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Coexpression cluster:C255: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.481682,0.24193,0.129135,0.0352482,0.346819,0.930217,0.800478,0.316884,0.188904,0.0424525,1.62077,0.256585,1.56536,0.439327,0.0291717,0.230197,0.48452,0.558757,0.217236,0.307217,0.266546,0.42954,0.313076,0.18453,0.182796,0.0829608,1.32483,0.309568,0.1978,0.174587,0.461914,0.182397,0.855791,0.29989,1.20129,0.63573,0.631899,0.59473,0.532811,1.54653,0.26038,0.0881102,0.0988443,0.0286566,0.372808,0.327431,0.462982,0.261018,0.182027,0.355091,0.0890171,0.485536,0.318527,0.231144,0.3402,0.201607,0.20506,0.684497,0.174273,0.681743,1.12906,0.810437,0.31025,0.875041,0.862736,0.399312,0.409209,0.727856,0.176167,0.58255,0.203487,0.336077,1.13495,0.338683,0.571037,1.10888,0.0114078,0.136087,0.517685,0.0665908,0.356801,0.444341,0.065229,0.201092,0.300427,1.66555,0.411529,0.252137,0.330571,0.819547,0.485902,0.280966,0.562326,0.0340674,0.807344,0.194711,0.124517,0.62667,0.102812,0.0693411,0.538347,0.55395,0.618126,0.948857,0.384166,0.111808,0.153835,0.195261,1.24693,0.0752699,0.141419,0.214289,0.256068,0.538506,0.446027,0.134123,0.740708,0.0227223,0.396218,0.467564,0.332425,0.327579,0.920211,0.244408,0.539181,0.423787,0.203834,0.19576,0.956872,0.196584,0.281458,0.46874,0.376217,0.240788,0.496746,0.0432911,1.06717,0.310482,0.461248,1.25501,0.868564,0.430601,0.452197,0.217405,0.386463,0.370366,0.736749,1.10041,0.216868,0.0814693,0.808946,1.11128,0.770319,0.283234,0.213312,0.609476,0.0933429,0.17073,0.359306,2.32995,0.429612,0.268633,0.17377,0.30594,0.81035,0.231403,0.583406,0.0572615,1.47727
|tfbs_overrepresentation_for_novel_motifs=0.481682,0.24193,0.129135,0.0352482,0.346819,0.930217,0.800478,0.316884,0.188904,0.0424525,1.62077,0.256585,1.56536,0.439327,0.0291717,0.230197,0.48452,0.558757,0.217236,0.307217,0.266546,0.42954,0.313076,0.18453,0.182796,0.0829608,1.32483,0.309568,0.1978,0.174587,0.461914,0.182397,0.855791,0.29989,1.20129,0.63573,0.631899,0.59473,0.532811,1.54653,0.26038,0.0881102,0.0988443,0.0286566,0.372808,0.327431,0.462982,0.261018,0.182027,0.355091,0.0890171,0.485536,0.318527,0.231144,0.3402,0.201607,0.20506,0.684497,0.174273,0.681743,1.12906,0.810437,0.31025,0.875041,0.862736,0.399312,0.409209,0.727856,0.176167,0.58255,0.203487,0.336077,1.13495,0.338683,0.571037,1.10888,0.0114078,0.136087,0.517685,0.0665908,0.356801,0.444341,0.065229,0.201092,0.300427,1.66555,0.411529,0.252137,0.330571,0.819547,0.485902,0.280966,0.562326,0.0340674,0.807344,0.194711,0.124517,0.62667,0.102812,0.0693411,0.538347,0.55395,0.618126,0.948857,0.384166,0.111808,0.153835,0.195261,1.24693,0.0752699,0.141419,0.214289,0.256068,0.538506