Personal tools

Coexpression cluster:C315: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C315_Osteoblast_Preadipocyte_mesenchymal_Smooth_Cardiac_leiomyoma_Adipocyte |id=C315 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C315_Osteoblast_Preadipocyte_mesenchymal_Smooth_Cardiac_leiomyoma_Adipocyte
|full_id=C315_Osteoblast_Preadipocyte_mesenchymal_Smooth_Cardiac_leiomyoma_Adipocyte
|gostat_on_coexpression_clusters=GO:0005509!calcium ion binding!0.0138219499543876!23770;1311;51150;6748;10398$GO:0051043!regulation of membrane protein ectodomain proteolysis!0.01680365693209!7076$GO:0051045!negative regulation of membrane protein ectodomain proteolysis!0.01680365693209!7076$GO:0048513!organ development!0.01680365693209!23770;1311;7076;1134$GO:0005789!endoplasmic reticulum membrane!0.01680365693209!23770;9415;6748$GO:0042175!nuclear envelope-endoplasmic reticulum network!0.01680365693209!23770;9415;6748$GO:0044432!endoplasmic reticulum part!0.0197111800970318!23770;9415;6748$GO:0044446!intracellular organelle part!0.0207947129244736!6141;23770;9415;51150;6748;10398$GO:0044422!organelle part!0.0207947129244736!6141;23770;9415;51150;6748;10398$GO:0003012!muscle system process!0.0207947129244736!1134;10398$GO:0006936!muscle contraction!0.0207947129244736!1134;10398$GO:0048731!system development!0.0207947129244736!23770;1311;7076;1134$GO:0005784!translocon complex!0.0207947129244736!6748$GO:0005796!Golgi lumen!0.0207947129244736!51150$GO:0033559!unsaturated fatty acid metabolic process!0.0207947129244736!9415$GO:0006636!unsaturated fatty acid biosynthetic process!0.0207947129244736!9415$GO:0044444!cytoplasmic part!0.0218859500403191!6141;23770;9415;51150;6748;10398$GO:0043249!erythrocyte maturation!0.0218859500403191!7076$GO:0045861!negative regulation of proteolysis!0.0218859500403191!7076$GO:0031594!neuromuscular junction!0.0249463112312134!1134$GO:0048821!erythrocyte development!0.0277140445166692!7076$GO:0005783!endoplasmic reticulum!0.0310440415863154!23770;9415;6748$GO:0048856!anatomical structure development!0.0311691245971762!23770;1311;7076;1134$GO:0007274!neuromuscular synaptic transmission!0.0311691245971762!1134$GO:0007528!neuromuscular junction development!0.0332421739419477!1134$GO:0030867!rough endoplasmic reticulum membrane!0.0348352846073642!6748$GO:0012505!endomembrane system!0.0348352846073642!23770;9415;6748$GO:0016717!oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water!0.0348352846073642!9415$GO:0033619!membrane protein proteolysis!0.0348352846073642!7076$GO:0005892!nicotinic acetylcholine-gated receptor-channel complex!0.0348352846073642!1134$GO:0006509!membrane protein ectodomain proteolysis!0.0348352846073642!7076$GO:0007224!smoothened signaling pathway!0.0354739566774395!23770$GO:0032501!multicellular organismal process!0.0354739566774395!23770;1311;7076;1134;10398$GO:0007275!multicellular organismal development!0.0354739566774395!23770;1311;7076;1134$GO:0001708!cell fate specification!0.0355904200985641!23770$GO:0030162!regulation of proteolysis!0.0371404727022243!7076$GO:0008191!metalloendopeptidase inhibitor activity!0.0371404727022243!7076$GO:0005791!rough endoplasmic reticulum!0.0371404727022243!6748$GO:0048468!cell development!0.0425221972773797!23770;7076;1134$GO:0015464!acetylcholine receptor activity!0.0435597955985175!1134$GO:0042166!acetylcholine binding!0.0445144965050405!1134$GO:0004889!nicotinic acetylcholine-activated cation-selective channel activity!0.0454231554612994!1134$GO:0005578!proteinaceous extracellular matrix!0.0467722061889542!1311;7076$GO:0005859!muscle myosin complex!0.047114905005606!10398$GO:0016460!myosin II complex!0.0479035766969372!10398
|id=C315
|id=C315
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C315_Osteoblast_Preadipocyte_mesenchymal_Smooth_Cardiac_leiomyoma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr11:1774382..1774391,-p@chr11:1774382..1774391
-
Hg19::chr11:61605283..61605303,+p@chr11:61605283..61605303
+
Hg19::chr11:61624925..61624946,+p10@FADS2
Hg19::chr11:61632639..61632653,+p@chr11:61632639..61632653
+
Hg19::chr15:74219788..74219809,+p@chr15:74219788..74219809
+
Hg19::chr15:74244185..74244207,+p@chr15:74244185..74244207
+
Hg19::chr16:55523576..55523615,+p@chr16:55523576..55523615
+
Hg19::chr16:57778334..57778362,+p@chr16:57778334..57778362
+
Hg19::chr17:19288479..19288518,-p@chr17:19288479..19288518
-
Hg19::chr17:41168059..41168088,-p@chr17:41168059..41168088
-
Hg19::chr17:74681202..74681205,-p@chr17:74681202..74681205
-
Hg19::chr17:76853662..76853675,-p@chr17:76853662..76853675
-
Hg19::chr18:47984183..47984184,+p1@ENST00000498296
Hg19::chr19:1105655..1105703,+p@chr19:1105655..1105703
+
Hg19::chr19:1105737..1105752,+p@chr19:1105737..1105752
+
Hg19::chr19:18652724..18652739,-p10@FKBP8
Hg19::chr19:18897406..18897417,-p6@COMP
Hg19::chr19:49119363..49119395,-p3@RPL18
Hg19::chr1:1153003..1153016,-p@chr1:1153003..1153016
-
Hg19::chr1:1164204..1164250,-p6@SDF4
Hg19::chr1:1290694..1290708,-p3@MXRA8
Hg19::chr1:150776569..150776581,-p@chr1:150776569..150776581
-
Hg19::chr1:17303641..17303660,-p@chr1:17303641..17303660
-
Hg19::chr1:19981535..19981580,+p4@NBL1
Hg19::chr1:19983866..19983874,+p@chr1:19983866..19983874
+
Hg19::chr20:35173298..35173317,+p5@MYL9
Hg19::chr20:35177518..35177532,+p@chr20:35177518..35177532
+
Hg19::chr22:31501233..31501245,-p@chr22:31501233..31501245
-
Hg19::chr2:175629374..175629385,-p5@CHRNA1
Hg19::chr2:219269059..219269083,+p@chr2:219269059..219269083
+
Hg19::chr3:52563245..52563281,-p5@NT5DC2
Hg19::chr3:8590309..8590333,+p@chr3:8590309..8590333
+
Hg19::chrX:153061882..153061933,+p4@SSR4
Hg19::chrX:47442814..47442835,+p6@TIMP1
Hg19::chrX:47444613..47444688,+p2@TIMP1
Hg19::chrX:47444935..47445039,+p@chrX:47444935..47445039
+
Hg19::chrX:47444981..47444990,-p@chrX:47444981..47444990
-
Hg19::chrX:47445910..47445992,+p@chrX:47445910..47445992
+


