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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.0724992894770213,0.

Latest revision as of 10:53, 17 September 2013


Full id: C193_Mesenchymal_Adipocyte_mature_Cardiac_heart_CD14CD16_CD14



Phase1 CAGE Peaks

Hg19::chr10:105211353..105211386,-p4@CALHM2
Hg19::chr10:73047521..73047525,+p@chr10:73047521..73047525
+
Hg19::chr10:99123608..99123611,-p4@RRP12
Hg19::chr11:113930128..113930159,-p@chr11:113930128..113930159
-
Hg19::chr11:114050496..114050536,+p@chr11:114050496..114050536
+
Hg19::chr11:3078838..3078876,-p6@CARS
Hg19::chr11:67134927..67134931,-p@chr11:67134927..67134931
-
Hg19::chr11:7687678..7687681,-p@chr11:7687678..7687681
-
Hg19::chr11:9781782..9781788,-p@chr11:9781782..9781788
-
Hg19::chr12:53455252..53455256,+p9@TENC1
Hg19::chr14:105818803..105818808,+p@chr14:105818803..105818808
+
Hg19::chr15:35731807..35731812,+p@chr15:35731807..35731812
+
Hg19::chr15:64448917..64448928,-p@chr15:64448917..64448928
-
Hg19::chr15:90328175..90328186,-p@chr15:90328175..90328186
-
Hg19::chr15:90344339..90344342,-p@chr15:90344339..90344342
-
Hg19::chr16:2819861..2819890,+p@chr16:2819861..2819890
+
Hg19::chr16:30662360..30662387,+p7@PRR14
Hg19::chr16:67701309..67701312,-p@chr16:67701309..67701312
-
Hg19::chr16:86797626..86797635,-p@chr16:86797626..86797635
-
Hg19::chr16:89595986..89595990,+p@chr16:89595986..89595990
+
Hg19::chr16:89628797..89628803,+p3@RPL13
Hg19::chr17:27894290..27894311,+p@chr17:27894290..27894311
+
Hg19::chr17:36862346..36862379,-p@chr17:36862346..36862379
-
Hg19::chr17:43013396..43013400,-p2@KIF18B
Hg19::chr17:61571793..61571795,+p@chr17:61571793..61571795
+
Hg19::chr17:79204340..79204344,-p@chr17:79204340..79204344
-
Hg19::chr19:11217362..11217367,+p6@LDLR
Hg19::chr19:17378331..17378339,+p3@BABAM1
Hg19::chr19:3620703..3620705,-p2@C19orf29
Hg19::chr19:36239576..36239581,+p6@LIN37
Hg19::chr19:45409274..45409280,+p6@APOE
Hg19::chr19:46894342..46894354,+p@chr19:46894342..46894354
+
Hg19::chr19:47778119..47778195,+p1@PRR24
Hg19::chr19:49977466..49977514,+p2@FLT3LG
Hg19::chr19:50143452..50143468,-p2@RRAS
Hg19::chr19:52097813..52097865,+p@chr19:52097813..52097865
+
Hg19::chr19:55758241..55758245,-p11@PPP6R1
Hg19::chr19:58987786..58987805,+p3@ZNF446
Hg19::chr19:7584815..7584829,+p2@ZNF358
Hg19::chr19:850817..850829,+p@chr19:850817..850829
