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Coexpression cluster:C576: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.514064,0.121261,0.167518,0.277483,0.429786,0.276158,0.338925,0.241,0.0669953,0.507384,0.252096,0.3759,0.177832,0.329255,0.137951,0.467196,0.534852,0.104074,0.431744,0.178501,0.16756,0.863227,0.26993,0.42122,0.581509,0.395548,0.348576,0.739386,1.38241,0.897048,0.662646,0.568576,0.0851517,1.55612,0.37247,0.908942,0.114552,0.27709,0.32965,0.0583135,0.115672,0.222502,0.246674,0.136946,0.783232,0.554944,0.339845,0.243586,0.394038,0.8571,0.407934,0.349819,0.698571,0.639823,0.784252,0.331716,0.143846,0.304469,0.567597,0.303639,0.606437,0.341844,0.512045,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,0.212516,0.532685,0.0195984,0.782342,0.388726,0.357608,1.33362,0.494371,0.556046,0.196113,0.443974,0.50868,0.356776,0.524924,0.733386,0.0363137,0.0669348,0.299485,0.430803,1.32629,0.95934,0.70782,0.584068,0.0892066,0.139351,0.0967938,0.750268,0.623577,0.434875,0.789337,0.33179,0.578851,0.618385,0.538198,0.468285,0.248535,0.523764,0.326366,0.20048,0.128402,0.175484,0.61581,0.49168,0.259545,0.912801,0.113572,0.117386,0.234099,0.476505,0.0908333,0.77444,0.428661,0.273941,0.959954,1.02031,0.495057,0.33358,0.588683,0.815183,0.321662,0.708473,0.667822,0.828971,0.953662,0.971853,0.118371,0.230408,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,0.620293,0.469857,0.297516,0.454976,1.61933,1.17609,0.0873523,0.943814,0.00708394,0.708834,0.489782,0.341434,1.09904,1.88113,0.406462,0.200711,0.179634,0.893382,0.691354,2.34273,0.181952,0.48429,0.937181,0.275921,0.89656,0.0958828
|tfbs_overrepresentation_jaspar=MA0003.1;0.0972587,MA0004.1;0.256222,MA0006.1;0.426713,MA0007.1;1.25763,MA0009.1;0.669377,MA0014.1;0.142864,MA0017.1;3.70421,MA0019.1;0.38027,MA0024.1;0.570967,MA0025.1;0.796882,MA0027.1;2.25966,MA0028.1;0.454219,MA0029.1;0.588958,MA0030.1;0.578277,MA0031.1;0.518602,MA0038.1;0.34128,MA0040.1;0.594421,MA0041.1;0.27117,MA0042.1;1.27338,MA0043.1;0.669676,MA0046.1;0.659066,MA0048.1;0.0932165,MA0050.1;0.688784,MA0051.1;0.337676,MA0052.1;0.598036,MA0055.1;0.120131,MA0056.1;0,MA0057.1;0.688135,MA0058.1;0.182945,MA0059.1;0.536577,MA0060.1;0.237888,MA0061.1;0.0537738,MA0063.1;0,MA0066.1;0.341645,MA0067.1;0.975379,MA0068.1;0.616525,MA0069.1;0.655419,MA0070.1;0.644843,MA0071.1;0.308534,MA0072.1;0.640598,MA0073.1;0.284448,MA0074.1;0.337035,MA0076.1;0.567195,MA0077.1;0.633326,MA0078.1;0.424186,MA0081.1;0.18212,MA0083.1;0.676499,MA0084.1;1.15904,MA0087.1;0.63829,MA0088.1;1.28272,MA0089.1;0,MA0090.1;0.593146,MA0091.1;0.258318,MA0092.1;1.2087,MA0093.1;0.139688,MA0095.1;0,MA0098.1;0,MA0100.1;0.930697,MA0101.1;0.141917,MA0103.1;0.411001,MA0105.1;0.0162551,MA0106.1;0.37688,MA0107.1;0.0950422,MA0108.2;0.515791,MA0109.1;0,MA0111.1;0.215855,MA0113.1;2.69148,MA0114.1;2.15005,MA0115.1;0.900969,MA0116.1;0.660297,MA0117.1;0.705104,MA0119.1;0.508209,MA0122.1;0.729811,MA0124.1;0.860724,MA0125.1;0.779672,MA0130.1;0,MA0131.1;0.440395,MA0132.1;0,MA0133.1;0,MA0135.1;0.698212,MA0136.1;0.347318,MA0139.1;0.181369,MA0140.1;0.30631,MA0141.1;1.02176,MA0142.1;0.489543,MA0143.1;0.391385,MA0144.1;0.596391,MA0145.1;0.7339,MA0146.1;1.07015,MA0147.1;0.326612,MA0148.1;0.758022,MA0149.1;0.298252,MA0062.2;0.745766,MA0035.2;0.305721,MA0039.2;0.072333,MA0138.2;0.425279,MA0002.2;0.82964,MA0137.2;0.465392,MA0104.2;0.236755,MA0047.2;0.959769,MA0112.2;0.124752,MA0065.2;2.27469,MA0150.1;0.201098,MA0151.1;0,MA0152.1;0.311809,MA0153.1;0.763487,MA0154.1;0.367546,MA0155.1;0.11478,MA0156.1;0.91467,MA0157.1;0.46471,MA0158.1;0,MA0159.1;1.64059,MA0160.1;0.786431,MA0161.1;0,MA0162.1;0.0065085,MA0163.1;0.563152,MA0164.1;0.402162,MA0080.2;0.851709,MA0018.2;0.378086,MA0099.2;0.312108,MA0079.2;0.0966405,MA0102.2;1.1957,MA0258.1;0.27007,MA0259.1;0.340204,MA0442.1;0
}}
}}