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:0005509calcium ion binding0.0138219499543876
GO:0051043regulation of membrane protein ectodomain proteolysis0.01680365693209
GO:0051045negative regulation of membrane protein ectodomain proteolysis0.01680365693209
GO:0048513organ development0.01680365693209
GO:0005789endoplasmic reticulum membrane0.01680365693209
GO:0042175nuclear envelope-endoplasmic reticulum network0.01680365693209
GO:0044432endoplasmic reticulum part0.0197111800970318
GO:0044446intracellular organelle part0.0207947129244736
GO:0044422organelle part0.0207947129244736
GO:0003012muscle system process0.0207947129244736
GO:0006936muscle contraction0.0207947129244736
GO:0048731system development0.0207947129244736
GO:0005784translocon complex0.0207947129244736
GO:0005796Golgi lumen0.0207947129244736
GO:0033559unsaturated fatty acid metabolic process0.0207947129244736
GO:0006636unsaturated fatty acid biosynthetic process0.0207947129244736
GO:0044444cytoplasmic part0.0218859500403191
GO:0043249erythrocyte maturation0.0218859500403191
GO:0045861negative regulation of proteolysis0.0218859500403191
GO:0031594neuromuscular junction0.0249463112312134
GO:0048821erythrocyte development0.0277140445166692
GO:0005783endoplasmic reticulum0.0310440415863154
GO:0048856anatomical structure development0.0311691245971762
GO:0007274neuromuscular synaptic transmission0.0311691245971762
GO:0007528neuromuscular junction development0.0332421739419477
GO:0030867rough endoplasmic reticulum membrane0.0348352846073642
GO:0012505endomembrane system0.0348352846073642
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 water0.0348352846073642
GO:0033619membrane protein proteolysis0.0348352846073642
GO:0005892nicotinic acetylcholine-gated receptor-channel complex0.0348352846073642
GO:0006509membrane protein ectodomain proteolysis0.0348352846073642
GO:0007224smoothened signaling pathway0.0354739566774395
GO:0032501multicellular organismal process0.0354739566774395
GO:0007275multicellular organismal development0.0354739566774395
GO:0001708cell fate specification0.0355904200985641
GO:0030162regulation of proteolysis0.0371404727022243
GO:0008191metalloendopeptidase inhibitor activity0.0371404727022243
GO:0005791rough endoplasmic reticulum0.0371404727022243
GO:0048468cell development0.0425221972773797
GO:0015464acetylcholine receptor activity0.0435597955985175
GO:0042166acetylcholine binding0.0445144965050405
GO:0004889nicotinic acetylcholine-activated cation-selective channel activity0.0454231554612994
GO:0005578proteinaceous extracellular matrix0.0467722061889542
GO:0005859muscle myosin complex0.047114905005606
GO:0016460myosin II complex0.0479035766969372



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:C315&oldid=1702962"