Personal tools

Coexpression cluster:C560: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic |id=C560 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic
|full_id=C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic
|gostat_on_coexpression_clusters=GO:0065007!biological regulation!0.00768606826536886!22900;5330;7940;57591;391;10800;10287;4987$GO:0007242!intracellular signaling cascade!0.00768606826536886!391;22900;10287;5330;4987$GO:0007165!signal transduction!0.00768606826536886!391;22900;10287;10800;257106;5330;4987$GO:0051480!cytosolic calcium ion homeostasis!0.00768606826536886!10800;4987$GO:0007204!elevation of cytosolic calcium ion concentration!0.00768606826536886!10800;4987$GO:0051345!positive regulation of hydrolase activity!0.00768606826536886!22900;5330$GO:0007154!cell communication!0.00768606826536886!391;22900;10287;10800;257106;5330;4987$GO:0008047!enzyme activator activity!0.00768606826536886!22900;10287;257106$GO:0032089!NACHT domain binding!0.00768606826536886!22900$GO:0009968!negative regulation of signal transduction!0.00963686219868977!22900;10287$GO:0006874!cellular calcium ion homeostasis!0.00963686219868977!10800;4987$GO:0055074!calcium ion homeostasis!0.00963686219868977!10800;4987$GO:0006875!cellular metal ion homeostasis!0.00963686219868977!10800;4987$GO:0055065!metal ion homeostasis!0.00963686219868977!10800;4987$GO:0007186!G-protein coupled receptor protein signaling pathway!0.0153133997986742!10287;10800;5330;4987$GO:0015051!X-opioid receptor activity!0.0164799494906198!4987$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0164799494906198!10800;4987$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0164799494906198!10800;4987$GO:0004974!leukotriene receptor activity!0.0173368271137648!10800$GO:0030003!cellular cation homeostasis!0.0173368271137648!10800;4987$GO:0055080!cation homeostasis!0.0173368271137648!10800;4987$GO:0043124!negative regulation of I-kappaB kinase/NF-kappaB cascade!0.0188533124660523!22900$GO:0055082!cellular chemical homeostasis!0.0202857552107383!10800;4987$GO:0006873!cellular ion homeostasis!0.0202857552107383!10800;4987$GO:0050718!positive regulation of interleukin-1 beta secretion!0.0202857552107383!22900$GO:0050706!regulation of interleukin-1 beta secretion!0.0202857552107383!22900$GO:0043085!positive regulation of catalytic activity!0.0202857552107383!22900;5330$GO:0050716!positive regulation of interleukin-1 secretion!0.0202857552107383!22900$GO:0050704!regulation of interleukin-1 secretion!0.0202857552107383!22900$GO:0050801!ion homeostasis!0.0202857552107383!10800;4987$GO:0019932!second-messenger-mediated signaling!0.0202857552107383!5330;4987$GO:0050702!interleukin-1 beta secretion!0.0215913114519548!22900$GO:0050672!negative regulation of lymphocyte proliferation!0.0217118145535234!7940$GO:0032945!negative regulation of mononuclear cell proliferation!0.0217118145535234!7940$GO:0050701!interleukin-1 secretion!0.0217118145535234!22900$GO:0048878!chemical homeostasis!0.021812809706439!10800;4987$GO:0051336!regulation of hydrolase activity!0.021812809706439!22900;5330$GO:0016358!dendrite development!0.021812809706439!7940$GO:0048523!negative regulation of cellular process!0.0222381094285401!22900;10287;7940$GO:0050715!positive regulation of cytokine secretion!0.0222381094285401!22900$GO:0007166!cell surface receptor linked signal transduction!0.0222381094285401!10287;10800;5330;4987$GO:0004985!opioid receptor activity!0.0224114206445887!4987$GO:0008656!caspase activator activity!0.0224114206445887!22900$GO:0048519!negative regulation of biological process!0.0224114206445887!22900;10287;7940$GO:0005096!GTPase activator activity!0.0225427971115012!10287;257106$GO:0050707!regulation of cytokine secretion!0.0225427971115012!22900$GO:0007202!phospholipase C activation!0.0225427971115012!5330$GO:0050714!positive regulation of protein secretion!0.0225427971115012!22900$GO:0016505!apoptotic protease activator activity!0.0225427971115012!22900$GO:0019725!cellular homeostasis!0.0238912041264944!10800;4987$GO:0016504!protease activator activity!0.0238912041264944!22900$GO:0007193!G-protein signaling, adenylate cyclase inhibiting