Personal tools

Coexpression cluster:C173

From FANTOM5_SSTAR

Revision as of 14:29, 5 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C173_Adipocyte_mature_skin_left_Hepatocyte_Osteoblast_adipose



Phase1 CAGE Peaks

Hg19::chr10:102107148..102107161,+p9@SCD
Hg19::chr10:102107168..102107180,+p11@SCD
Hg19::chr10:102107191..102107209,+p7@SCD
Hg19::chr10:102107808..102107865,+p8@SCD
Hg19::chr10:102107884..102107910,+p13@SCD
Hg19::chr10:102112119..102112137,+p@chr10:102112119..102112137
+
Hg19::chr10:102112150..102112189,+p@chr10:102112150..102112189
+
Hg19::chr10:102112191..102112213,+p@chr10:102112191..102112213
+
Hg19::chr10:102114285..102114307,+p@chr10:102114285..102114307
+
Hg19::chr10:102114326..102114340,+p@chr10:102114326..102114340
+
Hg19::chr10:102116281..102116301,+p@chr10:102116281..102116301
+
Hg19::chr10:102116352..102116360,+p@chr10:102116352..102116360
+
Hg19::chr10:102116406..102116419,+p@chr10:102116406..102116419
+
Hg19::chr10:102120488..102120498,+p@chr10:102120488..102120498
+
Hg19::chr10:102120684..102120716,+p@chr10:102120684..102120716
+
Hg19::chr10:102120837..102120873,+p@chr10:102120837..102120873
+
Hg19::chr10:102121513..102121533,+p2@ENST00000537595
Hg19::chr10:102122141..102122176,+p@chr10:102122141..102122176
+
Hg19::chr10:102122225..102122259,+p@chr10:102122225..102122259
+
Hg19::chr10:102122388..102122405,+p@chr10:102122388..102122405
+
Hg19::chr10:102122643..102122654,+p@chr10:102122643..102122654
+
Hg19::chr10:102122663..102122689,+p@chr10:102122663..102122689
+
Hg19::chr10:102123464..102123502,+p2@AF113690
Hg19::chr10:102123593..102123621,+p1@AF113690
Hg19::chr10:113915737..113915754,-p@chr10:113915737..113915754
-
Hg19::chr10:113928643..113928689,-p@chr10:113928643..113928689
-
Hg19::chr10:114136055..114136067,+p13@ACSL5
Hg19::chr10:53458765..53458768,+p@chr10:53458765..53458768
+
Hg19::chr10:53458769..53458785,+p@chr10:53458769..53458785
+
Hg19::chr11:111888022..111888037,+p17@DIXDC1
Hg19::chr11:111888043..111888056,+p22@DIXDC1
Hg19::chr11:111896321..111896332,+p4@DLAT
Hg19::chr11:111896671..111896691,+p@chr11:111896671..111896691
+
Hg19::chr11:111896693..111896701,+p@chr11:111896693..111896701
+
Hg19::chr11:35232781..35232791,+p1@U94903
Hg19::chr11:43702302..43702318,+p3@HSD17B12
Hg19::chr11:46615803..46615814,-p5@AMBRA1
Hg19::chr11:62439379..62439382,-p22@C11orf48
Hg19::chr11:62439729..62439747,-p2@C11orf48
Hg19::chr11:75271468..75271477,+p@chr11:75271468..75271477
+
Hg19::chr11:77775063..77775072,+p4@THRSP
Hg19::chr11:77775379..77775389,-p@chr11:77775379..77775389
-
Hg19::chr11:822386..822401,+p10@PNPLA2
Hg19::chr11:82828304..82828309,-p@chr11:82828304..82828309
-
Hg19::chr11:86667004..86667031,-p@chr11:86667004..86667031
-
Hg19::chr12:109665191..109665193,+p16@ACACB
Hg19::chr12:50503643..50503660,+p@chr12:50503643..50503660
