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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.15599724246889,

Latest revision as of 11:50, 17 September 2013


Full id: C1714_Hepatocyte_mature_liver_Synoviocyte_parotid_tenocyte_breast



Phase1 CAGE Peaks

Hg19::chr14:21152706..21152783,+p1@ANG
p1@RNASE4
Hg19::chr4:185726679..185726692,-p6@ACSL1
Hg19::chr4:77227797..77227808,+p4@STBD1
Hg19::chr4:77227809..77227820,+p5@STBD1
Hg19::chr4:77227845..77227860,+p3@STBD1


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:0032148activation of protein kinase B0.0104828061310714
GO:0032311angiogenin-PRI complex0.0104828061310714
GO:0032429regulation of phospholipase A2 activity0.0104828061310714
GO:0001556oocyte maturation0.0104828061310714
GO:0032431activation of phospholipase A20.0104828061310714
GO:0006651diacylglycerol biosynthetic process0.0104828061310714
GO:0032430positive regulation of phospholipase A2 activity0.0104828061310714
GO:0048662negative regulation of smooth muscle cell proliferation0.0114132670918778
GO:0001938positive regulation of endothelial cell proliferation0.0114132670918778
GO:0048599oocyte development0.0114132670918778
GO:0030246carbohydrate binding0.0114132670918778
GO:0046460neutral lipid biosynthetic process0.0114132670918778
GO:0009994oocyte differentiation0.0114132670918778
GO:0046339diacylglycerol metabolic process0.0114132670918778
GO:0046463acylglycerol biosynthetic process0.0114132670918778
GO:0046504glycerol ether biosynthetic process0.0115088380852527
GO:0045017glycerolipid biosynthetic process0.0115088380852527
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0128709689544981
GO:0015645fatty-acid ligase activity0.0128709689544981
GO:0048660regulation of smooth muscle cell proliferation0.0129699268652264
GO:0009303rRNA transcription0.0129699268652264
GO:0005624membrane fraction0.0129699268652264
GO:0048659smooth muscle cell proliferation0.0129699268652264
GO:0001890placenta development0.0129699268652264
GO:0007202phospholipase C activation0.0129699268652264
GO:0050714positive regulation of protein secretion0.0129699268652264
GO:0032501multicellular organismal process0.0129699268652264
GO:0001936regulation of endothelial cell proliferation0.0129699268652264
GO:0048477oogenesis0.0129699268652264
GO:0044255cellular lipid metabolic process0.0129699268652264
GO:0001541ovarian follicle development0.0129699268652264
GO:0030426growth cone0.0129699268652264
GO:0007281germ cell development0.0129699268652264
GO:0030427site of polarized growth0.0129699268652264
GO:0001935endothelial cell proliferation0.0129699268652264
GO:0033002muscle cell proliferation0.0129699268652264
GO:0051047positive regulation of secretion0.0129699268652264
GO:0004522pancreatic ribonuclease activity0.0129699268652264
GO:0042327positive regulation of phosphorylation0.0129699268652264
GO:0006638neutral lipid metabolic process0.0129699268652264
GO:0006639acylglycerol metabolic process0.0129699268652264
GO:0000267cell fraction0.0129699268652264
GO:0046486glycerolipid metabolic process0.0129699268652264
GO:0022601menstrual cycle phase0.0129699268652264
GO:0045937positive regulation of phosphate metabolic process0.0129699268652264
GO:0022602menstrual cycle process0.0129699268652264
GO:0006662glycerol ether metabolic process0.0129699268652264
GO:0006629lipid metabolic process0.0129699268652264
GO:0050708regulation of protein secretion0.0129699268652264
GO:0008585female gonad development0.0131258106267946
GO:0016892endoribonuclease activity, producing 3'-phosphomonoesters0.0131258106267946
GO:0016877ligase activity, forming carbon-sulfur bonds0.0131258106267946
GO:0046660female sex differentiation0.0131258106267946
GO:0046545development of primary female sexual characteristics0.0131258106267946
GO:0016894endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters0.013331151788889
GO:0030041actin filament polymerization0.0135291336434057
GO:0042698menstrual cycle0.0141484813821663
GO:0043025cell soma0.0144964345499042
GO:0007292female gamete generation0.0144964345499042
GO:0019843rRNA binding0.0146616763370218
GO:0005605basal lamina0.0160218026441832
GO:0017148negative regulation of translation0.0161569953268891
GO:0031327negative regulation of cellular biosynthetic process0.0166565806400099
GO:0005778peroxisomal membrane0.0166565806400099
GO:0048469cell maturation0.0166565806400099
GO:0031903microbody membrane0.0166565806400099
GO:0044439peroxisomal part0.016884205859888
GO:0044438microbody part0.016884205859888
GO:0001666response to hypoxia0.0169930388304039
GO:0009890negative regulation of biosynthetic process0.0176400003007381
GO:0048608reproductive structure development0.0176400003007381
GO:0008406gonad development0.0176400003007381
GO:0021700developmental maturation0.017732417975579
GO:0009306protein secretion0.0188107850763081
GO:0051046regulation of secretion0.0188545148732673
GO:0045137development of primary sexual characteristics0.0188545148732673
GO:0008154actin polymerization and/or depolymerization0.0188545148732673
GO:0048609reproductive process in a multicellular organism0.0188545148732673
GO:0032504multicellular organism reproduction0.0188545148732673
GO:0042325regulation of phosphorylation0.0195327876836674
GO:0051174regulation of phosphorus metabolic process0.0205421321007198
GO:0019220regulation of phosphate metabolic process0.0205421321007198
GO:0032147activation of protein kinase activity0.0205881552272556
GO:0004521endoribonuclease activity0.0209230556606885
GO:0005604basement membrane0.0210790797008298
GO:0009725response to hormone stimulus0.0210790797008298
GO:0008201heparin binding0.0210790797008298
GO:0051345positive regulation of hydrolase activity0.0210790797008298
GO:0007548sex differentiation0.0222101641048811
GO:0005741mitochondrial outer membrane0.0222338823698106
GO:0003006reproductive developmental process0.0233269439938313
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0233379140418386
GO:0031968organelle outer membrane0.0243951342809688
GO:0007586digestion0.024636467903827
GO:0019867outer membrane0.024636467903827
GO:0051258protein polymerization0.024636467903827
GO:0042579microbody0.024636467903827
GO:0004540ribonuclease activity0.024636467903827
GO:0005777peroxisome0.024636467903827
GO:0051248negative regulation of protein metabolic process0.0253627177922908
GO:0005539glycosaminoglycan binding0.0265556523991351
GO:0030247polysaccharide binding0.0276913871447646
GO:0005507copper ion binding0.0276913871447646
GO:0001871pattern binding0.0296569389378297
GO:0048015phosphoinositide-mediated signaling0.0296569389378297
GO:0001525angiogenesis0.0296569389378297
GO:0044420extracellular matrix part0.0298335129112542
GO:0045860positive regulation of protein kinase activity0.0318041813116468
GO:0033674positive regulation of kinase activity0.0321800304860929
GO:0051347positive regulation of transferase activity0.0322556951144632
GO:0048514blood vessel morphogenesis0.0322556951144632
GO:0004519endonuclease activity0.032833695199742
GO:0048646anatomical structure formation0.032972222229306
GO:0005792microsome0.0339570459220793
GO:0001568blood vessel development0.0339570459220793
GO:0003012muscle system process0.0339570459220793
GO:0006936muscle contraction0.0339570459220793
GO:0005730nucleolus0.0339570459220793
GO:0001944vasculature development0.0339570459220793
GO:0042598vesicular fraction0.0342796057165606
GO:0006417regulation of translation0.0369973583403696
GO:0006631fatty acid metabolic process0.0380822101533051
GO:0031326regulation of cellular biosynthetic process0.0393454125919087
GO:0042277peptide binding0.0407823737579117
GO:0009889regulation of biosynthetic process0.0421954160278696
GO:0008285negative regulation of cell proliferation0.0433935348567793
GO:0008284positive regulation of cell proliferation0.0442238454679207
GO:0016477cell migration0.0442238454679207
GO:0045859regulation of protein kinase activity0.0446290798871913
GO:0043549regulation of kinase activity0.0450999918537434
GO:0004518nuclease activity0.0450999918537434
GO:0030036actin cytoskeleton organization and biogenesis0.0450999918537434
GO:0051338regulation of transferase activity0.0450999918537434
GO:0043085positive regulation of catalytic activity0.046382160641243
GO:0030029actin filament-based process0.0467524227931329
GO:0007276gamete generation0.0471170717781419
GO:0019932second-messenger-mediated signaling0.0474762305321381