,0.446027,0.134123,0.740708,0.0227223,0.396218,0.467564,0.332425,0.327579,0.920211,0.244408,0.539181,0.423787,0.203834,0.19576,0.956872,0.196584,0.281458,0.46874,0.376217,0.240788,0.496746,0.0432911,1.06717,0.310482,0.461248,1.25501,0.868564,0.430601,0.452197,0.217405,0.386463,0.370366,0.736749,1.10041,0.216868,0.0814693,0.808946,1.11128,0.770319,0.283234,0.213312,0.609476,0.0933429,0.17073,0.359306,2.32995,0.429612,0.268633,0.17377,0.30594,0.81035,0.231403,0.583406,0.0572615,1.47727
|tfbs_overrepresentation_jaspar=MA0003.1;2.65757,MA0004.1;0.0287532,MA0006.1;0.0290142,MA0007.1;0.105058,MA0009.1;0.252434,MA0014.1;2.20334,MA0017.1;0.259054,MA0019.1;0.555905,MA0024.1;0.183969,MA0025.1;1.65237,MA0027.1;1.73105,MA0028.1;0.38452,MA0029.1;0.195946,MA0030.1;0.188804,MA0031.1;0.150659,MA0038.1;0.466212,MA0040.1;0.579034,MA0041.1;0.134241,MA0042.1;0.264815,MA0043.1;0.703596,MA0046.1;0.24494,MA0048.1;0.152472,MA0050.1;0.0259441,MA0051.1;0.0572096,MA0052.1;0.202085,MA0055.1;0.398929,MA0056.1;0,MA0057.1;0.570587,MA0058.1;0.0568651,MA0059.1;0.151766,MA0060.1;1.42636,MA0061.1;0.0300898,MA0063.1;0,MA0066.1;0.213568,MA0067.1;0.49981,MA0068.1;0.322801,MA0069.1;0.242306,MA0070.1;0.234718,MA0071.1;0.174636,MA0072.1;0.231695,MA0073.1;2.11352,MA0074.1;2.23582,MA0076.1;0.0138475,MA0077.1;1.20132,MA0078.1;1.09854,MA0081.1;0.151958,MA0083.1;0.715135,MA0084.1;0.664025,MA0087.1;0.230056,MA0088.1;0.148712,MA0089.1;0,MA0090.1;0.0160524,MA0091.1;0.534615,MA0092.1;0.441881,MA0093.1;0.00542575,MA0095.1;0,MA0098.1;0,MA0100.1;0.849289,MA0101.1;0.0312519,MA0103.1;0.751317,MA0105.1;0.472232,MA0106.1;0.547964,MA0107.1;0.0392752,MA0108.2;0.45517,MA0109.1;0,MA0111.1;0.209449,MA0113.1;0.0808928,MA0114.1;0.932237,MA0115.1;0.436009,MA0116.1;1.28368,MA0117.1;0.27892,MA0119.1;0.0482372,MA0122.1;0.806534,MA0124.1;0.402329,MA0125.1;0.8938,MA0130.1;0,MA0131.1;0.10574,MA0132.1;0,MA0133.1;0,MA0135.1;0.27375,MA0136.1;0.220509,MA0139.1;4.74703,MA0140.1;0.389168,MA0141.1;0.149727,MA0142.1;0.133251,MA0143.1;0.27686,MA0144.1;0.0751841,MA0145.1;0.79868,MA0146.1;0.289936,MA0147.1;0.012723,MA0148.1;0.0348816,MA0149.1;0.0422402,MA0062.2;0.122451,MA0035.2;0.387901,MA0039.2;3.32036,MA0138.2;0.0978028,MA0002.2;0.0875896,MA0137.2;0.402158,MA0104.2;0.00442204,MA0047.2;0.244302,MA0112.2;1.99723,MA0065.2;0.667807,MA0150.1;0.0704527,MA0151.1;0,MA0152.1;0.401045,MA0153.1;0.323801,MA0154.1;1.62697,MA0155.1;0.810786,MA0156.1;0.110132,MA0157.1;0.119034,MA0158.1;0,MA0159.1;0.751731,MA0160.1;0.152819,MA0161.1;0,MA0162.1;0.210045,MA0163.1;1.71766,MA0164.1;0.0861719,MA0080.2;0.0301046,MA0018.2;0.550787,MA0099.2;0.178704,MA0079.2;3.98856,MA0102.2;0.697711,MA0258.1;0.56487,MA0259.1;0.220187,MA0442.1;0
}}
}}

