0000475!1.31e-12!365;UBERON:0000468!1.46e-12!659;UBERON:0000490!1.95e-12!138;UBERON:0002100!9.09e-12!216;UBERON:0001009!3.42e-11!113;UBERON:0004535!5.21e-11!110;UBERON:0003102!6.69e-10!95;UBERON:0000119!1.81e-09!312;UBERON:0000483!2.12e-09!309;UBERON:0002199!2.90e-09!45;UBERON:0002416!2.90e-09!45;UBERON:0000947!3.73e-09!21;UBERON:0010191!3.73e-09!21;UBERON:0000467!5.01e-09!625;UBERON:0000480!8.88e-09!626;UBERON:0000948!2.63e-07!24;UBERON:0005498!2.63e-07!24;UBERON:0004140!2.63e-07!24;UBERON:0009881!2.63e-07!24;UBERON:0004141!2.63e-07!24;UBERON:0003084!2.63e-07!24;UBERON:0007005!2.63e-07!24;UBERON:0004139!2.63e-07!24;UBERON:0004291!2.63e-07!24;UBERON:0007100!2.80e-07!27;UBERON:0002097!3.15e-07!40;UBERON:0001135!3.38e-07!15
|tfbs_overrepresentation=0.00186981,0.136899,0.278627,0.0967951,0.686527,0.48911,0.374311,0.00235872,0.298722,0.242536,0.475592,0.512213,0.385725,0.0157331,0.0957444,0.494188,5.00775e-05,0.100098,0.439649,0.704702,0.186524,0.447884,0.598421,0.287605,0.0110686,0.0482168,0.00115955,0.637394,0.808975,0.004407,0.913399,0.140964,0.176416,1.21476e-05,0.520162,0.242689,0.927676,0.0807964,0.397005,0.521143,0.661152,0.233414,1.43572e-07,0.0692099,0.399393,0.325481,0.338616,0.0658052,0.715895,1.44134e-05,0.832161,0.0225422,0.539749,0.0880234,0.213794,0.341539,0.702569,0.921998,0.581042,0.032916,0.0411661,0.097151,0.126262,0.20657,0.450394,0.424558,0.0203694,0.142062,0.0731001,0.00395867,0.141913,0.00104912,0.262287,0.392911,0.0769244,0.168205,0.29451,0.379087,6.48377e-05,0.0747045,0.0940422,0.759424,0.370764,0.14318,0.166098,0.814561,0.50805,0.000278489,0.997261,0.152759,7.45258e-06,0.418708,0.656737,0.404099,0.614057,0.374401,0.593041,1.75854e-05,1.33787e-05,0.0591096,0.468213,0.00902891,0.485357,0.331615,0.739828,0.359661,0.522698,0.000201858,0.232573,0.430036,0.0672693,0.308536,0.0314232,0.015971,0.314977,0.306666,0.196824,0.463191,0.797425,0.607025,0.133147,0.728364,0.219309,0.000472389,0.68398,0.000311419,0.0198612,0.000594649,0.609403,0.0715622,0.0289199,0.563812,0.466589,0.217971,0.000715023,0.0355556,0.510977,0.00350256,0.301192,0.041392,0.217885,0.180229,0.100006,0.037066,0.179341,0.179133,0.304595,0.608798,0.345369,0.746821,0.218944,0.230811,0.627046,1.28656e-05,0.0799499,0.385137,0.563434,0.0230355,0.432331,0.306456,0.00744291,0.656334,0.0454184,0.244314,0.854048,0.14162,0.353248,0.0599126,0.355558,0.0210788,0.0633997,0.0226284,0.89815,0.447699,0.588777,0.634653,0.479233,8.08651e-05,0.160725,0.320931,2.38496e-05,0.40595,0.25652,0.37673,0.558198,0.390641,0.00174912,0.354278,0.602567,9.67166e-06,0.701465,0.0738173,0.000620231,0.764015,0.720592,0.40209,0.0578753,0.484825,0.526292,0.35146,0.0188536,0.0299678,0.283982,0.48668,0.79088,0.000501352,0.443688,0.000479988,0.104132,0.0616788,1.42949e-05,0.691369,0.0133856,0.137814,0.110459,0.316667,0.299862,0.313772,0.500449,0.111818,0.225136,0.0307512,2.02965e-05,0.0123985,0.558886,0.00