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{{Coexpression_clusters
{
|full_id=C1858_Hepatocyte_parotid_salivary_submaxillary_liver_small_cerebellum
 

Latest revision as of 11:53, 17 September 2013


Full id: C1858_Hepatocyte_parotid_salivary_submaxillary_liver_small_cerebellum



Phase1 CAGE Peaks

Hg19::chr1:41454160..41454176,+p6@CTPS
Hg19::chr1:41454185..41454224,+p5@CTPS
Hg19::chr1:41454251..41454260,+p21@CTPS
Hg19::chr6:46620445..46620463,-p1@CYP39A1
Hg19::chr6:46620465..46620476,-p3@CYP39A1


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:003378224-hydroxycholesterol 7alpha-hydroxylase activity0.00300247262451431
GO:0008387steroid 7-alpha-hydroxylase activity0.00300247262451431
GO:0008396oxysterol 7-alpha-hydroxylase activity0.00360286108933212
GO:0003883CTP synthase activity0.00360286108933212
GO:0030573bile acid catabolic process0.00360286108933212
GO:0006699bile acid biosynthetic process0.00500345816532559
GO:0006707cholesterol catabolic process0.00500345816532559
GO:0016127sterol catabolic process0.00500345816532559
GO:0019752carboxylic acid metabolic process0.00500345816532559
GO:0006082organic acid metabolic process0.00500345816532559
GO:0046395carboxylic acid catabolic process0.00500345816532559
GO:0016054organic acid catabolic process0.00500345816532559
GO:0008206bile acid metabolic process0.00643254415861032
GO:0008395steroid hydroxylase activity0.00643254415861032
GO:0006706steroid catabolic process0.00680400192983605
GO:0006541glutamine metabolic process0.00937941257394925
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0102888888512249
GO:0046036CTP metabolic process0.0102888888512249
GO:0009209pyrimidine ribonucleoside triphosphate biosynthetic process0.0102888888512249
GO:0009208pyrimidine ribonucleoside triphosphate metabolic process0.0102888888512249
GO:0006241CTP biosynthetic process0.0102888888512249
GO:0009220pyrimidine ribonucleotide biosynthetic process0.0106981654968376
GO:0009218pyrimidine ribonucleotide metabolic process0.0106981654968376
GO:0044242cellular lipid catabolic process0.0120012289244444
GO:0009147pyrimidine nucleoside triphosphate metabolic process0.0120012289244444
GO:0006221pyrimidine nucleotide biosynthetic process0.0122314812898656
GO:0044249cellular biosynthetic process0.0122882589398147
GO:0042493response to drug0.0134987973254267
GO:0006220pyrimidine nucleotide metabolic process0.0142733285258762
GO:0008203cholesterol metabolic process0.0150851187339486
GO:0009064glutamine family amino acid metabolic process0.0150851187339486
GO:0016053organic acid biosynthetic process0.0150851187339486
GO:0046394carboxylic acid biosynthetic process0.0150851187339486
GO:0009058biosynthetic process0.0152499402383358
GO:0006694steroid biosynthetic process0.0152499402383358
GO:0016125sterol metabolic process0.015396771212381
GO:0007586digestion0.015396771212381
GO:0009201ribonucleoside triphosphate biosynthetic process0.0190872381079814
GO:0009142nucleoside triphosphate biosynthetic process0.0193648990451604
GO:0009199ribonucleoside triphosphate metabolic process0.0197781111761532
GO:0016042lipid catabolic process0.0209721444520474
GO:0009141nucleoside triphosphate metabolic process0.0209721444520474
GO:0009260ribonucleotide biosynthetic process0.0218746911107329
GO:0005792microsome0.0220070949015963
GO:0042598vesicular fraction0.0220070949015963
GO:0009259ribonucleotide metabolic process0.0220070949015963
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0225557870057453
GO:0008202steroid metabolic process0.0278068183692588
GO:0004497monooxygenase activity0.028456624280113
GO:0009165nucleotide biosynthetic process0.0305107289082287
GO:0032787monocarboxylic acid metabolic process0.0328298187167133
GO:0020037heme binding0.0328298187167133
GO:0046906tetrapyrrole binding0.0328298187167133
GO:0008610lipid biosynthetic process0.0368495454127848
GO:0009117nucleotide metabolic process0.0369362602454575
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0388719701314618
GO:0016879ligase activity, forming carbon-nitrogen bonds0.0388719701314618
GO:0006066alcohol metabolic process0.0457713421174718
GO:0005789endoplasmic reticulum membrane0.0463011143602194
GO:0042175nuclear envelope-endoplasmic reticulum network0.0463365297057089
GO:0006520amino acid metabolic process0.0463365297057089
GO:0005506iron ion binding0.0483575825870521
GO:0044432endoplasmic reticulum part0.0491860097835861



