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Coexpression cluster:C4683: Difference between revisions

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{{Coexpression_clusters
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acid activation!0.000174999140341419!3376;2617$GO:0043039!tRNA aminoacylation!0.000174999140341419!3376;2617$GO:0006418!tRNA aminoacylation for protein translation!0.000174999140341419!3376;2617$GO:0016875!ligase activity, forming carbon-oxygen bonds!0.000174999140341419!3376;2617$GO:0016876!ligase activity, forming aminoacyl-tRNA and related compounds!0.000174999140341419!3376;2617$GO:0004812!aminoacyl-tRNA ligase activity!0.000174999140341419!3376;2617$GO:0006399!tRNA metabolic process!0.000386485029551408!3376;2617$GO:0005625!soluble fraction!0.000389759114775116!3376;2617$GO:0006520!amino acid metabolic process!0.00142466075754636!3376;2617$GO:0006519!amino acid and derivative metabolic process!0.0017073527239818!3376;2617$GO:0009308!amine metabolic process!0.0017073527239818!3376;2617$GO:0004820!glycine-tRNA ligase activity!0.0017073527239818!2617$GO:0006426!glycyl-tRNA aminoacylation!0.0017073527239818!2617$GO:0016874!ligase activity!0.0017073527239818!3376;2617$GO:0006807!nitrogen compound metabolic process!0.00175001427911881!3376;2617$GO:0004822!isoleucine-tRNA ligase activity!0.0019143533411074!3376$GO:0006428!isoleucyl-tRNA aminoacylation!0.0019143533411074!3376$GO:0019752!carboxylic acid metabolic process!0.0019143533411074!3376;2617$GO:0006082!organic acid metabolic process!0.0019143533411074!3376;2617$GO:0000267!cell fraction!0.00232389136198941!3376;2617$GO:0006412!translation!0.003964147193353!3376;2617$GO:0009059!macromolecule biosynthetic process!0.00624735990464482!3376;2617$GO:0030141!secretory granule!0.00624735990464482!2617$GO:0045055!regulated secretory pathway!0.00857402855122935!2617$GO:0044249!cellular biosynthetic process!0.00858732448264697!3376;2617$GO:0009058!biosynthetic process!0.0132407701752879!3376;2617$GO:0005524!ATP binding!0.0161792710118105!3376;2617$GO:0032559!adenyl ribonucleotide binding!0.0161792710118105!3376;2617$GO:0030554!adenyl nucleotide binding!0.0169818384858086!3376;2617$GO:0032553!ribonucleotide binding!0.0227218286099275!3376;2617$GO:0032555!purine ribonucleotide binding!0.0227218286099275!3376;2617$GO:0017076!purine nucleotide binding!0.0236857190230647!3376;2617$GO:0045045!secretory pathway!0.0281591605431612!2617$GO:0016070!RNA metabolic process!0.0290317417570611!3376;2617$GO:0000166!nucleotide binding!0.0297015403698842!3376;2617$GO:0032940!secretion by cell!0.0319161544909049!2617$GO:0016023!cytoplasmic membrane-bound vesicle!0.035806545811623!2617$GO:0031988!membrane-bound vesicle!0.035806545811623!2617$GO:0046903!secretion!0.0380420856223659!2617$GO:0031410!cytoplasmic vesicle!0.0404963451850661!2617$GO:0031982!vesicle!0.0404963451850661!2617$GO:0010467!gene expression!0.0404963451850661!3376;2617$GO:0044267!cellular protein metabolic process!0.0414628423752696!3376;2617$GO:0044260!cellular macromolecule metabolic process!0.0415722779567392!3376;2617$GO:0006139!nucleobase, nucleoside, nucleotide and nucleic acid metabolic process!0.0426561100799306!3376;2617$GO:0019538!protein metabolic process!0.0426561100799306!3376;2617|id=C4683|ontology_enrichment_celltype=CL:0000548!5.58e-25!679;CL:0000255!5.58e-25!679;CL:0000057!2.46e-12!76;CL:0000003!1.02e-11!722;CL:0002620!1.30e-08!23;CL:0002371!3.53e-08!588;CL:0000055!3.28e-07!106;CL:0002321!7.08e-07!250|ontology_enrichment_disease=DOID:14566!1.04e-26!239;DOID:162!1.03e-25!235;DOID:0050687!2.09e-15!143;DOID:0050686!2.52e-12!137;DOID:305!2.39e-08!106|ontology_enrichment_uberon=UBERON:0002097!2.31e-07!41;UBERON:0002199!3.98e-07!46;UBERON:0002416!3.98e-07!46|pathway_enrichment=4.79354634032066e-06;0.00151715741671149;2;63;Aminoacyl-tRNA biosynthesis (KEGG):00970!0.000216998173040322;0.045786614511508;2;421;Gene Expression (Reactome):REACT_71!2.5771754517853e-07;0.00016313520609801;2;15;{EPRS,15} (Static 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|full_id=C4683_Preadipocyte_giant_Smooth_Fibroblast_melanoma_Ewing_mesenchymal
|id=C4683
}}