+
Hg19::chr19:850985..851002,+p@chr19:850985..851002
+
Hg19::chr19:8590447..8590459,-p@chr19:8590447..8590459
-
Hg19::chr19:859425..859481,+p2@CFD
Hg19::chr19:859654..859672,+p1@CFD
Hg19::chr1:145556687..145556690,+p@chr1:145556687..145556690
+
Hg19::chr1:27269555..27269558,+p@chr1:27269555..27269558
+
Hg19::chr1:33834133..33834136,-p@chr1:33834133..33834136
-
Hg19::chr20:62293295..62293299,+p@chr20:62293295..62293299
+
Hg19::chr20:62371206..62371224,+p6@SLC2A4RG
Hg19::chr21:46386905..46386944,+p@chr21:46386905..46386944
+
Hg19::chr21:47423384..47423395,+p@chr21:47423384..47423395
+
Hg19::chr21:47680704..47680707,-p@chr21:47680704..47680707
-
Hg19::chr22:24577444..24577465,+p1@SUSD2
Hg19::chr22:24581731..24581748,+p@chr22:24581731..24581748
+
Hg19::chr22:24584625..24584636,+p@chr22:24584625..24584636
+
Hg19::chr22:45898503..45898514,+p11@FBLN1
Hg19::chr22:45898527..45898538,+p7@FBLN1
Hg19::chr22:46493889..46493892,+p@chr22:46493889..46493892
+
Hg19::chr3:10359730..10359734,-p4@SEC13
Hg19::chr3:45067642..45067645,+p7@CLEC3B
Hg19::chr3:52029054..52029058,-p@chr3:52029054..52029058
-
Hg19::chr3:9920487..9920502,-p2@CIDEC
Hg19::chr3:9920507..9920519,-p4@CIDEC
Hg19::chr3:9920535..9920548,-p3@CIDEC
Hg19::chr3:9956869..9956894,+p@chr3:9956869..9956894
+
Hg19::chr3:9956901..9956922,+p@chr3:9956901..9956922
+
Hg19::chr3:9956948..9956961,+p@chr3:9956948..9956961
+
Hg19::chr3:9958774..9958848,+p1@IL17RC
Hg19::chr3:9958849..9958863,+p2@IL17RC
Hg19::chr3:9958870..9958879,+p3@IL17RC
Hg19::chr4:5798958..5798961,+p@chr4:5798958..5798961
+
Hg19::chr4:891819..891820,-p@chr4:891819..891820
-
Hg19::chr5:149425247..149425250,+p@chr5:149425247..149425250
+
Hg19::chr6:31763316..31763327,-p7@VARS
Hg19::chr7:100201583..100201598,+p18@PCOLCE
Hg19::chr7:150711272..150711306,-p8@ATG9B
Hg19::chr7:150775644..150775650,-p5@FASTK
Hg19::chr8:143751707..143751730,+p2@PSCA
Hg19::chr8:21990868..21990906,-p2@HR
Hg19::chr8:22409352..22409361,+p24@SORBS3
Hg19::chr9:117004510..117004513,+p@chr9:117004510..117004513
+
Hg19::chr9:131903916..131903951,+p8@PPP2R4
Hg19::chr9:134165195..134165202,+p5@PPAPDC3
Hg19::chr9:139282891..139282896,-p@chr9:139282891..139282896
-
Hg19::chr9:21994750..21994776,-p13@CDKN2A
Hg19::chr9:38068437..38068455,-p3@ENST00000540557
Hg19::chrX:69623884..69623886,+p@chrX:69623884..69623886
+