+
Hg19::chr12:53224219..53224221,-p3@KRT79
Hg19::chr12:56710279..56710303,-p9@CNPY2
Hg19::chr12:57543246..57543251,+p@chr12:57543246..57543251
+
Hg19::chr12:89744674..89744686,+p6@LOC100131490
Hg19::chr15:83330979..83330982,-p23@AP3B2
Hg19::chr15:83330983..83330997,-p10@AP3B2
Hg19::chr16:68325453..68325473,+p@chr16:68325453..68325473
+
Hg19::chr16:69176140..69176147,+p@chr16:69176140..69176147
+
Hg19::chr16:85319990..85319997,+p@chr16:85319990..85319997
+
Hg19::chr17:20687806..20687810,+p3@SCDP1
Hg19::chr17:20688364..20688394,+p2@SCDP1
Hg19::chr17:20688808..20688832,+p@chr17:20688808..20688832
+
Hg19::chr17:22026633..22026638,+p@chr17:22026633..22026638
+
Hg19::chr17:41008915..41008925,+p@chr17:41008915..41008925
+
Hg19::chr17:48503603..48503622,+p1@ACSF2
Hg19::chr19:4512807..4512811,-p2@PLIN4
Hg19::chr1:109939715..109939728,+p@chr1:109939715..109939728
+
Hg19::chr1:9129347..9129370,-p11@SLC2A5
Hg19::chr1:9129735..9129762,-p4@SLC2A5
Hg19::chr20:42939371..42939377,+p@chr20:42939371..42939377
+
Hg19::chr21:47648451..47648462,-p3@LSS
Hg19::chr22:39916888..39916894,+p12@ATF4
Hg19::chr2:65356996..65357005,+p@chr2:65356996..65357005
+
Hg19::chr3:12190006..12190011,+p19@SYN2
Hg19::chr3:12190041..12190062,+p6@SYN2
Hg19::chr3:126008710..126008714,-p@chr3:126008710..126008714
-
Hg19::chr3:154797843..154797858,+p15@MME
Hg19::chr3:186570986..186570997,+p3@ADIPOQ
Hg19::chr3:186572016..186572028,+p@chr3:186572016..186572028
+
Hg19::chr3:186572114..186572128,+p@chr3:186572114..186572128
+
Hg19::chr3:186572221..186572231,+p@chr3:186572221..186572231
+
Hg19::chr3:186572288..186572301,+p@chr3:186572288..186572301
+
Hg19::chr3:186575301..186575315,+p@chr3:186575301..186575315
+
Hg19::chr3:186575349..186575368,+p@chr3:186575349..186575368
+
Hg19::chr3:52269260..52269269,-p@chr3:52269260..52269269
-
Hg19::chr3:52821997..52822012,+p3@ITIH1
Hg19::chr3:9911748..9911751,-p@chr3:9911748..9911751
-
Hg19::chr3:9911902..9911905,-p@chr3:9911902..9911905
-
Hg19::chr5:150138790..150138796,-p18@DCTN4
Hg19::chr5:74806597..74806605,+p@chr5:74806597..74806605
+
Hg19::chr5:76435093..76435109,+p1@ENST00000511547
p1@ENST00000515356
Hg19::chr5:80528491..80528513,+p@chr5:80528491..80528513
+
Hg19::chr6:127663543..127663559,-p5@ECHDC1
Hg19::chr6:127664628..127664661,-p4@ECHDC1
Hg19::chr6:53305337..53305366,-p@chr6:53305337..53305366
-
Hg19::chr6:83947539..83947555,-p@chr6:83947539..83947555
-
Hg19::chr8:19823146..19823158,+p@chr8:19823146..19823158
+
Hg19::chr8:27168021..27168026,+p@chr8:27168021..27168026
+
Hg19::chr8:82391082..82391095,-p@chr8:82391082..82391095
-
Hg19::chr8:82391711..82391737,-p2@FABP4
Hg19::chr8:82392752..82392769,-p@chr8:82392752..82392769
-
Hg19::chr9:95004537..95004561,-p@chr9:95004537..95004561
-
Hg19::chrX:151999438..151999444,-p3@CETN2