Latest revision as of 14:17, 17 September 2013


Full id: C4683_Preadipocyte_giant_Smooth_Fibroblast_melanoma_Ewing_mesenchymal



Phase1 CAGE Peaks

Hg19::chr7:30634439..30634572,+p1@GARS
Hg19::chr9:95055931..95055951,-p2@IARS
Hg19::chr9:95055956..95056004,-p1@IARS


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

p.valueFDRnGenesnPathwayName
4.79354634032066e-060.00151715741671149263Aminoacyl-tRNA biosynthesis (KEGG):00970
0.0002169981730403220.0457866145115082421Gene Expression (Reactome):REACT_71
2.5771754517853e-070.00016313520609801215{EPRS,15} (Static Module):NA



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:0043038amino acid activation0.000174999140341419
GO:0043039tRNA aminoacylation0.000174999140341419
GO:0006418tRNA aminoacylation for protein translation0.000174999140341419
GO:0016875ligase activity, forming carbon-oxygen bonds0.000174999140341419
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds0.000174999140341419
GO:0004812aminoacyl-tRNA ligase activity0.000174999140341419
GO:0006399tRNA metabolic process0.000386485029551408
GO:0005625soluble fraction0.000389759114775116
GO:0006520amino acid metabolic process0.00142466075754636
GO:0006519amino acid and derivative metabolic process0.0017073527239818
GO:0009308amine metabolic process0.0017073527239818
GO:0004820glycine-tRNA ligase activity0.0017073527239818
GO:0006426glycyl-tRNA aminoacylation0.0017073527239818
GO:0016874ligase activity0.0017073527239818
GO:0006807nitrogen compound metabolic process0.00175001427911881
GO:0004822isoleucine-tRNA ligase activity0.0019143533411074
GO:0006428isoleucyl-tRNA aminoacylation0.0019143533411074
GO:0019752carboxylic acid metabolic process0.0019143533411074
GO:0006082organic acid metabolic process0.0019143533411074
GO:0000267cell fraction0.00232389136198941
GO:0006412translation0.003964147193353
GO:0009059macromolecule biosynthetic process0.00624735990464482
GO:0030141secretory granule0.00624735990464482
GO:0045055regulated secretory pathway0.00857402855122935
GO:0044249cellular biosynthetic process0.00858732448264697
GO:0009058biosynthetic process0.0132407701752879
GO:0005524ATP binding0.0161792710118105
GO:0032559adenyl ribonucleotide binding0.0161792710118105
GO:0030554adenyl nucleotide binding0.0169818384858086
GO:0032553ribonucleotide binding0.0227218286099275
GO:0032555purine ribonucleotide binding0.0227218286099275
GO:0017076purine nucleotide binding0.0236857190230647
GO:0045045secretory pathway0.0281591605431612
GO:0016070RNA metabolic process0.0290317417570611
GO:0000166nucleotide binding0.0297015403698842
GO:0032940secretion by cell0.0319161544909049
GO:0016023cytoplasmic membrane-bound vesicle0.035806545811623
GO:0031988membrane-bound vesicle0.035806545811623
GO:0046903secretion0.0380420856223659
GO:0031410cytoplasmic vesicle0.0404963451850661
GO:0031982vesicle0.0404963451850661
GO:0010467gene expression0.0404963451850661
GO:0044267cellular protein metabolic process0.0414628423752696
GO:0044260cellular macromolecule metabolic process0.0415722779567392
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0426561100799306
GO:0019538protein metabolic process0.0426561100799306



