Personal tools

Coexpression cluster:C367: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular |id=C367 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular
|full_id=C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular
|gostat_on_coexpression_clusters=GO:0030574!collagen catabolic process!3.49113901529097e-05!4316;5653$GO:0044256!protein digestion!3.49113901529097e-05!4316;5653$GO:0044254!multicellular organismal protein catabolic process!3.49113901529097e-05!4316;5653$GO:0044266!multicellular organismal macromolecule catabolic process!3.49113901529097e-05!4316;5653$GO:0044259!multicellular organismal macromolecule metabolic process!3.49113901529097e-05!4316;5653$GO:0044268!multicellular organismal protein metabolic process!3.49113901529097e-05!4316;5653$GO:0044243!multicellular organismal catabolic process!3.49113901529097e-05!4316;5653$GO:0032963!collagen metabolic process!3.49113901529097e-05!4316;5653$GO:0044236!multicellular organismal metabolic process!3.738365344664e-05!4316;5653$GO:0007586!digestion!0.000592102168167378!4316;5653$GO:0004235!matrilysin activity!0.00137011228498335!4316$GO:0016316!phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity!0.00251176160996224!8821$GO:0004293!tissue kallikrein activity!0.00579560515052357!5653$GO:0030163!protein catabolic process!0.00592419392120253!4316;5653$GO:0007130!synaptonemal complex assembly!0.00602716320831794!10734$GO:0007129!synapsis!0.00659191867090141!10734$GO:0043285!biopolymer catabolic process!0.00790864191242954!4316;5653$GO:0042577!lipid phosphatase activity!0.0100426108972329!8821$GO:0000795!synaptonemal complex!0.0103064350029073!10734$GO:0042982!amyloid precursor protein metabolic process!0.0105438101975185!5653$GO:0042246!tissue regeneration!0.0111317409286778!5653$GO:0009057!macromolecule catabolic process!0.0111317409286778!4316;5653$GO:0050435!beta-amyloid metabolic process!0.0111317409286778!5653$GO:0031099!regeneration!0.0112949442082651!5653$GO:0042552!myelination!0.015656790337173!5653$GO:0004175!endopeptidase activity!0.0159698035176525!4316;5653$GO:0000794!condensed nuclear chromosome!0.0165549481747521!10734$GO:0007272!ensheathment of neurons!0.0165549481747521!5653$GO:0008366!axon ensheathment!0.0165549481747521!5653$GO:0007127!meiosis I!0.0165549481747521!10734$GO:0048589!developmental growth!0.0179596740625052!5653$GO:0001508!regulation of action potential!0.0183529399737562!5653$GO:0009056!catabolic process!0.0183529399737562!4316;5653$GO:0016540!protein autoprocessing!0.0203500138822008!5653$GO:0016787!hydrolase activity!0.0207309052081313!8821;4316;5653$GO:0000793!condensed chromosome!0.0217205866203829!10734$GO:0004437!inositol or phosphatidylinositol phosphatase activity!0.0231604999529081!8821$GO:0007059!chromosome segregation!0.0233402148347696!10734$GO:0008233!peptidase activity!0.0246856409289252!4316;5653$GO:0044454!nuclear chromosome part!0.0246856409289252!10734$GO:0051327!M phase of meiotic cell cycle!0.0246856409289252!10734$GO:0007126!meiosis!0.0246856409289252!10734$GO:0051321!meiotic cell cycle!0.0248082502336922!10734$GO:0006508!proteolysis!0.0248798947491532!4316;5653$GO:0042445!hormone metabolic process!0.0293596090777808!5653$GO:0016485!protein processing!0.0316086834367993!5653$GO:0000228!nuclear chromosome!0.0316086834367993!10734$GO:0042060!wound healing!0.0408964047267248!5653$GO:0045595!regulation of cell differentiation!0.0440120927780186!5653
|id=C367
|id=C367
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C367_papillotubular_Macrophage_clear_pharyngeal_Renal_endometrial_tubular