pathway!0.0238912041264944!4987$GO:0051250!negative regulation of lymphocyte activation!0.024739396424922!7940$GO:0050663!cytokine secretion!0.0255558362491887!22900$GO:0043028!caspase regulator activity!0.0258718582086354!22900$GO:0051047!positive regulation of secretion!0.0258718582086354!22900$GO:0006914!autophagy!0.0309068112179078!10287$GO:0050708!regulation of protein secretion!0.0309068112179078!22900$GO:0042127!regulation of cell proliferation!0.031677914247718!391;7940$GO:0042592!homeostatic process!0.0325735113717887!10800;4987$GO:0007585!respiratory gaseous exchange!0.032764573503621!10800$GO:0005834!heterotrimeric G-protein complex!0.0410853019415701!10287$GO:0022603!regulation of anatomical structure morphogenesis!0.0431284191752502!7940$GO:0022604!regulation of cell morphogenesis!0.0431284191752502!7940$GO:0050670!regulation of lymphocyte proliferation!0.0431284191752502!7940$GO:0032944!regulation of mononuclear cell proliferation!0.0431284191752502!7940$GO:0008360!regulation of cell shape!0.0431284191752502!7940$GO:0050790!regulation of catalytic activity!0.0442110780729895!22900;5330$GO:0004435!phosphoinositide phospholipase C activity!0.0442110780729895!5330$GO:0004434!inositol or phosphatidylinositol phosphodiesterase activity!0.0442110780729895!5330$GO:0019897!extrinsic to plasma membrane!0.0477272926776687!10287$GO:0043280!positive regulation of caspase activity!0.0477272926776687!22900$GO:0032943!mononuclear cell proliferation!0.048449248386039!7940$GO:0046651!lymphocyte proliferation!0.048449248386039!7940$GO:0065009!regulation of a molecular function!0.048449248386039!22900;5330$GO:0050794!regulation of cellular process!0.048449248386039!57591;391;22900;10287;7940$GO:0005624!membrane fraction!0.048449248386039!10287;10800$GO:0004629!phospholipase C activity!0.048449248386039!5330$GO:0009306!protein secretion!0.048449248386039!22900$GO:0005794!Golgi apparatus!0.048449248386039!10287;7940$GO:0030695!GTPase regulator activity!0.048449248386039!10287;257106$GO:0051046!regulation of secretion!0.048449248386039!22900$GO:0004871!signal transducer activity!0.048449248386039!10287;10800;5330;4987$GO:0060089!molecular transducer activity!0.048449248386039!10287;10800;5330;4987$GO:0043281!regulation of caspase activity!0.048449248386039!22900
|id=C560
|id=C560
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:3862154..3862165,-p3@RHOG
Hg19::chr15:40600066..40600089,-p3@PLCB2
Hg19::chr16:3137080..3137121,-p@chr16:3137080..3137121
-
Hg19::chr19:2282186..2282208,-p1@C19orf35
Hg19::chr19:48753064..48753095,-p1@CARD8
Hg19::chr1:161039493..161039519,-p3@ARHGAP30
Hg19::chr1:161039535..161039544,-p11@ARHGAP30
Hg19::chr20:62708698..62708701,+p@chr20:62708698..62708701
+
Hg19::chr20:62710832..62710879,-p1@RGS19
Hg19::chr20:62710880..62710898,-p3@RGS19
Hg19::chr20:62711425..62711470,+p2@OPRL1
Hg19::chr22:40859415..40859478,-p2@MKL1
Hg19::chr2:220042536..220042549,-p5@CNPPD1
Hg19::chr6:31554456..31554512,+p6@LST1
Hg19::chrX:109245878..109245916,+p2@TMEM164
Hg19::chrX:77583054..77583100,-p1@CYSLTR1


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:0065007biological regulation0.00768606826536886
GO:0007242intracellular signaling cascade0.00768606826536886
GO:0007165signal transduction0.00768606826536886
GO:0051480cytosolic calcium ion homeostasis0.00768606826536886
GO:0007204elevation of cytosolic calcium ion concentration0.00768606826536886
GO:0051345positive regulation of hydrolase activity0.00768606826536886
GO:0007154cell communication0.00768606826536886
GO:0008047enzyme activator activity0.00768606826536886
GO:0032089NACHT domain binding0.00768606826536886
GO:0009968negative regulation of signal transduction0.00963686219868977
GO:0006874cellular calcium ion homeostasis0.00963686219868977
GO:0055074calcium ion homeostasis0.00963686219868977
GO:0006875cellular metal ion homeostasis0.00963686219868977
GO:0055065metal ion homeostasis0.00963686219868977
GO:0007186G-protein coupled receptor protein signaling pathway0.0153133997986742
GO:0015051X-opioid receptor activity0.0164799494906198
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0164799494906198