Revision as of 19:17, 22 January 2013


Full id: C576_Hepatocyte_hepatocellular_liver_Intestinal_mature_breast_Prostate



Phase1 CAGE Peaks

Hg19::chr10:113987378..113987454,-p@chr10:113987378..113987454
-
Hg19::chr10:7755243..7755254,-p@chr10:7755243..7755254
-
Hg19::chr10:7773844..7773851,+p@chr10:7773844..7773851
+
Hg19::chr12:57828432..57828442,+p7@INHBC
Hg19::chr12:57828463..57828472,+p9@INHBC
Hg19::chr16:85570675..85570678,+p@chr16:85570675..85570678
+
Hg19::chr17:19437692..19437704,-p1@AK127534
Hg19::chr17:7082861..7082882,-p9@ASGR1
Hg19::chr1:21996247..21996270,-p6@RAP1GAP
Hg19::chr2:20793103..20793113,-p@chr2:20793103..20793113
-
Hg19::chr2:44066386..44066398,-p6@ABCG5
Hg19::chr5:149516966..149516977,-p8@PDGFRB
Hg19::chr5:32174797..32174803,-p17@GOLPH3
Hg19::chr6:64231645..64231678,+p6@PTP4A1
Hg19::chr8:144417558..144417572,-p7@TOP1MT


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:0042493response to drug0.0221113997876872
GO:0006855multidrug transport0.0363522643590524
GO:0005017platelet-derived growth factor receptor activity0.0363522643590524
GO:0004873asialoglycoprotein receptor activity0.0363522643590524
GO:0004992platelet activating factor receptor activity0.0387711830818315
GO:0030299cholesterol absorption0.0458376287579303
GO:0003917DNA topoisomerase type I activity0.0458376287579303
GO:0044241lipid digestion0.0458376287579303
GO:0050892intestinal absorption0.0458376287579303
GO:0003918DNA topoisomerase (ATP-hydrolyzing) activity0.0458376287579303
GO:0005160transforming growth factor beta receptor binding0.0458376287579303
GO:0016020membrane0.0458376287579303
GO:0010212response to ionizing radiation0.0458376287579303
GO:0006268DNA unwinding during replication0.0458376287579303
GO:0006265DNA topological change0.0458376287579303
GO:0003916DNA topoisomerase activity0.0458376287579303
GO:0015893drug transport0.0458376287579303
GO:0032392DNA geometric change0.0458376287579303
GO:0032508DNA duplex unwinding0.0458376287579303
GO:0022600digestive system process0.0459595450544434
GO:0015238drug transporter activity0.0483613875409549
GO:0005021vascular endothelial growth factor receptor activity0.0483613875409549



