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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast
|full_id=C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast
|gostat_on_coexpression_clusters=GO:0005739!mitochondrion!0.00620645344517677!25824;4713;572;64975;2876;51024$GO:0005737!cytoplasm!0.00761501180775182!64975;11316;2876;126003;51024;30851;25824;4713;572;29085;5372;51529;6881$GO:0044444!cytoplasmic part!0.00761501180775182!64975;11316;2876;126003;51024;4713;25824;572;29085;6881$GO:0006915!apoptosis!0.00761501180775182!9274;572;64975;2876;51024$GO:0012501!programmed cell death!0.00761501180775182!9274;572;64975;2876;51024$GO:0016265!death!0.00761501180775182!9274;572;64975;2876;51024$GO:0008219!cell death!0.00761501180775182!9274;572;64975;2876;51024$GO:0043231!intracellular membrane-bound organelle!0.00772619952853591!64975;11316;2876;126003;51024;30851;4713;25824;572;51529;6923;85359;6881$GO:0043227!membrane-bound organelle!0.00772619952853591!64975;11316;2876;126003;51024;30851;4713;25824;572;51529;6923;85359;6881$GO:0044429!mitochondrial part!0.012211775933763!4713;572;64975;51024$GO:0010269!response to selenium ion!0.0180924827404877!2876$GO:0048468!cell development!0.0180924827404877!9274;572;64975;2876;51024$GO:0004601!peroxidase activity!0.0180924827404877!25824;2876$GO:0016684!oxidoreductase activity, acting on peroxide as acceptor!0.0180924827404877!25824;2876$GO:0005741!mitochondrial outer membrane!0.019637546591411!572;51024$GO:0033598!mammary gland epithelial cell proliferation!0.019637546591411!2876$GO:0008539!proteasome inhibitor activity!0.019637546591411!2876$GO:0033599!regulation of mammary gland epithelial cell proliferation!0.019637546591411!2876$GO:0008969!phosphohistidine phosphatase activity!0.019637546591411!29085$GO:0008632!apoptotic program!0.019637546591411!572;2876$GO:0007005!mitochondrion organization and biogenesis!0.019637546591411!2876;51024$GO:0031968!organelle outer membrane!0.019637546591411!572;51024$GO:0019867!outer membrane!0.019637546591411!572;51024$GO:0044424!intracellular part!0.019637546591411!64975;11316;2876;126003;51024;30851;25824;4713;572;29085;5372;51529;6923;85359;6881$GO:0042579!microbody!0.019637546591411!25824;51024$GO:0005777!peroxisome!0.019637546591411!25824;51024$GO:0031966!mitochondrial membrane!0.019637546591411!4713;572;51024$GO:0043295!glutathione binding!0.019637546591411!2876$GO:0017057!6-phosphogluconolactonase activity!0.019637546591411!25796$GO:0000266!mitochondrial fission!0.019637546591411!51024$GO:0019307!mannose biosynthetic process!0.019637546591411!5372$GO:0004615!phosphomannomutase activity!0.019637546591411!5372$GO:0005740!mitochondrial envelope!0.021381196836168!4713;572;51024$GO:0006979!response to oxidative stress!0.0226387669961546!25824;2876$GO:0044455!mitochondrial membrane part!0.0226387669961546!4713;51024$GO:0008631!induction of apoptosis by oxidative stress!0.0226387669961546!2876$GO:0031307!integral to mitochondrial outer membrane!0.0226387669961546!51024$GO:0031306!intrinsic to mitochondrial outer membrane!0.0272464569702817!51024$GO:0043229!intracellular organelle!0.0272464569702817!64975;11316;2876;126003;51024;30851;4713;25824;572;51529;6923;85359;6881$GO:0043226!organelle!0.0272464569702817!64975;11316;2876;126003;51024;30851;4713;25824;572;51529;6923;85359;6881$GO:0048869!cellular developmental process!0.0272988937719487!9274;572;64975;2876;51024$GO:0030154!cell