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{{Coexpression_clusters
{{Coexpression_clusters|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0405018798333213,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.17777846941196,0.38470270793763,0.169385553164967,0,0.294157392104326,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0717872243853448,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.282468004036684,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.167529704189155,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.892279763218699,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0827735932201013,0,0,0.609788502995602,0.103551833417506,0,0,0,0,0,0,0,0,0,0,0.439188277874969,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.855282509242381,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.130127646808081,0.19240215837341,0.168690662036416,0.100775695696297,0,0,0,0,0,0,0,0,0,0,0.141477981839096,0.0524617670341519,0,0,0,0,0,0,0,0,0,0,0,0,0,0.111633612091231,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.125394621167623,0,0,0.0299437206513134,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0849077133655763,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.938801228533216,0,0,0,0,0,0,0,0,0,0,1.15292548286229,0.502166084918874,0,0,0,0,0,0,0,0,0,0,0,0,0,0.119065270453924,0,0,0,0,0,0.718685558632018,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0|full_id=C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver|gostat_on_coexpression_clusters=GO:0030299!cholesterol absorption!0.0135790157865837!29881$GO:0044241!lipid digestion!0.0135790157865837!29881$GO:0050892!intestinal absorption!0.0135790157865837!29881$GO:0008158!hedgehog receptor activity!0.0135790157865837!29881$GO:0015918!sterol transport!0.0135790157865837!29881$GO:0030301!cholesterol transport!0.0135790157865837!29881$GO:0022600!digestive system process!0.0135790157865837!29881$GO:0006695!cholesterol biosynthetic process!0.0156323542899154!29881$GO:0016126!sterol biosynthetic process!0.01833980188362!29881$GO:0006487!protein amino acid N-linked glycosylation!0.0249859883709692!7104$GO:0016324!apical plasma membrane!0.0249859883709692!29881$GO:0044459!plasma membrane part!0.0249859883709692!7104;29881$GO:0008203!cholesterol metabolic process!0.0249859883709692!29881$GO:0042157!lipoprotein metabolic process!0.0249859883709692!29881$GO:0045177!apical part of cell!0.0249859883709692!29881$GO:0009058!biosynthetic process!0.0249859883709692!7104;29881$GO:0006694!steroid biosynthetic process!0.0249859883709692!29881$GO:0016125!sterol metabolic process!0.0249859883709692!29881$GO:0007586!digestion!0.0249859883709692!29881$GO:0030659!cytoplasmic vesicle membrane!0.0254574086141063!29881$GO:0044433!cytoplasmic vesicle part!0.0254574086141063!29881$GO:0012506!vesicle membrane!0.0256606148778984!29881$GO:0006869!lipid transport!0.0293140852477049!29881$GO:0006486!protein amino acid glycosylation!0.0349355291417189!7104$GO:0043413!biopolymer glycosylation!0.0349355291417189!7104$GO:0009101!glycoprotein biosynthetic process!0.0349355291417189!7104$GO:0009100!glycoprotein metabolic process!0.0374071710405309!7104$GO:0005886!plasma membrane!0.0374071710405309!7104;29881$GO:0008202!steroid metabolic process!0.0374071710405309!29881$GO:0008285!negative regulation of cell 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A0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.729959,MA0155.1;1.25014,MA0156.1;0.257809,MA0157.1;1.4867,MA0158.1;0,MA0159.1;1.64451,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.108522,MA0163.1;0.0728181,MA0164.1;0.544294,MA0080.2;0.238846,MA0018.2;0.517858,MA0099.2;1.12985,MA0079.2;0.0179307,MA0102.2;1.36707,MA0258.1;0.472117,MA0259.1;0.191914,MA0442.1;0}}
|full_id=C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver
|gostat_on_coexpression_clusters=GO:0030299!cholesterol absorption!0.0135790157865837!29881$GO:0044241!lipid digestion!0.0135790157865837!29881$GO:0050892!intestinal absorption!0.0135790157865837!29881$GO:0008158!hedgehog receptor activity!0.0135790157865837!29881$GO:0015918!sterol transport!0.0135790157865837!29881$GO:0030301!cholesterol transport!0.0135790157865837!29881$GO:0022600!digestive system process!0.0135790157865837!29881$GO:0006695!cholesterol biosynthetic process!0.0156323542899154!29881$GO:0016126!sterol biosynthetic process!0.01833980188362!29881$GO:0006487!protein amino acid N-linked glycosylation!0.0249859883709692!7104$GO:0016324!apical plasma membrane!0.0249859883709692!29881$GO:0044459!plasma membrane part!0.0249859883709692!7104;29881$GO:0008203!cholesterol metabolic process!0.0249859883709692!29881$GO:0042157!lipoprotein metabolic process!0.0249859883709692!29881$GO:0045177!apical part of cell!0.0249859883709692!29881$GO:0009058!biosynthetic process!0.0249859883709692!7104;29881$GO:0006694!steroid biosynthetic process!0.0249859883709692!29881$GO:0016125!sterol metabolic process!0.0249859883709692!29881$GO:0007586!digestion!0.0249859883709692!29881$GO:0030659!cytoplasmic vesicle membrane!0.0254574086141063!29881$GO:0044433!cytoplasmic vesicle part!0.0254574086141063!29881$GO:0012506!vesicle membrane!0.0256606148778984!29881$GO:0006869!lipid transport!0.0293140852477049!29881$GO:0006486!protein amino acid glycosylation!0.0349355291417189!7104$GO:0043413!biopolymer glycosylation!0.0349355291417189!7104$GO:0009101!glycoprotein biosynthetic process!0.0349355291417189!7104$GO:0009100!glycoprotein metabolic process!0.0374071710405309!7104$GO:0005886!plasma membrane!0.0374071710405309!7104;29881$GO:0008202!steroid metabolic process!0.0374071710405309!29881$GO:0008285!negative regulation of cell proliferation!0.0374071710405309!7104
|id=C794
}}