GO:0055066di-, tri-valent inorganic cation homeostasis0.0164799494906198
GO:0004974leukotriene receptor activity0.0173368271137648
GO:0030003cellular cation homeostasis0.0173368271137648
GO:0055080cation homeostasis0.0173368271137648
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0188533124660523
GO:0055082cellular chemical homeostasis0.0202857552107383
GO:0006873cellular ion homeostasis0.0202857552107383
GO:0050718positive regulation of interleukin-1 beta secretion0.0202857552107383
GO:0050706regulation of interleukin-1 beta secretion0.0202857552107383
GO:0043085positive regulation of catalytic activity0.0202857552107383
GO:0050716positive regulation of interleukin-1 secretion0.0202857552107383
GO:0050704regulation of interleukin-1 secretion0.0202857552107383
GO:0050801ion homeostasis0.0202857552107383
GO:0019932second-messenger-mediated signaling0.0202857552107383
GO:0050702interleukin-1 beta secretion0.0215913114519548
GO:0050672negative regulation of lymphocyte proliferation0.0217118145535234
GO:0032945negative regulation of mononuclear cell proliferation0.0217118145535234
GO:0050701interleukin-1 secretion0.0217118145535234
GO:0048878chemical homeostasis0.021812809706439
GO:0051336regulation of hydrolase activity0.021812809706439
GO:0016358dendrite development0.021812809706439
GO:0048523negative regulation of cellular process0.0222381094285401
GO:0050715positive regulation of cytokine secretion0.0222381094285401
GO:0007166cell surface receptor linked signal transduction0.0222381094285401
GO:0004985opioid receptor activity0.0224114206445887
GO:0008656caspase activator activity0.0224114206445887
GO:0048519negative regulation of biological process0.0224114206445887
GO:0005096GTPase activator activity0.0225427971115012
GO:0050707regulation of cytokine secretion0.0225427971115012
GO:0007202phospholipase C activation0.0225427971115012
GO:0050714positive regulation of protein secretion0.0225427971115012
GO:0016505apoptotic protease activator activity0.0225427971115012
GO:0019725cellular homeostasis0.0238912041264944
GO:0016504protease activator activity0.0238912041264944
GO:0007193G-protein signaling, adenylate cyclase inhibiting pathway0.0238912041264944
GO:0051250negative regulation of lymphocyte activation0.024739396424922
GO:0050663cytokine secretion0.0255558362491887
GO:0043028caspase regulator activity0.0258718582086354
GO:0051047positive regulation of secretion0.0258718582086354
GO:0006914autophagy0.0309068112179078
GO:0050708regulation of protein secretion0.0309068112179078
GO:0042127regulation of cell proliferation0.031677914247718
GO:0042592homeostatic process0.0325735113717887
GO:0007585respiratory gaseous exchange0.032764573503621
GO:0005834heterotrimeric G-protein complex0.0410853019415701
GO:0022603regulation of anatomical structure morphogenesis0.0431284191752502
GO:0022604regulation of cell morphogenesis0.0431284191752502
GO:0050670regulation of lymphocyte proliferation0.0431284191752502
GO:0032944regulation of mononuclear cell proliferation0.0431284191752502
GO:0008360regulation of cell shape0.0431284191752502
GO:0050790regulation of catalytic activity0.0442110780729895
GO:0004435phosphoinositide phospholipase C activity0.0442110780729895
GO:0004434inositol or phosphatidylinositol phosphodiesterase activity0.0442110780729895
GO:0019897extrinsic to plasma membrane0.0477272926776687
GO:0043280positive regulation of caspase activity0.0477272926776687
GO:0032943mononuclear cell proliferation0.048449248386039
GO:0046651lymphocyte proliferation0.048449248386039
GO:0065009regulation of a molecular function0.048449248386039
GO:0050794regulation of cellular process0.048449248386039
GO:0005624membrane fraction0.048449248386039
GO:0004629phospholipase C activity0.048449248386039
GO:0009306protein secretion0.048449248386039
GO:0005794Golgi apparatus0.048449248386039
GO:0030695GTPase regulator activity0.048449248386039
GO:0051046regulation of secretion0.048449248386039
GO:0004871signal transducer activity0.048449248386039
GO:0060089molecular transducer activity0.048449248386039
GO:0043281regulation of caspase activity0.048449248386039



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C560&oldid=1703329"