differentiation!0.0272988937719487!9274;572;64975;2876;51024$GO:0009650!UV protection!0.0272988937719487!2876$GO:0016559!peroxisome fission!0.0272988937719487!51024$GO:0051920!peroxiredoxin activity!0.0272988937719487!25824$GO:0032592!integral to mitochondrial membrane!0.0272988937719487!51024$GO:0048285!organelle fission!0.034862420969153!51024$GO:0030503!regulation of cell redox homeostasis!0.034862420969153!2876$GO:0043154!negative regulation of caspase activity!0.0384090722914862!2876$GO:0031967!organelle envelope!0.0388818993684594!4713;572;51024$GO:0031975!envelope!0.0388818993684594!4713;572;51024$GO:0006368!RNA elongation from RNA polymerase II promoter!0.0402033875658268!6923$GO:0006917!induction of apoptosis!0.0431027183745183!572;2876$GO:0012502!induction of programmed cell death!0.0431027183745183!572;2876$GO:0006890!retrograde vesicle-mediated transport, Golgi to ER!0.0431027183745183!11316$GO:0042744!hydrogen peroxide catabolic process!0.0431027183745183!2876$GO:0044446!intracellular organelle part!0.0431027183745183!4713;572;64975;11316;51529;51024;6881$GO:0044422!organelle part!0.0431027183745183!4713;572;64975;11316;51529;51024;6881$GO:0005794!Golgi apparatus!0.0431027183745183!11316;126003;51024$GO:0001836!release of cytochrome c from mitochondria!0.0431027183745183!2876$GO:0006740!NADPH regeneration!0.0431027183745183!25796$GO:0006098!pentose-phosphate shunt!0.0431027183745183!25796$GO:0042743!hydrogen peroxide metabolic process!0.0431027183745183!2876$GO:0005515!protein binding!0.0443883691234917!5605;11316;2876;126003;51024;30851;10467;572;51529;6923;6881$GO:0006013!mannose metabolic process!0.0443883691234917!5372$GO:0005762!mitochondrial large ribosomal subunit!0.0443883691234917!64975$GO:0030663!COPI coated vesicle membrane!0.0443883691234917!11316$GO:0000315!organellar large ribosomal subunit!0.0443883691234917!64975$GO:0030126!COPI vesicle coat!0.0443883691234917!11316$GO:0005779!integral to peroxisomal membrane!0.0443883691234917!51024$GO:0031231!intrinsic to peroxisomal membrane!0.0443883691234917!51024$GO:0004602!glutathione peroxidase activity!0.0443883691234917!2876$GO:0065003!macromolecular complex assembly!0.0443883691234917!11316;6923;6881$GO:0043065!positive regulation of apoptosis!0.0443883691234917!572;2876$GO:0005622!intracellular!0.0443883691234917!64975;11316;2876;126003;51024;30851;25824;4713;572;29085;5372;51529;6923;85359;6881$GO:0006891!intra-Golgi vesicle-mediated transport!0.0443883691234917!11316$GO:0030137!COPI-coated vesicle!0.0443883691234917!11316$GO:0006739!NADP metabolic process!0.0443883691234917!25796$GO:0005680!anaphase-promoting complex!0.0443883691234917!51529$GO:0043068!positive regulation of programmed cell death!0.0443883691234917!572;2876$GO:0030178!negative regulation of Wnt receptor signaling pathway!0.0457598392455279!30851$GO:0006354!RNA elongation!0.0457598392455279!6923$GO:0031090!organelle membrane!0.0457598392455279!4713;572;11316;51024$GO:0019318!hexose metabolic process!0.0457863884821124!5372;25796$GO:0006749!glutathione metabolic process!0.0457888876222452!2876$GO:0008637!apoptotic mitochondrial changes!0.0457888876222452!2876$GO:0005996!monosaccharide metabolic process!0.0457888876222452!5372;25796$GO:0022607!cellular component assembly!0.0463276222825077!11316;6923;6881$GO:0042542!response to hydrogen peroxide!0.0463276222825077!2876$GO:0017124!SH3 domain binding!0.0463276222825077!2876$GO:0000152!nuclear ubiquitin ligase complex!0.0476122033922862!51529$GO:0006732!coenzyme metabolic process!0.0476122033922862!2876;25796