Latest revision as of 11:31, 17 September 2013


Full id: C794_small_signet_adenocarcinoma_colon_Hepatocyte_gall_liver



Phase1 CAGE Peaks

Hg19::chr11:123461510..123461537,+p@chr11:123461510..123461537
+
Hg19::chr12:49741821..49741836,+p@chr12:49741821..49741836
+
Hg19::chr20:60987744..60987756,-p@chr20:60987744..60987756
-
Hg19::chr3:149192427..149192438,+p2@TM4SF4
Hg19::chr7:155754002..155754015,+p@chr7:155754002..155754015
+
Hg19::chr7:155754027..155754046,+p@chr7:155754027..155754046
+
Hg19::chr7:15707836..15707857,+p1@ENST00000451240
p1@uc003ste.2
Hg19::chr7:44580861..44580912,-p1@NPC1L1
Hg19::chr7:44580918..44580934,-p2@NPC1L1
Hg19::chr9:130877633..130877641,-p@chr9:130877633..130877641
-


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:0030299cholesterol absorption0.0135790157865837
GO:0044241lipid digestion0.0135790157865837
GO:0050892intestinal absorption0.0135790157865837
GO:0008158hedgehog receptor activity0.0135790157865837
GO:0015918sterol transport0.0135790157865837
GO:0030301cholesterol transport0.0135790157865837
GO:0022600digestive system process0.0135790157865837
GO:0006695cholesterol biosynthetic process0.0156323542899154
GO:0016126sterol biosynthetic process0.01833980188362
GO:0006487protein amino acid N-linked glycosylation0.0249859883709692
GO:0016324apical plasma membrane0.0249859883709692
GO:0044459plasma membrane part0.0249859883709692
GO:0008203cholesterol metabolic process0.0249859883709692
GO:0042157lipoprotein metabolic process0.0249859883709692
GO:0045177apical part of cell0.0249859883709692
GO:0009058biosynthetic process0.0249859883709692
GO:0006694steroid biosynthetic process0.0249859883709692
GO:0016125sterol metabolic process0.0249859883709692
GO:0007586digestion0.0249859883709692
GO:0030659cytoplasmic vesicle membrane0.0254574086141063
GO:0044433cytoplasmic vesicle part0.0254574086141063
GO:0012506vesicle membrane0.0256606148778984
GO:0006869lipid transport0.0293140852477049
GO:0006486protein amino acid glycosylation0.0349355291417189
GO:0043413biopolymer glycosylation0.0349355291417189
GO:0009101glycoprotein biosynthetic process0.0349355291417189
GO:0009100glycoprotein metabolic process0.0374071710405309
GO:0005886plasma membrane0.0374071710405309
GO:0008202steroid metabolic process0.0374071710405309
GO:0008285negative regulation of cell proliferation0.0374071710405309