371553,0.215234,0.616679,6.82482e-05,0.48254,0.0219495,0.153024,0.366125,0.00182476,0.000863495,0.647777,0.000198911,0.111936,0.851077,0.0165231,0.0225614,0.0440065,0.668752,0.0670892,0.0112779,8.53266e-07,0.0138038,0.00950234,0.873308,1.41092e-06,0.551215,0.17755,0.37508,0.000970133,0.00546035,1.1733e-08,0.000263884,0.909736,0.0431117,0.453955,0.494312,0.871685,0.0443034,0.060981,0.312466,0.0631521,0.594611,0.0859425,0.738228,0.567231,0.861946,0.502135,0.0408778,0.444039,0.619431,0.33883,0.0179981,0.0158989,0.67878,0.0160616,0.198401,0.0656665,9.99753e-05,0.490011,0.0753871,0.267528,0.627186,0.000852001,0.0135307,0.0479929,7.15381e-06,0.426265,1.44922e-08,0.0303377,0.000818778,6.40118e-05,0.0568254,0.0133959,4.34618e-07,5.08435e-05,1.74744e-06,3.74036e-06,0.000487211,4.39203e-05,0.0660794,0.000414186,0.129942,0.0700124,0.0180599,0.0402097,0.00584516,0.000193612,0.324998,0.00378901,8.34174e-07,0.0297605,3.19718e-05,0.103421,0.205204,0.025123,0.338342,2.94767e-08,0.00320055,0.000119392,0.00440069,0.399407,0.285816,5.38977e-06,0.026059,0.00150442,0.013359,0.894172,0.00093165,0.504993,0.387674,0.000243195,0.558465,1.22593e-05,0.668789,0.00170661,0.544428,0.656411,0.607134,0.667036,1.05198e-05,0.374793,0.0418907,0.0729247,5.6835e-07,0.000561853,0.754048,0.246119,8.92187e-06,0.36379,0.146032,0.00026735,0.00345638,0.523033,0.00945388,0.000439219,0.0680699,0.669495,0.0284724,0.0137869,4.18455e-09,2.59206e-05,3.73873e-07,9.51156e-07,0.0513831,0.566824,0.00291612,0.00165665,0.00164468,0.000615461,0.237896,0.059693,0.751883,0.0363722,0.167135,0.538311,0.000409125,0.000133975,0.679496,0.674525,0.491089,0.0194485,4.11741e-08,0.000189081,0.000169928,0.00267266,0.0395341,4.03622e-05,0.0547225,0.00104787,2.10307e-05,0.954282,0.150631,1.02194e-05,0.813196,6.16722e-07,1.54314e-06,0.00230065,3.32254e-08,0.201879,0.103502,0.398722,0.466251,0.000498146,0.00511495,0.101017,2.87854e-06,0.0356583,0.00119691,0.000793507,3.571e-08,0.350256,0.00595041,0.218979,9.24464e-06,0.871613,0.111002,0.340495,2.15151e-07,0.197381,0.00640215,0.0107444,6.3965e-10,0.727458,0.00103129,0.0164198,0.164342,0.732105,0.0540398,0.452741,0.157591,0.067247,0.0830877,0.324578,0.0296753,0.011878,2.38935e-06,4.95883e-06,0.0251975,0.655385,0.630603,0.480575,0.032455,0.17224,0.0908266,0.000381741,0.000965956,3.42131e-06,0.00063233,2.90127e-05,0.000282009,0.0230135,0.537649,0.457265,0.897844,0.579461,0.468705,9.90729e-06,0.000496764,0.437864,0.000272955,0.867201,0.396289,0.718099,0.0125216,0.378006,0.342955,0.0159922,0.0714315,0.700554,0.00837627,0.000745284,0.994041,0.175332,0.344756,0.463584,0.00817266,0.398127,0.00432595,0.00221463,0.329412,0.266242,0.0170501,0.284852,0.340427,0.380259,0.0407279,0.168243,0.771249,0.919489,0.00256314,0.474649,0.00241593,0.602686,0.168499,4.51482e-07,0.000332998,0.0185395,0.146192,0.00981408,0.000970864,0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}}
}}

