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{{Coexpression_clusters
{
|full_id=C894_small_hepatoblastoma_colon_hepatocellular_liver_Intestinal_Prostate
|

Latest revision as of 11:33, 17 September 2013


Full id: C894_small_hepatoblastoma_colon_hepatocellular_liver_Intestinal_Prostate



Phase1 CAGE Peaks

Hg19::chr12:53497263..53497311,+p1@SOAT2
Hg19::chr15:65337469..65337477,+p9@OSTBETA
Hg19::chr15:65337671..65337680,+p4@OSTBETA
Hg19::chr15:65337778..65337794,+p3@OSTBETA
Hg19::chr17:28550048..28550058,-p@chr17:28550048..28550058
-
Hg19::chr19:49128245..49128254,+p13@SPHK2
Hg19::chr19:49128280..49128291,+p9@SPHK2
Hg19::chr3:38029450..38029458,+p12@VILL
Hg19::chr7:105517815..105517837,-p@chr7:105517815..105517837
-


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:0046511sphinganine biosynthetic process0.00576920244788202
GO:0006669sphinganine-1-phosphate biosynthetic process0.00576920244788202
GO:0006667sphinganine metabolic process0.00576920244788202
GO:0008481sphinganine kinase activity0.00576920244788202
GO:0006668sphinganine-1-phosphate metabolic process0.00576920244788202
GO:0004772sterol O-acyltransferase activity0.00576920244788202
GO:0046520sphingoid biosynthetic process0.0222457607846574
GO:0051693actin filament capping0.0305927686437621
GO:0051016barbed-end actin filament capping0.0305927686437621
GO:0030148sphingolipid biosynthetic process0.0305927686437621
GO:0030835negative regulation of actin filament depolymerization0.0305927686437621
GO:0030834regulation of actin filament depolymerization0.0305927686437621
GO:0030042actin filament depolymerization0.0305927686437621
GO:0044255cellular lipid metabolic process0.0311977777640363
GO:0004143diacylglycerol kinase activity0.0324737040564231
GO:0046519sphingoid metabolic process0.0324737040564231
GO:0008374O-acyltransferase activity0.0324737040564231
GO:0007205protein kinase C activation0.0324737040564231
GO:0001727lipid kinase activity0.0324737040564231
GO:0006629lipid metabolic process0.0324737040564231
GO:0008064regulation of actin polymerization and/or depolymerization0.0324737040564231
GO:0051261protein depolymerization0.0324737040564231
GO:0030832regulation of actin filament length0.0324737040564231
GO:0032535regulation of cellular component size0.0324737040564231
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0324737040564231
GO:0051129negative regulation of cellular component organization and biogenesis0.0333419790760655
GO:0048523negative regulation of cellular process0.0333419790760655
GO:0051493regulation of cytoskeleton organization and biogenesis0.0333419790760655
GO:0033043regulation of organelle organization and biogenesis0.0333419790760655
GO:0048519negative regulation of biological process0.0339362981913713
GO:0008154actin polymerization and/or depolymerization0.0339682814923601
GO:0006665sphingolipid metabolic process0.0366030174808241
GO:0032147activation of protein kinase activity0.0366030174808241
GO:0017016Ras GTPase binding0.038441991507084
GO:0008203cholesterol metabolic process0.038441991507084
GO:0031267small GTPase binding0.0396152345344609
GO:0005200structural constituent of cytoskeleton0.0396152345344609
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0399288269016283
GO:0016125sterol metabolic process0.0415466116649148
GO:0051020GTPase binding0.0417952136990352
GO:0051128regulation of cellular component organization and biogenesis0.0420313551711835
GO:0051248negative regulation of protein metabolic process0.042664293013026
GO:0046467membrane lipid biosynthetic process0.045260339858271



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 cell5.91e-1712
endopolyploid cell5.91e-1712
parenchymal cell5.91e-1712
polyploid cell5.91e-1712
hepatocyte5.91e-1712
intestinal epithelial cell2.08e-134
endodermal cell5.41e-1058
epithelial cell of large intestine1.99e-072
Uber Anatomy
Ontology termp-valuen
intestine2.08e-3317
small intestine3.47e-234
gastrointestinal system5.39e-2325
subdivision of digestive tract1.16e-13118
intestinal mucosa2.08e-134
wall of intestine2.08e-134
gastrointestinal system mucosa2.08e-134
gastrointestinal system epithelium2.08e-134
intestinal epithelium2.08e-134
colon4.41e-139
digestive system7.52e-11145
digestive tract7.52e-11145
primitive gut7.52e-11145
liver8.24e-1119
digestive gland8.24e-1119
liver bud8.24e-1119
large intestine8.26e-1111
gut epithelium8.88e-1154
endoderm-derived structure1.08e-09160
endoderm1.08e-09160
presumptive endoderm1.08e-09160
hepatic diverticulum2.29e-0922
liver primordium2.29e-0922
digestive tract diverticulum5.72e-0923
epithelial sac2.88e-0825
epithelium of foregut-midgut junction2.88e-0825
anatomical boundary2.88e-0825
hepatobiliary system2.88e-0825
foregut-midgut junction2.88e-0825
septum transversum2.88e-0825
sac5.89e-0826
abdomen element6.21e-0854
abdominal segment element6.21e-0854
organ system subdivision1.12e-07223
epithelium of mucosa3.78e-078
abdominal segment of trunk4.21e-0760
abdomen4.21e-0760
endo-epithelium6.93e-0782


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)
MA0003.10.0149552
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.12.25785
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.432181
MA0063.10
MA0066.12.21042
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.11.20007
MA0072.10.840664
MA0073.12.69853
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.01254
MA0089.10
MA0090.11.66392
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.11.73095
MA0115.11.11137
MA0116.10.208403
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.11.55341
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.11.3662
MA0147.10.211483
MA0148.11.95811
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.0512596
MA0138.20.608783
MA0002.21.45266
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.21.04513
MA0065.21.56252
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.12.22353
MA0154.10.225151
MA0155.10.645215
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.12.52807
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.604232
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.289676
MA0102.21.41188
MA0258.10.532421
MA0259.10.218904
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
BHLHE40#8553314.95727118232580.0008400100540424580.00633656988328929
FOXA2#317038.210154584221750.00467281236756890.0220525915434491
HDAC2#306645.9624978829450.002864271980786230.0155220891138093
HEY1#2346273.142308589082220.001258763462843770.00845808385099018
HNF4A#3172615.42152690863584.88730097228247e-072.29921092902797e-05
HNF4G#3174722.36377307612532.07633960554806e-091.78625067597886e-07
RXRA#625648.9220520618370.0006332213048085760.00519750077435577



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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