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>disease_data<br>

Cell Type
Ontology termp-valuen
metabolising cell1.15e-1212
endopolyploid cell1.15e-1212
parenchymal cell1.15e-1212
polyploid cell1.15e-1212
hepatocyte1.15e-1212
Uber Anatomy
Ontology termp-valuen
exocrine gland1.83e-1831
exocrine system1.83e-1831
subdivision of digestive tract2.28e-18118
gland3.80e-1559
liver3.87e-1519
digestive gland3.87e-1519
liver bud3.87e-1519
digestive system3.63e-14145
digestive tract3.63e-14145
primitive gut3.63e-14145
major salivary gland5.51e-142
hepatic diverticulum5.89e-1322
liver primordium5.89e-1322
endoderm-derived structure1.92e-12160
endoderm1.92e-12160
presumptive endoderm1.92e-12160
digestive tract diverticulum2.35e-1223
intestine9.62e-1217
small intestine1.04e-114
abdomen element1.07e-1154
abdominal segment element1.07e-1154
epithelial sac2.69e-1125
epithelium of foregut-midgut junction2.69e-1125
anatomical boundary2.69e-1125
hepatobiliary system2.69e-1125
foregut-midgut junction2.69e-1125
septum transversum2.69e-1125
sac7.91e-1126
adult organism2.23e-10114
saliva-secreting gland2.49e-106
gland of oral region2.49e-106
gland of foregut2.49e-106
oral gland2.49e-106
oral cavity2.49e-106
abdominal segment of trunk2.51e-1060
abdomen2.51e-1060
gut epithelium1.44e-0954
foregut1.98e-0987
male genital duct5.51e-093
internal male genitalia5.51e-093
gastrointestinal system5.86e-0825
parotid gland7.50e-081
cheek7.50e-081
parotid gland primordium7.50e-081
submandibular gland8.00e-081
submandibular gland primordium8.00e-081
endocrine gland8.11e-0835
multi-tissue structure1.09e-07342
trunk region element1.18e-07101
organ system subdivision1.41e-07223
immaterial anatomical entity1.56e-07117
seminal vesicle1.72e-071
seminal fluid secreting gland1.72e-071
mitral valve1.83e-071
epididymis3.20e-071
uterus or analog3.62e-071
intralobular bile duct3.84e-071
acinus3.84e-071
intrahepatic bile duct3.84e-071
portal lobule3.84e-071
hepatic acinus3.84e-071
duct of male reproductive system6.07e-074
Disease
Ontology termp-valuen
vascular disease2.66e-071
ischemia2.66e-071
extrinsic cardiomyopathy2.66e-071
myocardial ischemia2.66e-071
myocardial infarction2.66e-071


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)
MA0003.10.136928
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.14.50736
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.12.51533
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.12.79236
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.11.36977
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.11.83541
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.11.40074
MA0113.11.8711
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.11.87149
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.21.65235
MA0039.20.0575907
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.12.71958
MA0154.10.172764
MA0155.10.409315
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.11.60707
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0442129
MA0102.21.66336
MA0258.10.914277
MA0259.10.395396
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

No analysis results for this cluster

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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