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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 11:31, 17 September 2013


Full id: C830_Renal_Endothelial_adipose_Mast_ovary_testis_Lymphatic



Phase1 CAGE Peaks

Hg19::chr14:54421190..54421212,-p5@BMP4
Hg19::chr19:50192842..50192863,+p2@C19orf76
Hg19::chr2:20647026..20647047,+p5@RHOB
Hg19::chr2:20647862..20647881,+p4@RHOB
Hg19::chr2:26700331..26700340,-p@chr2:26700331..26700340
-
Hg19::chr2:26700872..26700884,-p5@OTOF
Hg19::chr2:26700900..26700918,-p4@OTOF
Hg19::chr2:26700923..26700934,-p9@OTOF
Hg19::chr2:26700984..26700993,-p7@OTOF
Hg19::chr5:150019594..150019618,+p@chr5:150019594..150019618
+


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:0001525angiogenesis0.00352018488905965
GO:0048514blood vessel morphogenesis0.00352018488905965
GO:0048646anatomical structure formation0.00352018488905965
GO:0001568blood vessel development0.00352018488905965
GO:0001944vasculature development0.00352018488905965
GO:0021904dorsoventral neural tube patterning0.00365006475921347
GO:0045786negative regulation of progression through cell cycle0.0043799487752665
GO:0032331negative regulation of chondrocyte differentiation0.0043799487752665
GO:0021532neural tube patterning0.0043799487752665
GO:0021978telencephalon regionalization0.0043799487752665
GO:0006927transformed cell apoptosis0.00461020095924032
GO:0045662negative regulation of myoblast differentiation0.00461020095924032
GO:0030501positive regulation of bone mineralization0.00461020095924032
GO:0000074regulation of progression through cell cycle0.00461020095924032
GO:0051726regulation of cell cycle0.00461020095924032
GO:0009887organ morphogenesis0.00461020095924032
GO:0032330regulation of chondrocyte differentiation0.00461020095924032
GO:0007500mesodermal cell fate determination0.00461020095924032
GO:0021871forebrain regionalization0.00461020095924032
GO:0045669positive regulation of osteoblast differentiation0.00547445247884972
GO:0008333endosome to lysosome transport0.00571230398792825
GO:0045778positive regulation of ossification0.00571230398792825
GO:0045661regulation of myoblast differentiation0.00571230398792825
GO:0046852positive regulation of bone remodeling0.00589521710383024
GO:0001710mesodermal cell fate commitment0.00589521710383024
GO:0048333mesodermal cell differentiation0.00589521710383024
GO:0051145smooth muscle cell differentiation0.00625596459095219
GO:0045843negative regulation of striated muscle development0.00625596459095219
GO:0002062chondrocyte differentiation0.00679507183798379
GO:0045667regulation of osteoblast differentiation0.00706276996781126
GO:0001658ureteric bud branching0.00706276996781126
GO:0030500regulation of bone mineralization0.00752578033711717
GO:0022402cell cycle process0.00752578033711717
GO:0045766positive regulation of angiogenesis0.00772704627624871
GO:0016202regulation of striated muscle development0.00813155691880163
GO:0007041lysosomal transport0.00851355894503422
GO:0001707mesoderm formation0.00887487737891711
GO:0032501multicellular organismal process0.00904102041585094
GO:0048332mesoderm morphogenesis0.00904102041585094
GO:0001704formation of primary germ layer0.00904102041585094
GO:0030509BMP signaling pathway0.00904102041585094
GO:0001657ureteric bud development0.00904102041585094
GO:0042475odontogenesis of dentine-containing teeth0.00904102041585094
GO:0021915neural tube development0.00904102041585094
GO:0030278regulation of ossification0.00904102041585094
GO:0007281germ cell development0.00904102041585094
GO:0030282bone mineralization0.00928784922746442
GO:0007049cell cycle0.00928784922746442
GO:0046850regulation of bone remodeling0.0101319072928017
GO:0001656metanephros development0.0101319072928017
GO:0042476odontogenesis0.0101319072928017
GO:0001649osteoblast differentiation0.0101319072928017
GO:0007034vacuolar transport0.0101319072928017
GO:0007369gastrulation0.0101319072928017
GO:0045445myoblast differentiation0.0101872075412325
GO:0001934positive regulation of protein amino acid phosphorylation0.0101872075412325
GO:0033240positive regulation of amine metabolic process0.0101872075412325
GO:0045764positive regulation of amino acid metabolic process0.0101872075412325
GO:0048754branching morphogenesis of a tube0.0102120604434338
GO:0009953dorsal/ventral pattern formation0.0102120604434338
GO:0031902late endosome membrane0.010235289153024
GO:0001709cell fate determination0.010235289153024
GO:0009653anatomical structure morphogenesis0.0109402046955137
GO:0001763morphogenesis of a branching structure0.0109402046955137
GO:0030218erythrocyte differentiation0.0111081884375619
GO:0043010camera-type eye development0.0112710622458616
GO:0051216cartilage development0.0115459537040865
GO:0001822kidney development0.0115459537040865
GO:0006944membrane fusion0.0115459537040865
GO:0048523negative regulation of cellular process0.0115459537040865
GO:0048513organ development0.0115459537040865
GO:0045765regulation of angiogenesis0.0115459537040865
GO:0001655urogenital system development0.0116809668371001
GO:0016197endosome transport0.0116809668371001
GO:0048519negative regulation of biological process0.0116809668371001
GO:0048741skeletal muscle fiber development0.0116809668371001
GO:0030324lung development0.0116809668371001
GO:0048747muscle fiber development0.0116809668371001
GO:0030323respiratory tube development0.0116809668371001
GO:0007498mesoderm development0.0116809668371001
GO:0048468cell development0.0116809668371001
GO:0001932regulation of protein amino acid phosphorylation0.0116809668371001
GO:0030900forebrain development0.0116809668371001
GO:0033238regulation of amine metabolic process0.0116809668371001
GO:0042692muscle cell differentiation0.0116809668371001
GO:0006521regulation of amino acid metabolic process0.0116809668371001
GO:0045597positive regulation of cell differentiation0.0116809668371001
GO:0001654eye development0.0116809668371001
GO:0005770late endosome0.0125311986003383
GO:0042325regulation of phosphorylation0.01554474559342
GO:0045596negative regulation of cell differentiation0.0156136818634785
GO:0007519skeletal muscle development0.0158747785825665
GO:0051094positive regulation of developmental process0.0158747785825665
GO:0051174regulation of phosphorus metabolic process0.0158747785825665
GO:0019220regulation of phosphate metabolic process0.0158747785825665
GO:0045165cell fate commitment0.0161638094001479
GO:0048729tissue morphogenesis0.0162220066069993
GO:0048731system development0.0164026782168303
GO:0008201heparin binding0.0164956866080014
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0164956866080014
GO:0030099myeloid cell differentiation0.0164956866080014
GO:0051093negative regulation of developmental process0.0164956866080014
GO:0035239tube morphogenesis0.0174754790541053
GO:0007423sensory organ development0.0174754790541053
GO:0044440endosomal part0.0174754790541053
GO:0010008endosome membrane0.0174754790541053
GO:0003002regionalization0.0174754790541053
GO:0014706striated muscle development0.0174754790541053
GO:0001503ossification0.0174754790541053
GO:0031214biomineral formation0.0174754790541053
GO:0048869cellular developmental process0.0180416102903668
GO:0030154cell differentiation0.0180416102903668
GO:0007507heart development0.0180416102903668
GO:0009792embryonic development ending in birth or egg hatching0.0180416102903668
GO:0043009chordate embryonic development0.0180416102903668
GO:0046849bone remodeling0.0180738211415503
GO:0051240positive regulation of multicellular organismal process0.0194280340625341
GO:0048771tissue remodeling0.0194280340625341
GO:0005539glycosaminoglycan binding0.0201791700177027
GO:0048856anatomical structure development0.020737575069496
GO:0030247polysaccharide binding0.0209244188058977
GO:0035295tube development0.0209311946862125
GO:0007389pattern specification process0.0219985960043331
GO:0001871pattern binding0.0223471439314306
GO:0050954sensory perception of mechanical stimulus0.0228549025510702
GO:0007605sensory perception of sound0.0228549025510702
GO:0007420brain development0.0238724756048115
GO:0045595regulation of cell differentiation0.0245343689107644
GO:0007275multicellular organismal development0.0252121697359094
GO:0030097hemopoiesis0.0269952425986517
GO:0007517muscle development0.0285576995570027
GO:0048534hemopoietic or lymphoid organ development0.0285576995570027
GO:0002520immune system development0.0298095579949197
GO:0007266Rho protein signal transduction0.0305570901556772
GO:0005768endosome0.0311328188244837
GO:0001501skeletal development0.0334500930167917
GO:0007417central nervous system development0.0369267618751606
GO:0009790embryonic development0.0369267618751606
GO:0050793regulation of developmental process0.0369267618751606
GO:0008083growth factor activity0.0392842670450358
GO:0007276gamete generation0.0406883426001273
GO:0003924GTPase activity0.0419198021015244
GO:0051239regulation of multicellular organismal process0.0420786967399136
GO:0016044membrane organization and biogenesis0.0428336082681813
GO:0016043cellular component organization and biogenesis0.0446058764501163
GO:0007167enzyme linked receptor protein signaling pathway0.0446058764501163
GO:0009888tissue development0.0450341605435387
GO:0005125cytokine activity0.0452741436959324
GO:0032502developmental process0.0452741436959324
GO:0019953sexual reproduction0.045567020297071



