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Coexpression cluster:C254: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.00994446,0.31273,0.129135,0.596001,0.551135,1.33367,0.210268,0.10658,0.103045,0.0424525,0.277529,0.256585,0.429629,0.439327,0.546222,0.230197,0.48452,0.558757,0.0657141,0.307217,0.460478,0.111715,0.0328631,0.18453,0.182796,0.0829608,0.0745653,0.131203,1.12048,0.103661,0.0992195,0.182397,0.623456,0.29989,0.00318612,1.36554,0.0183901,0.0351221,0.348556,0.757282,0.26038,0.0881102,0.676349,0.00512216,0.0831551,0.0616916,0.0580955,0.0252168,0.733322,0.355091,0.299055,0.223593,0.219096,0.231144,0.901894,0.201607,0.578264,0.044455,0.541586,0.169121,0.207824,0.0589178,0.465675,0.875041,0.0653592,0.126911,0.409209,0.727856,0.176167,0.58255,0.0175642,1.20339,0.135729,0.898518,0.0204379,0.497936,1.48205,0.422759,0.174236,0.175042,0.706298,0.444341,0.861697,0.201092,0.300427,0.000200356,0.699045,1.90529,0.100673,0.819547,0.485902,0.768577,0.192665,1.49126,0.0891866,0.194711,0.124517,0.219696,0.687073,0.562547,0.0133748,0.55395,0.216077,0.162843,0.384166,1.17233,0.153835,0.432928,0.597506,0.494852,0.141419,0.613899,0.687351,0.122517,0.446027,0.134123,0.0154566,0.0227223,0.125708,0.467564,0.332425,0.327579,0.584558,1.86676,0.539181,0.423787,0.203834,1.70239,0.365014,0.196584,0.769699,0.248918,5.75074,0.240788,0.496746,1.80121,0.447768,0.567543,0.461248,1.25501,0.868564,0.430601,0.205577,0.217405,0.121929,0.0419814,0.113636,1.10041,0.416162,0.284107,0.0153812,0.0275181,0.28173,0.0923161,0.466559,0.609476,0.0933429,0.0250763,0.0701495,0.0110894,0.429612,0.268633,0.17377,0.0561604,0.130191,0.499875,0.14284,0.208912,0.0780672
|tfbs_overrepresentation_jaspar=MA0003.1;0.00892823,MA0004.1;0.0287532,MA0006.1;0.342164,MA0007.1;0.105058,MA0009.1;0.703091,MA0014.1;0.148222,MA0017.1;0.124978,MA0019.1;0.555905,MA0024.1;0.183969,MA0025.1;0.350278,MA0027.1;1.73105,MA0028.1;0.0348968,MA0029.1;0.195946,MA0030.1;0.188804,MA0031.1;0.459469,MA0038.1;0.466212,MA0040.1;1.09698,MA0041.1;0.134241,MA0042.1;0.10898,MA0043.1;0.252653,MA0046.1;0.685727,MA0048.1;0.0247203,MA0050.1;0.0259441,MA0051.1;0.208758,MA0052.1;0.584895,MA0055.1;0.0782628,MA0056.1;0,MA0057.1;0.0812865,MA0058.1;0.0116659,MA0059.1;0.0561949,MA0060.1;0.00449395,MA0061.1;0.693887,MA0063.1;0,MA0066.1;0.213568,MA0067.1;0.49981,MA0068.1;0.00408205,MA0069.1;0.242306,MA0070.1;0.234718,MA0071.1;1.52405,MA0072.1;0.231695,MA0073.1;0.00021799,MA0074.1;0.0569489,MA0076.1;0.0138475,MA0077.1;0.642781,MA0078.1;0.097239,MA0081.1;0.306407,MA0083.1;0.715135,MA0084.1;0.664025,MA0087.1;0.230056,MA0088.1;0.301993,MA0089.1;0,MA0090.1;0.924123,MA0091.1;0.121304,MA0092.1;0.441881,MA0093.1;0.00542575,MA0095.1;0,MA0098.1;0,MA0100.1;0.0636797,MA0101.1;0.0925848,MA0103.1;0.318689,MA0105.1;0.0312901,MA0106.1;0.0741862,MA0107.1;0.0959267,MA0108.2;0.45517,MA0109.1;0,MA0111.1;0.403858,MA0113.1;0.0808928,MA0114.1;0.307147,MA0115.1;0.436009,MA0116.1;0.98806,MA0117.1;0.27892,MA0119.1;2.69146,MA0122.1;0.297683,MA0124.1;1.03875,MA0125.1;0.8938,MA0130.1;0,MA0131.1;0.10574,MA0132.1;0,MA0133.1;0,MA0135.1;0.752104,MA0136.1;0.829173,MA0139.1;0.0557015,MA0140.1;0.389168,MA0141.1;0.0552982,MA0142.1;0.133251,MA0143.1;0.0809666,MA0144.1;0.611919,MA0145.1;0.047384,MA0146.1;0.00670092,MA0147.1;0.0431895,MA0148.1;0.592302,MA0149.1;0.0422402,MA0062.2;0.00915808,MA0035.2;0.387901,MA0039.2;0.0502555,MA0138.2;0.322872,MA0002.2;0.589195,MA0137.2;0.402158,MA0104.2;0.0475142,MA0047.2;0.523412,MA0112.2;0.241563,MA0065.2;1.43999,MA0150.1;0.360429,MA0151.1;0,MA0152.1;1.09269,MA0153.1;0.323801,MA0154.1;1.37971,MA0155.1;0.294601,MA0156.1;0.408437,MA0157.1;1.24443,MA0158.1;0,MA0159.1;0.344759,MA0160.1;0.35201,MA0161.1;0,MA0162.1;0.0107448,MA0163.1;0.0624314,MA0164.1;0.0861719,MA0080.2;0.81016,MA0018.2;0.0747401,MA0099.2;0.178704,MA0079.2;0.0281189,MA0102.2;0.697711,MA0258.1;0.24184,MA0259.1;0.368662,MA0442.1;0
}}
}}