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
1.9629592890301e-060.001242553229956058740TGF beta receptor down reg. targets (Netpath):NetPath_7



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:0048518positive regulation of biological process0.00140632531219541
GO:0048522positive regulation of cellular process0.00388887713003141
GO:0006917induction of apoptosis0.00392172611206062
GO:0012502induction of programmed cell death0.00392172611206062
GO:0005625soluble fraction0.00392172611206062
GO:0045936negative regulation of phosphate metabolic process0.00392172611206062
GO:0043065positive regulation of apoptosis0.00392172611206062
GO:0043068positive regulation of programmed cell death0.00392172611206062
GO:0042632cholesterol homeostasis0.00392172611206062
GO:0055092sterol homeostasis0.00392172611206062
GO:0055088lipid homeostasis0.00438854313126638
GO:0015918sterol transport0.00438854313126638
GO:0030301cholesterol transport0.00438854313126638
GO:0008034lipoprotein binding0.0107484795777597
GO:0065007biological regulation0.0178024265771723
GO:0050789regulation of biological process0.0191590005068112
GO:0003817complement factor D activity0.0191590005068112
GO:0050749apolipoprotein E receptor binding0.0191590005068112
GO:0032515negative regulation of phosphoprotein phosphatase activity0.0191590005068112
GO:0030229very-low-density lipoprotein receptor activity0.0191590005068112
GO:0032516positive regulation of phosphoprotein phosphatase activity0.0191590005068112
GO:0035305negative regulation of dephosphorylation0.0191590005068112
GO:0035308negative regulation of protein amino acid dephosphorylation0.0191590005068112
GO:0042981regulation of apoptosis0.0259099367043505
GO:0043067regulation of programmed cell death0.0259099367043505
GO:0050794regulation of cellular process0.0259099367043505
GO:0051174regulation of phosphorus metabolic process0.0259099367043505
GO:0019220regulation of phosphate metabolic process0.0259099367043505
GO:0008160protein tyrosine phosphatase activator activity0.0259099367043505
GO:0048156tau protein binding0.0259099367043505
GO:0035306positive regulation of dephosphorylation0.0259099367043505
GO:0035304regulation of protein amino acid dephosphorylation0.0259099367043505
GO:0035307positive regulation of protein amino acid dephosphorylation0.0259099367043505
GO:0010149senescence0.0259099367043505
GO:0008203cholesterol metabolic process0.030957613977377
GO:0042157lipoprotein metabolic process0.0319799892743909
GO:0051496positive regulation of stress fiber formation0.0319799892743909
GO:0051004regulation of lipoprotein lipase activity0.0319799892743909
GO:0051495positive regulation of cytoskeleton organization and biogenesis0.0319799892743909
GO:0032233positive regulation of actin filament bundle formation0.0319799892743909
GO:0031232extrinsic to external side of plasma membrane0.0319799892743909
GO:0043086negative regulation of catalytic activity0.0319799892743909
GO:0016125sterol metabolic process0.0363570142838911
GO:0005319lipid transporter activity0.0370265024419312
GO:0051721protein phosphatase 2A binding0.0374547283925113
GO:0045192low-density lipoprotein catabolic process0.0374547283925113
GO:0032088inhibition of NF-kappaB transcription factor0.0374547283925113
GO:0031589cell-substrate adhesion0.0389496332072172
GO:0035303regulation of dephosphorylation0.0439905280809569
GO:0017166vinculin binding0.0439905280809569
GO:0031324negative regulation of cellular metabolic process0.0444126921707153
GO:0051346negative regulation of hydrolase activity0.0454880282252511
GO:0006423cysteinyl-tRNA aminoacylation0.0454880282252511
GO:0004817cysteine-tRNA ligase activity0.0454880282252511
GO:0033344cholesterol efflux0.0454880282252511
GO:0042159lipoprotein catabolic process0.0454880282252511
GO:0051492regulation of stress fiber formation0.0454880282252511
GO:0032231regulation of actin filament bundle formation0.0454880282252511
GO:0043038amino acid activation0.0456459809016163
GO:0006418tRNA aminoacylation for protein translation0.0456459809016163
GO:0043039tRNA aminoacylation0.0456459809016163
GO:0001953negative regulation of cell-matrix adhesion0.0456459809016163
GO:0043149stress fiber formation0.0456459809016163
GO:0006869lipid transport0.0456459809016163
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds0.0456459809016163
GO:0016875ligase activity, forming carbon-oxygen bonds0.0456459809016163
GO:0004812aminoacyl-tRNA ligase activity0.0456459809016163
GO:0006915apoptosis0.0456459809016163
GO:0009892negative regulation of metabolic process0.0456459809016163
GO:0012501programmed cell death0.0456459809016163
GO:0030299cholesterol absorption0.0456459809016163
GO:0043410positive regulation of MAPKKK cascade0.0456459809016163
GO:0000045autophagic vacuole formation0.0456459809016163
GO:0042627chylomicron0.0456459809016163
GO:0044241lipid digestion0.0456459809016163
GO:0050750low-density lipoprotein receptor binding0.0456459809016163
GO:0045471response to ethanol0.0456459809016163
GO:0000267cell fraction0.0469230363482118
GO:0045736negative regulation of cyclin-dependent protein kinase activity0.0469230363482118
GO:0016236macroautophagy0.0469230363482118
GO:0006707cholesterol catabolic process0.0469230363482118
GO:0016127sterol catabolic process0.0469230363482118
GO:0048168regulation of neuronal synaptic plasticity0.0469230363482118
GO:0016265death0.0469230363482118
GO:0008219cell death0.0469230363482118
GO:0050892intestinal absorption0.0498827202411778
GO:0001540beta-amyloid binding0.0498827202411778
GO:0022408negative regulation of cell-cell adhesion0.0498827202411778