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 cell1.61e-2712
endopolyploid cell1.61e-2712
parenchymal cell1.61e-2712
polyploid cell1.61e-2712
hepatocyte1.61e-2712
endodermal cell3.47e-1058
intestinal epithelial cell8.25e-084
Uber Anatomy
Ontology termp-valuen
epithelium of foregut-midgut junction6.64e-2625
anatomical boundary6.64e-2625
hepatobiliary system6.64e-2625
foregut-midgut junction6.64e-2625
septum transversum6.64e-2625
hepatic diverticulum7.26e-2422
liver primordium7.26e-2422
intestine1.00e-2317
small intestine6.95e-234
digestive tract diverticulum9.07e-2323
liver3.58e-2219
digestive gland3.58e-2219
liver bud3.58e-2219
epithelial sac7.72e-2125
gastrointestinal system2.81e-2025
sac5.52e-2026
gut epithelium5.09e-1954
abdomen element3.95e-1654
abdominal segment element3.95e-1654
subdivision of digestive tract2.76e-15118
abdominal segment of trunk2.68e-1460
abdomen2.68e-1460
digestive system2.01e-13145
digestive tract2.01e-13145
primitive gut2.01e-13145
exocrine gland3.63e-1331
exocrine system3.63e-1331
endoderm-derived structure7.92e-12160
endoderm7.92e-12160
presumptive endoderm7.92e-12160
endo-epithelium1.07e-1182
endocrine gland1.56e-1135
endocrine system5.11e-1145
duodenum3.75e-102
trunk region element4.70e-09101
gland4.79e-0859
hepatopancreatic ampulla7.16e-081
extrahepatic bile duct7.16e-081
common bile duct7.16e-081
duodenal papilla7.16e-081
intestinal mucosa8.25e-084
wall of intestine8.25e-084
gastrointestinal system mucosa8.25e-084
gastrointestinal system epithelium8.25e-084
intestinal epithelium8.25e-084
colon2.05e-079
organ system subdivision2.62e-07223


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)
MA0003.10.0586157
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.15363
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.11.73868
MA0031.10.669876
MA0038.11.20033
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.13.17924
MA0048.10.480635
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.211138
MA0058.10.796055
MA0059.10.79343
MA0060.10.848451
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.00880943
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.11.95087
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.422512
MA0106.10.516528
MA0107.10.529721
MA0108.21.6011
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.11.5848
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.12.22106
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.740103
MA0035.20.437071
MA0039.20.0721026
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.313961
MA0065.20.963081
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.729959
MA0155.11.25014
MA0156.10.257809
MA0157.11.4867
MA0158.10
MA0159.11.64451
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.0728181
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.21.12985
MA0079.20.0179307
MA0102.21.36707
MA0258.10.472117
MA0259.10.191914
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
EP300#203353.38697086311160.009216261698114180.0348391905128618
FOSL2#235546.772080241824680.001913955163860850.0112608621124705
HNF4A#3172511.56614518147683.16474693899284e-050.00063549895320414
HNF4G#3174411.50136901057870.0002593045920322360.00278129940302503
MAFF#23764211.2630712979890.01290318508912210.0464064102594036
SREBF2#6721287.38865248226950.0002323059271552280.00255306731833788



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.

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