Revision as of 18:52, 22 January 2013


Full id: C254_prostate_rhabdomyosarcoma_seminal_Fibroblast_transitionalcell_Smooth_Iris



Phase1 CAGE Peaks

Hg19::chr10:33624520..33624578,-p@chr10:33624520..33624578
-
Hg19::chr10:38146468..38146475,-p12@ZNF248
Hg19::chr10:38146482..38146507,-p4@ZNF248
Hg19::chr10:4808729..4808734,-p@chr10:4808729..4808734
-
Hg19::chr11:1221057..1221104,+p1@uc009ycs.1
Hg19::chr11:66583418..66583427,+p6@C11orf80
Hg19::chr12:52679734..52679755,-p@chr12:52679734..52679755
-
Hg19::chr13:66882589..66882629,+p@chr13:66882589..66882629
+
Hg19::chr14:62393999..62394005,+p@chr14:62393999..62394005
+
Hg19::chr14:62583348..62583354,+p3@FLJ43390
Hg19::chr15:69339407..69339410,+p3@NOX5
Hg19::chr15:74220458..74220472,-p11@LOC100287616
Hg19::chr15:74220487..74220499,-p9@LOC100287616
Hg19::chr15:74220519..74220531,-p8@LOC100287616
Hg19::chr15:74220536..74220564,-p3@LOC100287616
Hg19::chr15:74220590..74220602,-p15@LOC100287616
Hg19::chr15:74220651..74220670,-p5@LOC100287616
Hg19::chr17:46806016..46806029,-p5@HOXB13
Hg19::chr17:46806373..46806386,-p6@HOXB13
Hg19::chr17:46806404..46806415,-p7@HOXB13
Hg19::chr17:46806554..46806558,-p9@HOXB13
Hg19::chr17:49141793..49141801,-p@chr17:49141793..49141801
-
Hg19::chr1:85395365..85395368,-p6@MCOLN2
Hg19::chr20:24115408..24115418,+p@chr20:24115408..24115418
+
Hg19::chr20:58410917..58410928,+p12@PHACTR3
Hg19::chr20:58411263..58411271,+p34@PHACTR3
Hg19::chr21:46331846..46331872,-p29@ITGB2
Hg19::chr22:39410287..39410302,+p2@APOBEC3C
Hg19::chr2:189992577..189992580,-p@chr2:189992577..189992580
-
Hg19::chr2:36806022..36806034,-p20@FEZ2
Hg19::chr3:108160535..108160548,-p@chr3:108160535..108160548
-
Hg19::chr3:146464294..146464304,+p@chr3:146464294..146464304
+
Hg19::chr4:69614262..69614265,-p@chr4:69614262..69614265
-
Hg19::chr5:147297683..147297729,-p@chr5:147297683..147297729
-
Hg19::chr5:151055872..151055921,-p14@SPARC
Hg19::chr6:47010258..47010273,-p5@GPR110
Hg19::chr6:47010286..47010292,-p11@GPR110
Hg19::chr6:47010305..47010311,-p8@GPR110
Hg19::chr7:103086717..103086724,+p@chr7:103086717..103086724
+
Hg19::chr7:103086740..103086747,+p@chr7:103086740..103086747
+
Hg19::chr7:103310094..103310097,+p@chr7:103310094..103310097
+
Hg19::chr7:31855776..31855807,-p@chr7:31855776..31855807
-
Hg19::chr7:48251843..48251884,+p@chr7:48251843..48251884
+
Hg19::chr8:38687332..38687338,+p@chr8:38687332..38687338
+
Hg19::chr9:123788118..123788127,-p@chr9:123788118..123788127
-
Hg19::chr9:35753022..35753030,-p4@CU674847
Hg19::chr9:35753038..35753047,-p2@CU674847
Hg19::chr9:35753063..35753064,-p5@CU674847
Hg19::chr9:35754222..35754237,-p3@MSMP
Hg19::chr9:35754253..35754279,-p1@MSMP
Hg19::chr9:35754350..35754382,-p4@MSMP