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
muscle tissue3.91e-1364
musculature3.91e-1364
musculature of body3.91e-1364
skeletal muscle tissue1.05e-1262
striated muscle tissue1.05e-1262
myotome1.05e-1262
somite3.50e-1271
presomitic mesoderm3.50e-1271
presumptive segmental plate3.50e-1271
dermomyotome3.50e-1271
trunk paraxial mesoderm3.50e-1271
paraxial mesoderm6.62e-1272
presumptive paraxial mesoderm6.62e-1272
dense mesenchyme tissue1.23e-1173
articulation1.67e-118
skeletal joint1.67e-118
articular system1.67e-118
multilaminar epithelium2.92e-1183
epithelial vesicle2.10e-1078
intervertebral cartilage3.23e-105
symphysis3.23e-105
nonsynovial joint3.23e-105
fibrous joint3.23e-105
cartilaginous joint3.23e-105
developing mesenchymal condensation3.23e-105
pre-cartilage condensation3.23e-105
cartilaginous condensation3.23e-105
cartilage element3.23e-105
post-cranial axial skeletal system3.23e-105
vertebral column3.23e-105
intervertebral disk3.23e-105
intervertebral joint3.23e-105
mesenchyme3.43e-08160
entire embryonic mesenchyme3.43e-08160
trunk mesenchyme2.13e-07122
vasculature of eye6.44e-076
uvea6.44e-076
vasculature of head6.44e-076
surface structure9.12e-0799


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)
MA0003.11.86458
MA0004.10.162186
MA0006.10.637472
MA0007.11.89588
MA0009.10.123344
MA0014.11.88201
MA0017.10.636189
MA0019.10.685569
MA0024.10.563692
MA0025.10.197015
MA0027.11.50196
MA0028.10.238402
MA0029.10.0849308
MA0030.10.275143
MA0031.10.208537
MA0038.10.0619426
MA0040.10.0873223
MA0041.10.0858974
MA0042.10.442249
MA0043.10.123499
MA0046.10.376386
MA0048.13.76681
MA0050.10.14606
MA0051.10.541159
MA0052.10.088923
MA0055.11.82916
MA0056.10
MA0057.10.198798
MA0058.10.232977
MA0059.10.367999
MA0060.10.0141011
MA0061.10.228336
MA0063.10
MA0066.11.17279
MA0067.10.321182
MA0068.11.00889
MA0069.10.116197
MA0070.10.110912
MA0071.10.124821
MA0072.10.352222
MA0073.12.0539
MA0074.10.319007
MA0076.10.42201
MA0077.10.105288
MA0078.10.530438
MA0081.10.0620248
MA0083.10.127065
MA0084.10.467465
MA0087.10.107695
MA0088.12.73976
MA0089.10
MA0090.10.677112
MA0091.11.00123
MA0092.10.814442
MA0093.10.120838
MA0095.10
MA0098.10
MA0100.10.180464
MA0101.10.215169
MA0103.10.786514
MA0105.10.435336
MA0106.11.37549
MA0107.10.139901
MA0108.20.0561432
MA0109.10
MA0111.10.998505
MA0113.10.446129
MA0114.11.19136
MA0115.10.736328
MA0116.13.55016
MA0117.10.142504
MA0119.10.902961
MA0122.10.473907
MA0124.10.238942
MA0125.10.546863
MA0130.10
MA0131.10.133596
MA0132.10
MA0133.10
MA0135.10.138714
MA0136.10.172629
MA0139.12.08921
MA0140.10.0434794
MA0141.10.12667
MA0142.10.178954
MA0143.10.724853
MA0144.10.103591
MA0145.14.00051
MA0146.14.85741
MA0147.10.355764
MA0148.10.197037
MA0149.10.0397429
MA0062.20.401099
MA0035.20.0431997
MA0039.25.43545
MA0138.20.288975
MA0002.20.531836
MA0137.20.254546
MA0104.20.462936
MA0047.20.385808
MA0112.23.17444
MA0065.22.50072
MA0150.10.0831624
MA0151.10
MA0152.10.0461403
MA0153.10.176346
MA0154.13.92417
MA0155.10.829881
MA0156.10.260353
MA0157.10.155276
MA0158.10
MA0159.11.87301
MA0160.10.220119
MA0161.10
MA0162.11.23937
MA0163.12.74971
MA0164.10.102678
MA0080.20.120967
MA0018.20.215507
MA0099.20.12892
MA0079.26.30506
MA0102.20.498347
MA0258.10.599574
MA0259.10.173277
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
HNF4G#317482.643992875995110.01092635257248610.0402134593620846
NR3C1#2908122.065244597403180.01288410733778660.0463441806871393



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

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