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
animal cell5.58e-25679
eukaryotic cell5.58e-25679
fibroblast2.46e-1276
native cell1.02e-11722
skin fibroblast1.30e-0823
somatic cell3.53e-08588
non-terminally differentiated cell3.28e-07106
embryonic cell7.08e-07250
Uber Anatomy
Ontology termp-valuen
skin of body2.31e-0741
integument3.98e-0746
integumental system3.98e-0746
Disease
Ontology termp-valuen
disease of cellular proliferation1.04e-26239
cancer1.03e-25235
cell type cancer2.09e-15143
organ system cancer2.52e-12137
carcinoma2.39e-08106


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)
MA0003.11.0927
MA0004.11.93041
MA0006.12.61424
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.14.27202
MA0061.11.15625
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.12.626
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.10.348055
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
ATF3#467322.46317452600878.81932387510763e-050.00130077865582879
BATF#10538324.35780179230366.91705216281876e-050.00110241112594633
BCL3#602223.03140186915890.002464674760842910.0138622525363602
CCNT2#90536.336201576962630.003930750035764890.0191118995803189
CEBPB#105137.971147625824820.001974187055288560.0115813133666956
CTCFL#140690213.16431623931620.007433367036996010.0306948212864473
E2F1#186934.907389214879320.008460985347239390.0327680813097614
E2F4#1874312.66806031528440.0004917987006298980.0043896217840429
E2F6#187635.017155731697390.00791769806886330.03242682516819
EGR1#195834.988179094810140.008056488137383440.0322441680237666
ELF1#199734.258097958807540.01295179875054610.0464899955220059
ETS1#211339.728760922202340.001085840092584840.00765157907222642
FOS#235338.99795530889440.001372499272417130.00901921924822076
FOSL2#2355316.93020060456170.0002060162053171620.00244085382497097
GABPB1#255337.067683836182170.002832212825417420.0154800855805825
GATA1#2623313.56030814380040.0004009615963782630.00389435768289309
GTF2B#2959221.29588662288280.002878180589911410.0155901821808909
GTF2F1#2962312.73966087675770.0004835525047438590.00435923522166111
HDAC2#3066313.41562023662630.0004140761399857210.0039353624519036
HMGN3#932438.178547723350590.001827766942164210.0109192398851784
IRF1#365937.63716375356390.002244692747297240.0128717655430174
IRF3#3661231.32130147432640.001339514673320110.0088795666751431
JUN#3725312.51282919233630.0005103313992726250.00446423494502334
JUND#372736.994663941871030.002921845042734990.0157670029150666
MAX#414936.452555509007120.003721913834265510.0187412833969845
MXI1#460139.96157162875930.001011470541259020.00723342727051157
MYC#460935.22228187160940.007020843755740150.0296047279152837
NANOG#79923329.24477848101273.99627955670032e-050.000741195952090615
NFKB1#479035.488063424193840.006049381815655430.0270818032253949
NFYA#4800212.28372046655370.008516011403724430.0324991308873306
NFYB#4801211.17319550235760.01025467135054530.0381623297170609
PAX5#507936.669565531177830.003370290999677260.0173659194689079
POU2F2#545239.106124057742520.001324165192682130.00885651543762593
REST#597839.650028716128020.001112636247114590.00771239244789279
SIN3A#2594235.408884726815140.006318961977991520.0278246930609434
SMARCB1#6598318.25271578115740.000164397760679890.00204034910607808
SP1#666735.69838137814090.005403962701712170.0247863179887623
SREBF1#6720231.33723296032550.00133816265136180.0088784936881758
SRF#6722313.79717826216780.0003806615025800190.00376440741103632
STAT1#6772320.70658749719920.0001125992441046670.00155346795971563
TAF7#6879311.43306940492390.0006690181981945830.00545658661470083
TCF7L2#6934310.77017656313730.0008003181298398380.00617406006517528
THAP1#55145331.36914460285133.23800758564397e-050.000649086898727583
TRIM28#10155212.39368336350830.008368344129438470.0329431395602874
USF1#739136.361499277207960.00388404057290560.0191188817171932
USF2#7392312.99219738506960.0004558979393427810.00423268956236294
YY1#752834.911170749853860.008441455341808260.0331223336380175



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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