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>

Uber Anatomy
Ontology termp-valuen
adult organism1.51e-23114
lymphatic vessel2.75e-108
lymph vasculature2.75e-108
lymphatic part of lymphoid system2.75e-108
anatomical cluster2.25e-08373
anatomical conduit2.36e-08240
lymphoid system3.91e-0810
brainstem6.84e-086
throat2.53e-072


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)
MA0003.10.456919
MA0004.10.380329
MA0006.10.665232
MA0007.11.69684
MA0009.10.828613
MA0014.10.15363
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.577037
MA0056.10
MA0057.11.22133
MA0058.10.796055
MA0059.10.291897
MA0060.10.430116
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.11.12112
MA0072.10.798564
MA0073.10.311193
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.11.31824
MA0114.10.174997
MA0115.11.06753
MA0116.12.31128
MA0117.10.865782
MA0119.10.760742
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
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.945459
MA0146.10.0551603
MA0147.10.543675
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.360905
MA0138.20.569505
MA0002.20.407187
MA0137.20.255808
MA0104.20.845907
MA0047.20.504873
MA0112.23.406
MA0065.20.963081
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.729959
MA0155.13.30773
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.11.07255
MA0161.10
MA0162.10.108522
MA0163.10.484115
MA0164.10.544294
MA0080.20.238846
MA0018.23.27184
MA0099.20.444294
MA0079.20.48867
MA0102.21.36707
MA0258.14.43327
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
NR3C1#290845.989209332469220.003010390809148850.015987907740488
TFAP2A#702058.259317186522480.0001581829523935980.00199402164937054
TFAP2C#702255.404614304930110.001145270868237330.007834093804548



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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