|id=C385
|id=C385
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C385_Mesenchymal_Alveolar_Osteoblast_Smooth_Renal_Placental_Fibroblast



Phase1 CAGE Peaks

Hg19::chr11:129903123..129903147,-p1@TCEB2P2
Hg19::chr11:63993738..63993778,+p1@NUDT22
Hg19::chr11:64052114..64052210,-p1@BAD
Hg19::chr11:64085563..64085736,+p1@PRDX5
Hg19::chr11:6633406..6633456,-p1@TAF10
Hg19::chr14:94595896..94595949,-p1@IFI27L2
Hg19::chr15:44084503..44084563,+p1@SERF2
Hg19::chr16:1401799..1401896,-p1@C16orf42
Hg19::chr16:2827261..2827299,-p1@TCEB2
Hg19::chr16:30905311..30905428,-p1@BCL7C
Hg19::chr17:3571887..3571918,-p2@TAX1BP3
Hg19::chr17:79849591..79849644,+p1@ANAPC11
Hg19::chr19:14682838..14682894,-p1@NDUFB7
Hg19::chr19:17622415..17622481,+p1@PGLS
Hg19::chr19:19030157..19030210,-p1@COPE
Hg19::chr19:4124133..4124149,-p2@MAP2K2
Hg19::chr19:51014430..51014455,-p2@JOSD2
Hg19::chr19:51014460..51014503,-p1@JOSD2
Hg19::chr19:7745708..7745752,+p1@TRAPPC5
Hg19::chr22:20307537..20307590,-p1@DGCR6L
Hg19::chr22:41985798..41985852,-p1@PMM1
Hg19::chr3:49395773..49395819,-p1@GPX1
Hg19::chr3:9834088..9834176,-p1@TADA3
Hg19::chr7:100861427..100861471,+p1@ZNHIT1
Hg19::chr7:100888337..100888377,-p1@FIS1
Hg19::chr7:100888385..100888396,-p3@FIS1
Hg19::chr9:139743853..139743878,+p1@PHPT1
Hg19::chr9:140446314..140446398,+p1@MRPL41


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:0005739mitochondrion0.00620645344517677
GO:0005737cytoplasm0.00761501180775182
GO:0044444cytoplasmic part0.00761501180775182
GO:0006915apoptosis0.00761501180775182
GO:0012501programmed cell death0.00761501180775182
GO:0016265death0.00761501180775182
GO:0008219cell death0.00761501180775182
GO:0043231intracellular membrane-bound organelle0.00772619952853591
GO:0043227membrane-bound organelle0.00772619952853591
GO:0044429mitochondrial part0.012211775933763
GO:0010269response to selenium ion0.0180924827404877
GO:0048468cell development0.0180924827404877
GO:0004601peroxidase activity0.0180924827404877
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.0180924827404877
GO:0005741mitochondrial outer membrane0.019637546591411
GO:0033598mammary gland epithelial cell proliferation0.019637546591411
GO:0008539proteasome inhibitor activity0.019637546591411
GO:0033599regulation of mammary gland epithelial cell proliferation0.019637546591411
GO:0008969phosphohistidine phosphatase activity0.019637546591411
GO:0008632apoptotic program0.019637546591411
GO:0007005mitochondrion organization and biogenesis0.019637546591411
GO:0031968organelle outer membrane0.019637546591411
GO:0019867outer membrane0.019637546591411
GO:0044424intracellular part0.019637546591411
GO:0042579microbody0.019637546591411
GO:0005777peroxisome0.019637546591411
GO:0031966mitochondrial membrane0.019637546591411
GO:0043295glutathione binding0.019637546591411
GO:00170576-phosphogluconolactonase activity0.019637546591411
GO:0000266mitochondrial fission0.019637546591411
GO:0019307mannose biosynthetic process0.019637546591411
GO:0004615phosphomannomutase activity0.019637546591411
GO:0005740mitochondrial envelope0.021381196836168
GO:0006979response to oxidative stress0.0226387669961546
GO:0044455mitochondrial membrane part0.0226387669961546
GO:0008631induction of apoptosis by oxidative stress0.0226387669961546