Revision as of 18:52, 22 January 2013


Full id: C255_Wilms_leiomyoblastoma_kidney_adrenal_MCF7_epithelioid_Mast



Phase1 CAGE Peaks

Hg19::chr10:43867077..43867098,+p1@FXYD4
Hg19::chr10:84983078..84983087,+p@chr10:84983078..84983087
+
Hg19::chr11:121513919..121513924,-p@chr11:121513919..121513924
-
Hg19::chr11:77792240..77792241,+p@chr11:77792240..77792241
+
Hg19::chr11:77792301..77792328,+p@chr11:77792301..77792328
+
Hg19::chr12:42983782..42983815,-p2@PRICKLE1
Hg19::chr12:42983843..42983865,-p3@PRICKLE1
Hg19::chr12:43946001..43946016,-p1@ADAMTS20
Hg19::chr15:39561378..39561415,-p@chr15:39561378..39561415
-
Hg19::chr15:88119982..88120003,+p2@LINC00052
Hg19::chr15:88120158..88120161,+p1@LINC00052
Hg19::chr15:88799370..88799383,-p6@NTRK3
Hg19::chr16:80838418..80838432,-p5@CDYL2
Hg19::chr16:80838441..80838473,-p2@CDYL2
Hg19::chr16:80838479..80838508,-p1@CDYL2
Hg19::chr17:41132410..41132418,-p8@AARSD1
Hg19::chr19:46651474..46651514,+p1@IGFL2
Hg19::chr19:50381565..50381605,-p4@AKT1S1
Hg19::chr1:153517273..153517295,-p5@S100A4
Hg19::chr1:172347750..172347761,+p11@DNM3
Hg19::chr1:180601188..180601207,+p2@XPR1
Hg19::chr1:180601215..180601233,+p4@XPR1
Hg19::chr1:183387723..183387763,-p7@NMNAT2
Hg19::chr1:201438498..201438583,-p3@PHLDA3
Hg19::chr1:201532249..201532262,+p@chr1:201532249..201532262
+
Hg19::chr1:201532269..201532289,+p@chr1:201532269..201532289
+
Hg19::chr1:43387667..43387671,-p@chr1:43387667..43387671
-
Hg19::chr1:62785019..62785032,-p4@KANK4
Hg19::chr1:62902308..62902335,+p9@USP1
Hg19::chr1:62902336..62902387,+p2@USP1
Hg19::chr1:62902414..62902438,+p5@USP1
Hg19::chr1:63213403..63213406,+p@chr1:63213403..63213406
+
Hg19::chr1:69521584..69521593,+p2@ENST00000425517
Hg19::chr20:42545244..42545247,-p@chr20:42545244..42545247
-
Hg19::chr21:18218138..18218142,-p@chr21:18218138..18218142
-
Hg19::chr2:139791638..139791647,+p@chr2:139791638..139791647
+
Hg19::chr2:140592929..140592932,+p@chr2:140592929..140592932
+
Hg19::chr3:47088671..47088676,-p28@SETD2
Hg19::chr3:96532316..96532327,+p@chr3:96532316..96532327
+
Hg19::chr3:96533452..96533467,+p3@EPHA6
Hg19::chr5:103006456..103006466,+p@chr5:103006456..103006466
+
Hg19::chr5:103012042..103012047,+p@chr5:103012042..103012047
+
Hg19::chr5:159343481..159343528,+p1@ADRA1B
Hg19::chr5:159343688..159343754,+p2@ADRA1B
Hg19::chr5:159343995..159344006,+p5@ADRA1B
Hg19::chr5:56247250..56247252,-p@chr5:56247250..56247252
-
Hg19::chr5:56248032..56248039,-p3@MIER3
Hg19::chr7:116070621..116070623,-p@chr7:116070621..116070623
-
Hg19::chr7:139168434..139168465,-p2@KLRG2
Hg19::chr9:15552504..15552550,+p13@C9orf93
Hg19::chrX:13062697..13062745,-p1@FAM9C


