Personal tools

Coexpression cluster:C296: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed |id=C296 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed
|full_id=C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed
|gostat_on_coexpression_clusters=GO:0009101!glycoprotein biosynthetic process!0.0153040198506013!25825;6480$GO:0009100!glycoprotein metabolic process!0.0153040198506013!25825;6480$GO:0042985!negative regulation of amyloid precursor protein biosynthetic process!0.0153040198506013!25825$GO:0042983!amyloid precursor protein biosynthetic process!0.0153040198506013!25825$GO:0003835!beta-galactoside alpha-2,6-sialyltransferase activity!0.0153040198506013!6480$GO:0042984!regulation of amyloid precursor protein biosynthetic process!0.0153040198506013!25825$GO:0009049!aspartic-type signal peptidase activity!0.0163961987631881!25825$GO:0016486!peptide hormone processing!0.0187766779372494!25825$GO:0032488!Cdc42 protein signal transduction!0.0187766779372494!89846$GO:0043088!regulation of Cdc42 GTPase activity!0.0187766779372494!89846$GO:0032489!regulation of Cdc42 protein signal transduction!0.0187766779372494!89846$GO:0032319!regulation of Rho GTPase activity!0.0198846865302194!89846$GO:0033619!membrane protein proteolysis!0.0198846865302194!25825$GO:0009003!signal peptidase activity!0.0198846865302194!25825$GO:0006509!membrane protein ectodomain proteolysis!0.0198846865302194!25825$GO:0042982!amyloid precursor protein metabolic process!0.0200747034966908!25825$GO:0050435!beta-amyloid metabolic process!0.0229384663849809!25825$GO:0009311!oligosaccharide metabolic process!0.0275148176906598!6480$GO:0046847!filopodium formation!0.0275148176906598!89846$GO:0030035!microspike biogenesis!0.0275148176906598!89846$GO:0004194!pepsin A activity!0.0283849614143019!25825$GO:0005794!Golgi apparatus!0.0284450184777538!89846;6480$GO:0004175!endopeptidase activity!0.0339601840165598!25825;11098$GO:0008373!sialyltransferase activity!0.0339601840165598!6480$GO:0030027!lamellipodium!0.0339601840165598!89846$GO:0022603!regulation of anatomical structure morphogenesis!0.0339601840165598!89846$GO:0022604!regulation of cell morphogenesis!0.0339601840165598!89846$GO:0008360!regulation of cell shape!0.0339601840165598!89846$GO:0001726!ruffle!0.0339601840165598!89846$GO:0030031!cell projection biogenesis!0.0381565712327612!89846$GO:0009306!protein secretion!0.0420779689934136!25825$GO:0030173!integral to Golgi membrane!0.0436133239286936!6480$GO:0031228!intrinsic to Golgi membrane!0.0484185353590127!6480$GO:0031252!leading edge!0.0484185353590127!89846$GO:0006959!humoral immune response!0.0489862934759819!6480
|id=C296
|id=C296
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C296_gall_small_mesothelioma_acute_bronchioalveolar_epidermoid_mixed