Revision as of 19:14, 8 August 2012


Full id: C351_Fibroblast_Smooth_mesenchymal_Adipocyte_tenocyte_Synoviocyte_Hair



Phase1 CAGE Peaks

Hg19::chr14:75070388..75070409,-p@chr14:75070388..75070409
-
Hg19::chr16:4431001..4431014,+p4@VASN
Hg19::chr16:55513074..55513088,+p2@MMP2
Hg19::chr16:55513101..55513124,+p1@MMP2
Hg19::chr16:55516814..55516833,+p@chr16:55516814..55516833
+
Hg19::chr16:55516984..55517009,+p@chr16:55516984..55517009
+
Hg19::chr16:55519282..55519295,+p@chr16:55519282..55519295
+
Hg19::chr16:55519314..55519342,-p@chr16:55519314..55519342
-
Hg19::chr16:55519541..55519560,+p@chr16:55519541..55519560
+
Hg19::chr16:55519569..55519597,+p@chr16:55519569..55519597
+
Hg19::chr16:55519605..55519627,+p@chr16:55519605..55519627
+
Hg19::chr16:55522512..55522527,+p6@MMP2
Hg19::chr16:55522536..55522599,+p4@MMP2
Hg19::chr16:55523690..55523729,-p@chr16:55523690..55523729
-
Hg19::chr16:55525707..55525728,+p@chr16:55525707..55525728
+
Hg19::chr16:55525755..55525774,+p@chr16:55525755..55525774
+
Hg19::chr16:55525781..55525812,+p@chr16:55525781..55525812
+
Hg19::chr16:55527062..55527078,+p7@MMP2
Hg19::chr16:55527084..55527124,+p5@MMP2
Hg19::chr16:55532232..55532249,+p@chr16:55532232..55532249
+
Hg19::chr16:55536741..55536782,+p@chr16:55536741..55536782
+
Hg19::chr16:55539240..55539261,+p@chr16:55539240..55539261
+
Hg19::chr16:55539265..55539280,+p@chr16:55539265..55539280
+
Hg19::chr16:55539338..55539366,+p@chr16:55539338..55539366
+
Hg19::chr16:55539371..55539383,+p@chr16:55539371..55539383
+
Hg19::chr16:55539430..55539443,+p@chr16:55539430..55539443
+
Hg19::chr16:55539539..55539552,+p@chr16:55539539..55539552
+
Hg19::chr16:55539559..55539581,+p@chr16:55539559..55539581
+
Hg19::chr16:55539785..55539877,+p@chr16:55539785..55539877
+
Hg19::chr16:55539883..55539894,+p@chr16:55539883..55539894
+
Hg19::chr16:55539899..55539914,+p@chr16:55539899..55539914
+
Hg19::chr16:55540311..55540323,+p@chr16:55540311..55540323
+


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


GO IDGO nameFDR corrected p-value
GO:0001955blood vessel maturation0.00182503237960673
GO:0004228gelatinase A activity0.00182503237960673
GO:0030574collagen catabolic process0.00762948231814427
GO:0044256protein digestion0.00762948231814427
GO:0044254multicellular organismal protein catabolic process0.00762948231814427
GO:0044266multicellular organismal macromolecule catabolic process0.00762948231814427
GO:0044259multicellular organismal macromolecule metabolic process0.00762948231814427
GO:0044268multicellular organismal protein metabolic process0.00762948231814427
GO:0032963collagen metabolic process0.00762948231814427
GO:0044243multicellular organismal catabolic process0.00762948231814427
GO:0044236multicellular organismal metabolic process0.00762948231814427
GO:0030017sarcomere0.0138075264980836
GO:0021700developmental maturation0.0138075264980836
GO:0030016myofibril0.0138075264980836
GO:0044449contractile fiber part0.014586720778938
GO:0043292contractile fiber0.014586720778938
GO:0007586digestion0.0203692002083057
GO:0001568blood vessel development0.031812593175251
GO:0001944vasculature development0.031812593175251
GO:0004222metalloendopeptidase activity0.0360308646701287



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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
somite7.14e-2183
paraxial mesoderm7.14e-2183
presomitic mesoderm7.14e-2183
presumptive segmental plate7.14e-2183
trunk paraxial mesoderm7.14e-2183
presumptive paraxial mesoderm7.14e-2183
multilaminar epithelium3.62e-2082
dermomyotome7.96e-2070
splanchnic layer of lateral plate mesoderm2.98e-1984
muscle tissue1.13e-1863
musculature1.13e-1863
musculature of body1.13e-1863
skeletal muscle tissue1.27e-1861
striated muscle tissue1.27e-1861
myotome1.27e-1861
blood vessel5.02e-1660
epithelial tube open at both ends5.02e-1660
blood vasculature5.02e-1660
vascular cord5.02e-1660
trunk mesenchyme5.17e-16143
vasculature5.21e-1679
vascular system5.21e-1679
artery4.16e-1542
arterial blood vessel4.16e-1542
arterial system4.16e-1542
vessel3.77e-1469
systemic artery5.13e-1333
systemic arterial system5.13e-1333
epithelial tube7.62e-13118
organism subdivision1.31e-12365
multi-cellular organism1.46e-12659
unilaminar epithelium1.95e-12138
trunk9.09e-12216
circulatory system3.42e-11113
cardiovascular system5.21e-11110
surface structure6.69e-1095
cell layer1.81e-09312
epithelium2.12e-09309
integument2.90e-0945
integumental system2.90e-0945
aorta3.73e-0921
aortic system3.73e-0921
anatomical system5.01e-09625
anatomical group8.88e-09626
heart2.63e-0724
primitive heart tube2.63e-0724
primary heart field2.63e-0724
anterior lateral plate mesoderm2.63e-0724
heart tube2.63e-0724
heart primordium2.63e-0724
cardiac mesoderm2.63e-0724
cardiogenic plate2.63e-0724
heart rudiment2.63e-0724
primary circulatory organ2.80e-0727
skin of body3.15e-0740
smooth muscle tissue3.38e-0715
Disease
Ontology termp-valuen
ovarian cancer7.08e-0714


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)

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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


No analysis results for this cluster

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.