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
0.0001789219686142740.0188762676888059221Biosynthesis of unsaturated fatty acids (KEGG):01040
5.90386057604479e-070.000186857187231817471PPAR signaling pathway (KEGG):03320
3.79223521833263e-050.00480096978640911369Adipocytokine signaling pathway (KEGG):04920
0.0004743660284216810.0428962422844178234Fatty Acid Beta Oxidation (Wikipathways):WP143
4.58745353739527e-092.90385808917121e-06422Fatty Acid Biosynthesis (Wikipathways):WP357
6.90977631174787e-060.00145796280177885289Metabolism of lipids and lipoproteins (Reactome):REACT_22258
1.5244952903819e-050.00241251379702936351{RXRA,51} (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:0032787monocarboxylic acid metabolic process1.73275744464493e-05
GO:0006629lipid metabolic process3.68303076272497e-05
GO:0006090pyruvate metabolic process0.000158056992643084
GO:0006631fatty acid metabolic process0.00093611946455349
GO:0044255cellular lipid metabolic process0.00093611946455349
GO:0019752carboxylic acid metabolic process0.00093611946455349
GO:0006082organic acid metabolic process0.00093611946455349
GO:0005737cytoplasm0.00274374696519734
GO:0008610lipid biosynthetic process0.00388723994990565
GO:0044444cytoplasmic part0.00524267132803325
GO:0006094gluconeogenesis0.00547635957551173
GO:0015758glucose transport0.00661975714474225
GO:0005975carbohydrate metabolic process0.00661975714474225
GO:0008645hexose transport0.00661975714474225
GO:0015749monosaccharide transport0.00661975714474225
GO:0019319hexose biosynthetic process0.00738804011175958
GO:0006006glucose metabolic process0.00738804011175958
GO:0046165alcohol biosynthetic process0.00738804011175958
GO:0046364monosaccharide biosynthetic process0.00738804011175958
GO:0005783endoplasmic reticulum0.00763820596210189
GO:0044262cellular carbohydrate metabolic process0.00763820596210189
GO:0000250lanosterol synthase activity0.0119816319321794
GO:0031559oxidosqualene cyclase activity0.0119816319321794
GO:0015755fructose transport0.0119816319321794
GO:0005967mitochondrial pyruvate dehydrogenase complex0.0119816319321794
GO:0019318hexose metabolic process0.0143270588232775
GO:0005996monosaccharide metabolic process0.0145494156568869
GO:0009058biosynthetic process0.0178195177213405
GO:0006633fatty acid biosynthetic process0.017823864636361
GO:0045254pyruvate dehydrogenase complex0.018714962284046
GO:0003989acetyl-CoA carboxylase activity0.018714962284046
GO:0045721negative regulation of gluconeogenesis0.018714962284046
GO:0016053organic acid biosynthetic process0.0196013790796282
GO:0046394carboxylic acid biosynthetic process0.0196013790796282
GO:0006694steroid biosynthetic process0.0218552600591857
GO:0004075biotin carboxylase activity0.0219027833096744
GO:0030523dihydrolipoamide S-acyltransferase activity0.0219027833096744
GO:0005353fructose transmembrane transporter activity0.0219027833096744
GO:0006085acetyl-CoA biosynthetic process0.0219027833096744
GO:0004742dihydrolipoyllysine-residue acetyltransferase activity0.0219027833096744
GO:0045912negative regulation of carbohydrate metabolic process0.0219027833096744
GO:0008643carbohydrate transport0.0260205847257939
GO:0006111regulation of gluconeogenesis0.0260205847257939
GO:0016418S-acetyltransferase activity0.0260205847257939
GO:0046326positive regulation of glucose import0.0260205847257939
GO:0004768stearoyl-CoA 9-desaturase activity0.0260205847257939
GO:0005886plasma membrane0.031762335050145
GO:0006066alcohol metabolic process0.0322854011259591
GO:0005813centrosome0.0322854011259591
GO:0005789endoplasmic reticulum membrane0.0322854011259591
GO:0042175nuclear envelope-endoplasmic reticulum network0.0322854011259591
GO:0016421CoA carboxylase activity0.0322854011259591
GO:0045923positive regulation of fatty acid metabolic process0.0322854011259591
GO:0050811GABA receptor binding0.0322854011259591
GO:0043255regulation of carbohydrate biosynthetic process0.0322854011259591
GO:0016051carbohydrate biosynthetic process0.0322854011259591
GO:0005815microtubule organizing center0.0352497886411914
GO:0030135coated vesicle0.0352497886411914
GO:0016885ligase activity, forming carbon-carbon bonds0.0354666323447513
GO:0006109regulation of carbohydrate metabolic process0.0363860662134483
GO:0005869dynactin complex0.0363860662134483
GO:0019217regulation of fatty acid metabolic process0.0363860662134483
GO:0046323glucose import0.0363860662134483
GO:0046324regulation of glucose import0.0363860662134483
GO:0044446intracellular organelle part0.0363860662134483
GO:0044432endoplasmic reticulum part0.0363860662134483
GO:0044422organelle part0.0363860662134483
GO:0016417S-acyltransferase activity0.0409081858716647
GO:0045834positive regulation of lipid metabolic process0.0409081858716647
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0409081858716647
GO:0005811lipid particle0.0409081858716647
GO:0015645fatty-acid ligase activity0.0409081858716647
GO:0030212hyaluronan metabolic process0.0409081858716647
GO:0044424intracellular part0.0415672940808074
GO:0031405lipoic acid binding0.0415672940808074
GO:0009746response to hexose stimulus0.0415672940808074
GO:0050729positive regulation of inflammatory response0.0415672940808074
GO:0009749response to glucose stimulus0.0415672940808074
GO:0031349positive regulation of defense response0.0415672940808074
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.044211523486239
GO:0004303estradiol 17-beta-dehydrogenase activity0.044211523486239
GO:0031406carboxylic acid binding0.049790421721825
GO:0004245neprilysin activity0.049790421721825
GO:0009308amine metabolic process0.049790421721825