Phase1 CAGE Peaks

Hg19::chr10:103952998..103953003,-p@chr10:103952998..103953003
-
Hg19::chr10:124050589..124050596,+p15@BTBD16
Hg19::chr10:73818867..73818877,-p@chr10:73818867..73818877
-
Hg19::chr11:63331619..63331629,-p7@AK025029
Hg19::chr11:86501675..86501685,+p29@PRSS23
Hg19::chr11:86501763..86501768,+p33@PRSS23
Hg19::chr14:68633950..68633964,-p@chr14:68633950..68633964
-
Hg19::chr14:94582961..94582978,+p@chr14:94582961..94582978
+
Hg19::chr17:5813133..5813142,-p@chr17:5813133..5813142
-
Hg19::chr1:27992626..27992630,-p@chr1:27992626..27992630
-
Hg19::chr1:27992654..27992665,-p@chr1:27992654..27992665
-
Hg19::chr1:27992698..27992702,-p@chr1:27992698..27992702
-
Hg19::chr1:27992756..27992763,-p@chr1:27992756..27992763
-
Hg19::chr1:27992774..27992780,-p@chr1:27992774..27992780
-
Hg19::chr1:79107935..79107976,+p@chr1:79107935..79107976
+
Hg19::chr1:94583454..94583465,-p@chr1:94583454..94583465
-
Hg19::chr20:4100484..4100497,+p1@BC027448
Hg19::chr20:4100520..4100530,+p2@BC027448
Hg19::chr20:4100562..4100570,+p4@BC027448
Hg19::chr20:4100596..4100603,+p5@BC027448
Hg19::chr21:42613665..42613680,+p10@BACE2
Hg19::chr22:31985409..31985436,+p@chr22:31985409..31985436
+
Hg19::chr22:31985448..31985465,+p@chr22:31985448..31985465
+
Hg19::chr22:50983547..50983560,-p@chr22:50983547..50983560
-
Hg19::chr2:121003683..121003689,-p@chr2:121003683..121003689
-
Hg19::chr2:42157172..42157179,-p@chr2:42157172..42157179
-
Hg19::chr2:42157397..42157411,-p@chr2:42157397..42157411
-
Hg19::chr3:186648149..186648166,+p12@ST6GAL1
Hg19::chr3:195516631..195516648,-p@chr3:195516631..195516648
-
Hg19::chr3:195516657..195516687,-p@chr3:195516657..195516687
-
Hg19::chr3:23688310..23688316,+p@chr3:23688310..23688316
+
Hg19::chr4:6698835..6698866,+p@chr4:6698835..6698866
+
Hg19::chr5:147644551..147644576,+p@chr5:147644551..147644576
+
Hg19::chr5:147645292..147645302,+p@chr5:147645292..147645302
+
Hg19::chr5:84867331..84867340,-p@chr5:84867331..84867340
-
Hg19::chr5:84943630..84943645,-p@chr5:84943630..84943645
-
Hg19::chr9:95736745..95736757,+p9@FGD3
Hg19::chr9:95736758..95736771,+p7@FGD3
Hg19::chr9:95736796..95736808,+p11@FGD3
Hg19::chr9:95736917..95736936,+p10@FGD3
Hg19::chr9:95737369..95737393,+p18@FGD3
Hg19::chr9:95737958..95737978,+p@chr9:95737958..95737978
+


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:0009101glycoprotein biosynthetic process0.0153040198506013
GO:0009100glycoprotein metabolic process0.0153040198506013
GO:0042985negative regulation of amyloid precursor protein biosynthetic process0.0153040198506013
GO:0042983amyloid precursor protein biosynthetic process0.0153040198506013
GO:0003835beta-galactoside alpha-2,6-sialyltransferase activity0.0153040198506013
GO:0042984regulation of amyloid precursor protein biosynthetic process0.0153040198506013
GO:0009049aspartic-type signal peptidase activity0.0163961987631881
GO:0016486peptide hormone processing0.0187766779372494
GO:0032488Cdc42 protein signal transduction0.0187766779372494
GO:0043088regulation of Cdc42 GTPase activity0.0187766779372494
GO:0032489regulation of Cdc42 protein signal transduction0.0187766779372494
GO:0032319regulation of Rho GTPase activity0.0198846865302194
GO:0033619membrane protein proteolysis0.0198846865302194
GO:0009003signal peptidase activity0.0198846865302194
GO:0006509membrane protein ectodomain proteolysis0.0198846865302194
GO:0042982amyloid precursor protein metabolic process0.0200747034966908
GO:0050435beta-amyloid metabolic process0.0229384663849809
GO:0009311oligosaccharide metabolic process0.0275148176906598
GO:0046847filopodium formation0.0275148176906598
GO:0030035microspike biogenesis0.0275148176906598
GO:0004194pepsin A activity0.0283849614143019
GO:0005794Golgi apparatus0.0284450184777538
GO:0004175endopeptidase activity0.0339601840165598
GO:0008373sialyltransferase activity0.0339601840165598
GO:0030027lamellipodium0.0339601840165598
GO:0022603regulation of anatomical structure morphogenesis0.0339601840165598
GO:0022604regulation of cell morphogenesis0.0339601840165598
GO:0008360regulation of cell shape0.0339601840165598
GO:0001726ruffle0.0339601840165598
GO:0030031cell projection biogenesis0.0381565712327612
GO:0009306protein secretion0.0420779689934136
GO:0030173integral to Golgi membrane0.0436133239286936
GO:0031228intrinsic to Golgi membrane0.0484185353590127
GO:0031252leading edge0.0484185353590127
GO:0006959humoral immune response0.0489862934759819



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

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C296&oldid=1702903"