Phase1 CAGE Peaks

Hg19::chr11:102401469..102401488,-p1@MMP7
Hg19::chr13:107026326..107026335,-p@chr13:107026326..107026335
-
Hg19::chr15:20093569..20093572,+p@chr15:20093569..20093572
+
Hg19::chr17:70636802..70636818,+p@chr17:70636802..70636818
+
Hg19::chr19:15923954..15923958,-p@chr19:15923954..15923958
-
Hg19::chr19:49522727..49522759,-p@chr19:49522727..49522759
-
Hg19::chr19:49545646..49545652,+p@chr19:49545646..49545652
+
Hg19::chr19:49545660..49545673,+p@chr19:49545660..49545673
+
Hg19::chr19:49545674..49545685,+p@chr19:49545674..49545685
+
Hg19::chr19:49545691..49545692,+p@chr19:49545691..49545692
+
Hg19::chr19:49553696..49553725,-p@chr19:49553696..49553725
-
Hg19::chr19:49553788..49553818,-p@chr19:49553788..49553818
-
Hg19::chr19:51472014..51472030,-p2@KLK6
Hg19::chr1:218785863..218785866,+p@chr1:218785863..218785866
+
Hg19::chr1:222159603..222159607,+p@chr1:222159603..222159607
+
Hg19::chr20:56283735..56283746,+p@chr20:56283735..56283746
+
Hg19::chr2:106016186..106016205,+p@chr2:106016186..106016205
+
Hg19::chr2:30440814..30440823,+p@chr2:30440814..30440823
+
Hg19::chr3:139035972..139036016,-p@chr3:139035972..139036016
-
Hg19::chr4:143369478..143369483,-p@chr4:143369478..143369483
-
Hg19::chr4:143395551..143395584,-p3@INPP4B
Hg19::chr4:143395591..143395600,-p16@INPP4B
Hg19::chr4:143395603..143395614,-p14@INPP4B
Hg19::chr6:1054763..1054800,-p@chr6:1054763..1054800
-
Hg19::chr7:98796685..98796688,-p@chr7:98796685..98796688
-
Hg19::chr7:98807901..98807908,-p@chr7:98807901..98807908
-
Hg19::chr7:98822527..98822533,+p@chr7:98822527..98822533
+
Hg19::chr7:99779265..99779276,+p15@STAG3
Hg19::chr9:132337683..132337714,+p1@ENST00000443993
p1@uc004bya.1
Hg19::chrX:46121582..46121588,-p@chrX:46121582..46121588
-


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:0030574collagen catabolic process3.49113901529097e-05
GO:0044256protein digestion3.49113901529097e-05
GO:0044254multicellular organismal protein catabolic process3.49113901529097e-05
GO:0044266multicellular organismal macromolecule catabolic process3.49113901529097e-05
GO:0044259multicellular organismal macromolecule metabolic process3.49113901529097e-05
GO:0044268multicellular organismal protein metabolic process3.49113901529097e-05
GO:0044243multicellular organismal catabolic process3.49113901529097e-05
GO:0032963collagen metabolic process3.49113901529097e-05
GO:0044236multicellular organismal metabolic process3.738365344664e-05
GO:0007586digestion0.000592102168167378
GO:0004235matrilysin activity0.00137011228498335
GO:0016316phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity0.00251176160996224
GO:0004293tissue kallikrein activity0.00579560515052357
GO:0030163protein catabolic process0.00592419392120253
GO:0007130synaptonemal complex assembly0.00602716320831794
GO:0007129synapsis0.00659191867090141
GO:0043285biopolymer catabolic process0.00790864191242954
GO:0042577lipid phosphatase activity0.0100426108972329
GO:0000795synaptonemal complex0.0103064350029073
GO:0042982amyloid precursor protein metabolic process0.0105438101975185
GO:0042246tissue regeneration0.0111317409286778
GO:0009057macromolecule catabolic process0.0111317409286778
GO:0050435beta-amyloid metabolic process0.0111317409286778
GO:0031099regeneration0.0112949442082651
GO:0042552myelination0.015656790337173
GO:0004175endopeptidase activity0.0159698035176525
GO:0000794condensed nuclear chromosome0.0165549481747521
GO:0007272ensheathment of neurons0.0165549481747521
GO:0008366axon ensheathment0.0165549481747521
GO:0007127meiosis I0.0165549481747521
GO:0048589developmental growth0.0179596740625052
GO:0001508regulation of action potential0.0183529399737562
GO:0009056catabolic process0.0183529399737562
GO:0016540protein autoprocessing0.0203500138822008
GO:0016787hydrolase activity0.0207309052081313
GO:0000793condensed chromosome0.0217205866203829
GO:0004437inositol or phosphatidylinositol phosphatase activity0.0231604999529081
GO:0007059chromosome segregation0.0233402148347696
GO:0008233peptidase activity0.0246856409289252
GO:0044454nuclear chromosome part0.0246856409289252
GO:0051327M phase of meiotic cell cycle0.0246856409289252
GO:0007126meiosis0.0246856409289252
GO:0051321meiotic cell cycle0.0248082502336922
GO:0006508proteolysis0.0248798947491532
GO:0042445hormone metabolic process0.0293596090777808
GO:0016485protein processing0.0316086834367993
GO:0000228nuclear chromosome0.0316086834367993
GO:0042060wound healing0.0408964047267248
GO:0045595regulation of cell differentiation0.0440120927780186



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:C367&oldid=1703074"