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:0043012regulation of fusion of sperm to egg plasma membrane0.0376730967742162
GO:0010155regulation of proton transport0.0376730967742162
GO:0015252hydrogen ion channel activity0.0376730967742162
GO:0016175superoxide-generating NADPH oxidase activity0.0376730967742162



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><br>uberon_data<br><br>


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)
MA0003.10.00892823
MA0004.10.0287532
MA0006.10.342164
MA0007.10.105058
MA0009.10.703091
MA0014.10.148222
MA0017.10.124978
MA0019.10.555905
MA0024.10.183969
MA0025.10.350278
MA0027.11.73105
MA0028.10.0348968
MA0029.10.195946
MA0030.10.188804
MA0031.10.459469
MA0038.10.466212
MA0040.11.09698
MA0041.10.134241
MA0042.10.10898
MA0043.10.252653
MA0046.10.685727
MA0048.10.0247203
MA0050.10.0259441
MA0051.10.208758
MA0052.10.584895
MA0055.10.0782628
MA0056.10
MA0057.10.0812865
MA0058.10.0116659
MA0059.10.0561949
MA0060.10.00449395
MA0061.10.693887
MA0063.10
MA0066.10.213568
MA0067.10.49981
MA0068.10.00408205
MA0069.10.242306
MA0070.10.234718
MA0071.11.52405
MA0072.10.231695
MA0073.10.00021799
MA0074.10.0569489
MA0076.10.0138475
MA0077.10.642781
MA0078.10.097239
MA0081.10.306407
MA0083.10.715135
MA0084.10.664025
MA0087.10.230056
MA0088.10.301993
MA0089.10
MA0090.10.924123
MA0091.10.121304
MA0092.10.441881
MA0093.10.00542575
MA0095.10
MA0098.10
MA0100.10.0636797
MA0101.10.0925848
MA0103.10.318689
MA0105.10.0312901
MA0106.10.0741862
MA0107.10.0959267
MA0108.20.45517
MA0109.10
MA0111.10.403858
MA0113.10.0808928
MA0114.10.307147
MA0115.10.436009
MA0116.10.98806
MA0117.10.27892
MA0119.12.69146
MA0122.10.297683
MA0124.11.03875
MA0125.10.8938
MA0130.10
MA0131.10.10574
MA0132.10
MA0133.10
MA0135.10.752104
MA0136.10.829173
MA0139.10.0557015
MA0140.10.389168
MA0141.10.0552982
MA0142.10.133251
MA0143.10.0809666
MA0144.10.611919
MA0145.10.047384
MA0146.10.00670092
MA0147.10.0431895
MA0148.10.592302
MA0149.10.0422402
MA0062.20.00915808
MA0035.20.387901
MA0039.20.0502555
MA0138.20.322872
MA0002.20.589195
MA0137.20.402158
MA0104.20.0475142
MA0047.20.523412
MA0112.20.241563
MA0065.21.43999
MA0150.10.360429
MA0151.10
MA0152.11.09269
MA0153.10.323801
MA0154.11.37971
MA0155.10.294601
MA0156.10.408437
MA0157.11.24443
MA0158.10
MA0159.10.344759
MA0160.10.35201
MA0161.10
MA0162.10.0107448
MA0163.10.0624314
MA0164.10.0861719
MA0080.20.81016
MA0018.20.0747401
MA0099.20.178704
MA0079.20.0281189
MA0102.20.697711
MA0258.10.24184
MA0259.10.368662
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
ZZZ3#26009314.0831301432490.001302033896730150.0087224578666196



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

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