GO:0031307integral to mitochondrial outer membrane0.0226387669961546
GO:0031306intrinsic to mitochondrial outer membrane0.0272464569702817
GO:0043229intracellular organelle0.0272464569702817
GO:0043226organelle0.0272464569702817
GO:0048869cellular developmental process0.0272988937719487
GO:0030154cell differentiation0.0272988937719487
GO:0009650UV protection0.0272988937719487
GO:0016559peroxisome fission0.0272988937719487
GO:0051920peroxiredoxin activity0.0272988937719487
GO:0032592integral to mitochondrial membrane0.0272988937719487
GO:0048285organelle fission0.034862420969153
GO:0030503regulation of cell redox homeostasis0.034862420969153
GO:0043154negative regulation of caspase activity0.0384090722914862
GO:0031967organelle envelope0.0388818993684594
GO:0031975envelope0.0388818993684594
GO:0006368RNA elongation from RNA polymerase II promoter0.0402033875658268
GO:0006917induction of apoptosis0.0431027183745183
GO:0012502induction of programmed cell death0.0431027183745183
GO:0006890retrograde vesicle-mediated transport, Golgi to ER0.0431027183745183
GO:0042744hydrogen peroxide catabolic process0.0431027183745183
GO:0044446intracellular organelle part0.0431027183745183
GO:0044422organelle part0.0431027183745183
GO:0005794Golgi apparatus0.0431027183745183
GO:0001836release of cytochrome c from mitochondria0.0431027183745183
GO:0006740NADPH regeneration0.0431027183745183
GO:0006098pentose-phosphate shunt0.0431027183745183
GO:0042743hydrogen peroxide metabolic process0.0431027183745183
GO:0005515protein binding0.0443883691234917
GO:0006013mannose metabolic process0.0443883691234917
GO:0005762mitochondrial large ribosomal subunit0.0443883691234917
GO:0030663COPI coated vesicle membrane0.0443883691234917
GO:0000315organellar large ribosomal subunit0.0443883691234917
GO:0030126COPI vesicle coat0.0443883691234917
GO:0005779integral to peroxisomal membrane0.0443883691234917
GO:0031231intrinsic to peroxisomal membrane0.0443883691234917
GO:0004602glutathione peroxidase activity0.0443883691234917
GO:0065003macromolecular complex assembly0.0443883691234917
GO:0043065positive regulation of apoptosis0.0443883691234917
GO:0005622intracellular0.0443883691234917
GO:0006891intra-Golgi vesicle-mediated transport0.0443883691234917
GO:0030137COPI-coated vesicle0.0443883691234917
GO:0006739NADP metabolic process0.0443883691234917
GO:0005680anaphase-promoting complex0.0443883691234917
GO:0043068positive regulation of programmed cell death0.0443883691234917
GO:0030178negative regulation of Wnt receptor signaling pathway0.0457598392455279
GO:0006354RNA elongation0.0457598392455279
GO:0031090organelle membrane0.0457598392455279
GO:0019318hexose metabolic process0.0457863884821124
GO:0006749glutathione metabolic process0.0457888876222452
GO:0008637apoptotic mitochondrial changes0.0457888876222452
GO:0005996monosaccharide metabolic process0.0457888876222452
GO:0022607cellular component assembly0.0463276222825077
GO:0042542response to hydrogen peroxide0.0463276222825077
GO:0017124SH3 domain binding0.0463276222825077
GO:0000152nuclear ubiquitin ligase complex0.0476122033922862
GO:0006732coenzyme metabolic process0.0476122033922862



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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

No analysis results for this cluster

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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