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
fat cell2.20e-0815
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.87e-18656
anatomical system4.92e-15624
anatomical group1.04e-14625
organ5.58e-12503
multi-tissue structure1.06e-09342
embryo1.44e-09592
organism subdivision1.50e-09264
developing anatomical structure7.08e-09581
embryonic structure2.01e-08564
germ layer6.48e-08560
germ layer / neural crest6.48e-08560
embryonic tissue6.48e-08560
presumptive structure6.48e-08560
germ layer / neural crest derived structure6.48e-08560
epiblast (generic)6.48e-08560
mesenchyme9.09e-08160
entire embryonic mesenchyme9.09e-08160
adult organism9.81e-08114
trunk1.18e-07199
endoderm-derived structure7.52e-07160
endoderm7.52e-07160
presumptive endoderm7.52e-07160


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)
MA0003.14.3611
MA0004.11.51734
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.14.38573
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
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
MA0043.11.11288
MA0046.11.10134
MA0048.11.7027
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.189508
MA0058.11.29981
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.362215
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
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.12.99362
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
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
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.946108
MA0147.11.77656
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.22.38271
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.11.57192
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.22.12087
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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
E2F1#186943.925911371903460.007214984547106360.0298745498598597
ZNF263#1012746.577473309608540.0009875103237900160.00709072469620526



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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