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
stuff accumulating cell3.43e-1239
fat cell1.55e-0915
epithelial cell8.09e-08254
Uber Anatomy
Ontology termp-valuen
organism subdivision1.77e-21365
multi-tissue structure7.35e-20347
ectoderm-derived structure1.07e-14169
cell layer2.66e-14312
epithelium3.28e-14309
ectoderm5.17e-14173
presumptive ectoderm5.17e-14173
head1.90e-13123
organ part3.94e-12219
organ4.71e-12511
anterior region of body5.93e-12129
craniocervical region5.93e-12129
anatomical cluster1.02e-11286
embryo1.64e-11612
embryonic structure1.99e-11605
developing anatomical structure1.99e-11605
germ layer2.04e-11604
embryonic tissue2.04e-11604
presumptive structure2.04e-11604
epiblast (generic)2.04e-11604
multi-cellular organism2.57e-11659
endoderm-derived structure1.89e-10169
endoderm1.89e-10169
presumptive endoderm1.89e-10169
trunk1.27e-09216
digestive system3.56e-09155
digestive tract3.56e-09155
primitive gut3.56e-09155
central nervous system5.83e-0982
neural plate5.85e-0986
presumptive neural plate5.85e-0986
anatomical group6.13e-09626
anatomical system6.59e-09625
regional part of brain2.12e-0859
mesenchyme2.22e-08238
entire embryonic mesenchyme2.22e-08238
brain2.68e-0869
future brain2.68e-0869
neurectoderm3.19e-0890
trunk mesenchyme5.13e-08143
neural tube6.48e-0857
neural rod6.48e-0857
future spinal cord6.48e-0857
neural keel6.48e-0857
regional part of nervous system6.73e-0894
nervous system6.73e-0894
anatomical conduit2.27e-07241
organ segment2.77e-0797
pre-chordal neural plate9.03e-0761


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)

{{{tfbs_overrepresentation_jaspar}}}



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
SREBF1#672073.290409460834180.005635517670162610.0254725106013205
SREBF2#6721521.84716312056743.860722311979e-060.000126003117981492



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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C173&oldid=2133414"