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:0031330negative regulation of cellular catabolic process0.0243337650614231
GO:0045818negative regulation of glycogen catabolic process0.0243337650614231
GO:0045819positive regulation of glycogen catabolic process0.0243337650614231
GO:0031329regulation of cellular catabolic process0.0243337650614231
GO:0005981regulation of glycogen catabolic process0.0243337650614231
GO:0001987vasoconstriction of artery involved in baroreceptor response to lowering of systemic arterial blood pressure0.0243337650614231
GO:0043278response to morphine0.0243337650614231
GO:0031331positive regulation of cellular catabolic process0.0243337650614231
GO:0014072response to isoquinoline alkaloid0.0243337650614231
GO:0001982baroreceptor response to decreased systemic arterial blood pressure0.0291923521403618
GO:0003099positive regulation of the force of heart contraction by chemical signal0.0291923521403618
GO:0001996positive regulation of heart rate by epinephrine-norepinephrine0.0291923521403618
GO:0048148behavioral response to cocaine0.0291923521403618
GO:0003057regulation of the force of heart contraction by chemical signal0.0291923521403618
GO:0001997positive regulation of the force of heart contraction by epinephrine-norepinephrine0.0291923521403618
GO:0004813alanine-tRNA ligase activity0.0298474661164654
GO:0045912negative regulation of carbohydrate metabolic process0.0298474661164654
GO:0010460positive regulation of heart rate0.0298474661164654
GO:0006419alanyl-tRNA aminoacylation0.0298474661164654
GO:0000309nicotinamide-nucleotide adenylyltransferase activity0.0298474661164654
GO:0042220response to cocaine0.0298474661164654
GO:0014073response to tropane0.0298474661164654
GO:0004714transmembrane receptor protein tyrosine kinase activity0.030184957028829
GO:0001978carotid sinus baroreceptor feedback regulation of systemic arterial blood pressure0.0312600309926838
GO:0003025baroreceptor regulation of systemic arterial blood pressure0.0312600309926838
GO:0001975response to amphetamine0.0312600309926838
GO:0014075response to amine stimulus0.0312600309926838
GO:0043526neuroprotection0.0312600309926838
GO:0019199transmembrane receptor protein kinase activity0.0321704466659882
GO:0004937alpha1-adrenergic receptor activity0.0321704466659882
GO:0043121neurotrophin binding0.0321704466659882
GO:0035265organ growth0.0321704466659882
GO:0045823positive regulation of heart contraction0.0321704466659882
GO:0001993regulation of systemic arterial blood pressure by norepinephrine-epinephrine0.0321704466659882
GO:0002027regulation of heart rate0.0347831181905141
GO:0005980glycogen catabolic process0.0347831181905141
GO:0009251glucan catabolic process0.0347831181905141
GO:0045913positive regulation of carbohydrate metabolic process0.0347831181905141
GO:0007512adult heart development0.0347831181905141
GO:0002026regulation of the force of heart contraction0.0347831181905141
GO:0009896positive regulation of catabolic process0.0347831181905141
GO:0001974blood vessel remodeling0.0347831181905141
GO:0003084positive regulation of systemic arterial blood pressure0.0347831181905141
GO:0008542visual learning0.0347831181905141
GO:0001976regulation of systemic arterial blood pressure by neurological process0.0364292713497891
GO:0006109regulation of carbohydrate metabolic process0.0364292713497891
GO:0000299integral to membrane of membrane fraction0.0364292713497891
GO:0043279response to alkaloid0.0364292713497891
GO:0009895negative regulation of catabolic process0.0393326162769219
GO:0004936alpha-adrenergic receptor activity0.0393326162769219
GO:0007632visual behavior0.0420102813890101
GO:0045777positive regulation of blood pressure0.0420102813890101
GO:0014070response to organic cyclic substance0.0444873434181894
GO:0001837epithelial to mesenchymal transition0.0444873434181894
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0454180426281821
GO:0003044regulation of systemic arterial blood pressure mediated by a chemical signal0.0467852967057092