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
metabolising cell3.55e-4612
endopolyploid cell3.55e-4612
parenchymal cell3.55e-4612
polyploid cell3.55e-4612
hepatocyte3.55e-4612
endodermal cell9.15e-1058
Uber Anatomy
Ontology termp-valuen
liver1.67e-5619
digestive gland1.67e-5619
liver bud1.67e-5619
hepatic diverticulum7.93e-4922
liver primordium7.93e-4922
digestive tract diverticulum1.03e-4623
epithelial sac5.45e-4325
epithelium of foregut-midgut junction5.45e-4325
anatomical boundary5.45e-4325
hepatobiliary system5.45e-4325
foregut-midgut junction5.45e-4325
septum transversum5.45e-4325
sac2.42e-4126
exocrine gland1.07e-3431
exocrine system1.07e-3431
endocrine gland9.61e-3135
endocrine system6.32e-2445
gut epithelium6.12e-2054
abdomen element6.12e-2054
abdominal segment element6.12e-2054
gland3.01e-1859
abdominal segment of trunk6.06e-1860
abdomen6.06e-1860
endo-epithelium4.14e-1382
foregut2.38e-1287
trunk region element1.29e-10101
subdivision of trunk1.48e-09112
immaterial anatomical entity3.86e-09117
epithelial tube3.86e-09117
subdivision of digestive tract5.54e-09118
trunk mesenchyme9.32e-09122
digestive system2.81e-07145
digestive tract2.81e-07145
primitive gut2.81e-07145
unilaminar epithelium3.55e-07148


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)
MA0003.10.0972587
MA0004.10.256222
MA0006.10.426713
MA0007.11.25763
MA0009.10.669377
MA0014.10.142864
MA0017.13.70421
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.11.27338
MA0043.10.669676
MA0046.10.659066
MA0048.10.0932165
MA0050.10.688784
MA0051.10.337676
MA0052.10.598036
MA0055.10.120131
MA0056.10
MA0057.10.688135
MA0058.10.182945
MA0059.10.536577
MA0060.10.237888
MA0061.10.0537738
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.616525
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.10.284448
MA0074.10.337035
MA0076.10.567195
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.11.28272
MA0089.10
MA0090.10.593146
MA0091.10.258318
MA0092.11.2087
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.10.141917
MA0103.10.411001
MA0105.10.0162551
MA0106.10.37688
MA0107.10.0950422
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.12.69148
MA0114.12.15005
MA0115.10.900969
MA0116.10.660297
MA0117.10.705104
MA0119.10.508209
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.30631
MA0141.11.02176
MA0142.10.489543
MA0143.10.391385
MA0144.10.596391
MA0145.10.7339
MA0146.11.07015
MA0147.10.326612
MA0148.10.758022
MA0149.10.298252
MA0062.20.745766
MA0035.20.305721
MA0039.20.072333
MA0138.20.425279
MA0002.20.82964
MA0137.20.465392
MA0104.20.236755
MA0047.20.959769
MA0112.20.124752
MA0065.22.27469
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.367546
MA0155.10.11478
MA0156.10.91467
MA0157.10.46471
MA0158.10
MA0159.11.64059
MA0160.10.786431
MA0161.10
MA0162.10.0065085
MA0163.10.563152
MA0164.10.402162
MA0080.20.851709
MA0018.20.378086
MA0099.20.312108
MA0079.20.0966405
MA0102.21.1957
MA0258.10.27007
MA0259.10.340204
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
CEBPB#105163.188459050329930.007086617758029420.02955157804076
EP300#203383.612768920652370.0005452671939171080.00470949061077645
FOXA1#316953.693806583128480.008293763036037370.0326741726790157
FOXA2#317058.210154584221750.0002349349652283730.00256442023761351
HDAC2#306654.471873412208750.003658657523086560.0184753182986963
HEY1#23462123.232088834484571.10567306413993e-050.00028597174132172
HNF4A#3172913.87937421777222.07194282394466e-091.78393764707301e-07
HNF4G#31741019.16894835096456.57815993221828e-128.41931918089393e-10
RXRA#625668.02984685565335.16480117100425e-050.000878941941499939
SP1#666793.419028826884540.0002830127128465880.00301085512040184
TCF7L2#693453.590058854379110.009346606803531750.0353038071592786



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:C576&oldid=2569087"