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><br><br>

Cell Type
Ontology termp-valuen
embryonic stem cell2.94e-115


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)
MA0003.12.65757
MA0004.10.0287532
MA0006.10.0290142
MA0007.10.105058
MA0009.10.252434
MA0014.12.20334
MA0017.10.259054
MA0019.10.555905
MA0024.10.183969
MA0025.11.65237
MA0027.11.73105
MA0028.10.38452
MA0029.10.195946
MA0030.10.188804
MA0031.10.150659
MA0038.10.466212
MA0040.10.579034
MA0041.10.134241
MA0042.10.264815
MA0043.10.703596
MA0046.10.24494
MA0048.10.152472
MA0050.10.0259441
MA0051.10.0572096
MA0052.10.202085
MA0055.10.398929
MA0056.10
MA0057.10.570587
MA0058.10.0568651
MA0059.10.151766
MA0060.11.42636
MA0061.10.0300898
MA0063.10
MA0066.10.213568
MA0067.10.49981
MA0068.10.322801
MA0069.10.242306
MA0070.10.234718
MA0071.10.174636
MA0072.10.231695
MA0073.12.11352
MA0074.12.23582
MA0076.10.0138475
MA0077.11.20132
MA0078.11.09854
MA0081.10.151958
MA0083.10.715135
MA0084.10.664025
MA0087.10.230056
MA0088.10.148712
MA0089.10
MA0090.10.0160524
MA0091.10.534615
MA0092.10.441881
MA0093.10.00542575
MA0095.10
MA0098.10
MA0100.10.849289
MA0101.10.0312519
MA0103.10.751317
MA0105.10.472232
MA0106.10.547964
MA0107.10.0392752
MA0108.20.45517
MA0109.10
MA0111.10.209449
MA0113.10.0808928
MA0114.10.932237
MA0115.10.436009
MA0116.11.28368
MA0117.10.27892
MA0119.10.0482372
MA0122.10.806534
MA0124.10.402329
MA0125.10.8938
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.27375
MA0136.10.220509
MA0139.14.74703
MA0140.10.389168
MA0141.10.149727
MA0142.10.133251
MA0143.10.27686
MA0144.10.0751841
MA0145.10.79868
MA0146.10.289936
MA0147.10.012723
MA0148.10.0348816
MA0149.10.0422402
MA0062.20.122451
MA0035.20.387901
MA0039.23.32036
MA0138.20.0978028
MA0002.20.0875896
MA0137.20.402158
MA0104.20.00442204
MA0047.20.244302
MA0112.21.99723
MA0065.20.667807
MA0150.10.0704527
MA0151.10
MA0152.10.401045
MA0153.10.323801
MA0154.11.62697
MA0155.10.810786
MA0156.10.110132
MA0157.10.119034
MA0158.10
MA0159.10.751731
MA0160.10.152819
MA0161.10
MA0162.10.210045
MA0163.11.71766
MA0164.10.0861719
MA0080.20.0301046
MA0018.20.550787
MA0099.20.178704
MA0079.23.98856
MA0102.20.697711
MA0258.10.56487
MA0259.10.220187
MA0442.10



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
CTCF#10664171.786752124358340.009002194809137830.0341300404280519



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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C255&oldid=2568766"