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Coexpression cluster:C365: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0005201!extracellular matrix structural constituent!0.000213322837143487!4146;1297;10143$GO:0044421!extracellular region part!0.00111610238361664!4146;1297;10143;92304$GO:0005578!proteinaceous extracellular matrix!0.00282570299014515!4146;1297;10143$GO:0048856!anatomical structure development!0.0121855798442595!4146;1297;10143;92304$GO:0005594!collagen type IX!0.0164400489879395!1297$GO:0001501!skeletal development!0.017181818860989!4146;10143$GO:0048513!organ development!0.0205446175102198!4146;1297;10143$GO:0005593!FACIT collagen!0.0205446175102198!1297$GO:0030934!anchoring collagen!0.0273855671839068!1297$GO:0001502!cartilage condensation!0.0291932207385848!4146$GO:0032502!developmental process!0.0291932207385848!4146;1297;10143;92304$GO:0000146!microfilament motor activity!0.0291932207385848!8735$GO:0048731!system development!0.0291932207385848!4146;1297;10143$GO:0032982!myosin filament!0.0291932207385848!8735$GO:0005863!striated muscle thick filament!0.0291932207385848!8735$GO:0032501!multicellular organismal process!0.0351270622408377!4146;1297;10143;8735$GO:0005859!muscle myosin complex!0.0374187747719306!8735$GO:0016460!myosin II complex!0.0374187747719306!8735$GO:0050381!unspecific monooxygenase activity!0.0374187747719306!1572$GO:0030424!axon!0.0459438181410297!5816$GO:0051216!cartilage development!0.0459438181410297!4146$GO:0006941!striated muscle contraction!0.0459438181410297!8735
|gostat_on_coexpression_clusters=GO:0005201!extracellular matrix structural constituent!0.000213322837143487!4146;1297;10143$GO:0044421!extracellular region part!0.00111610238361664!4146;1297;10143;92304$GO:0005578!proteinaceous extracellular matrix!0.00282570299014515!4146;1297;10143$GO:0048856!anatomical structure development!0.0121855798442595!4146;1297;10143;92304$GO:0005594!collagen type IX!0.0164400489879395!1297$GO:0001501!skeletal development!0.017181818860989!4146;10143$GO:0048513!organ development!0.0205446175102198!4146;1297;10143$GO:0005593!FACIT collagen!0.0205446175102198!1297$GO:0030934!anchoring collagen!0.0273855671839068!1297$GO:0001502!cartilage condensation!0.0291932207385848!4146$GO:0032502!developmental process!0.0291932207385848!4146;1297;10143;92304$GO:0000146!microfilament motor activity!0.0291932207385848!8735$GO:0048731!system development!0.0291932207385848!4146;1297;10143$GO:0032982!myosin filament!0.0291932207385848!8735$GO:0005863!striated muscle thick filament!0.0291932207385848!8735$GO:0032501!multicellular organismal process!0.0351270622408377!4146;1297;10143;8735$GO:0005859!muscle myosin complex!0.0374187747719306!8735$GO:0016460!myosin II complex!0.0374187747719306!8735$GO:0050381!unspecific monooxygenase activity!0.0374187747719306!1572$GO:0030424!axon!0.0459438181410297!5816$GO:0051216!cartilage development!0.0459438181410297!4146$GO:0006941!striated muscle contraction!0.0459438181410297!8735
|id=C365
|id=C365
|ontology_enrichment_celltype=CL:0002057!6.71e-09!42;CL:0000860!1.26e-08!45
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.65e-26!115;UBERON:0001049!1.16e-08!57;UBERON:0005068!1.16e-08!57;UBERON:0006241!1.16e-08!57;UBERON:0007135!1.16e-08!57;UBERON:0001017!5.34e-08!82;UBERON:0005743!1.28e-07!86;UBERON:0002616!4.84e-07!59;UBERON:0000073!6.88e-07!94;UBERON:0001016!6.88e-07!94
}}
}}

Revision as of 14:39, 21 May 2012


Full id: C365_trachea_throat_aorta_lung_parotid_salivary_umbilical



Phase1 CAGE Peaks

Hg19::chr10:13276329..13276338,-p3@UCMA
Hg19::chr10:13276352..13276361,-p2@UCMA
Hg19::chr10:13276368..13276379,-p1@UCMA
Hg19::chr11:34909983..34910006,-p@chr11:34909983..34910006
-
Hg19::chr12:10998450..10998451,+p@chr12:10998450..10998451
+
Hg19::chr12:119772810..119772834,+p4@CCDC60
Hg19::chr12:48390329..48390340,+p@chr12:48390329..48390340
+
Hg19::chr16:78056435..78056451,+p1@CLEC3A
Hg19::chr17:10276319..10276324,-p1@MYH13
Hg19::chr19:41620335..41620338,+p1@CYP2F1
Hg19::chr1:31196427..31196433,-p1@MATN1
Hg19::chr22:37215541..37215544,-p3@PVALB
Hg19::chr2:180524914..180524925,-p17@ZNF385B
Hg19::chr5:147261651..147261660,+p@chr5:147261651..147261660
+
Hg19::chr5:147526410..147526417,+p@chr5:147526410..147526417
+
Hg19::chr5:180017106..180017107,+p@chr5:180017106..180017107
+
Hg19::chr5:180017127..180017161,-p@chr5:180017127..180017161
-
Hg19::chr5:180017171..180017202,+p@chr5:180017171..180017202
+
Hg19::chr5:180017205..180017215,-p@chr5:180017205..180017215
-
Hg19::chr5:180017253..180017257,-p@chr5:180017253..180017257
-
Hg19::chr5:180017672..180017683,-p11@SCGB3A1
Hg19::chr5:180017691..180017700,-p8@SCGB3A1
Hg19::chr5:180017732..180017767,-p3@SCGB3A1
Hg19::chr5:180017818..180017830,-p7@SCGB3A1
Hg19::chr5:180018490..180018505,-p1@SCGB3A1
Hg19::chr5:180018695..180018706,-p9@SCGB3A1
Hg19::chr6:70937124..70937126,-p@chr6:70937124..70937126
-
Hg19::chr6:71012780..71012794,-p2@COL9A1
Hg19::chr7:75368627..75368651,+p@chr7:75368627..75368651
+
Hg19::chr9:38720126..38720131,-p@chr9:38720126..38720131
-


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:0005201extracellular matrix structural constituent0.000213322837143487
GO:0044421extracellular region part0.00111610238361664
GO:0005578proteinaceous extracellular matrix0.00282570299014515
GO:0048856anatomical structure development0.0121855798442595
GO:0005594collagen type IX0.0164400489879395
GO:0001501skeletal development0.017181818860989
GO:0048513organ development0.0205446175102198
GO:0005593FACIT collagen0.0205446175102198
GO:0030934anchoring collagen0.0273855671839068
GO:0001502cartilage condensation0.0291932207385848
GO:0032502developmental process0.0291932207385848
GO:0000146microfilament motor activity0.0291932207385848
GO:0048731system development0.0291932207385848
GO:0032982myosin filament0.0291932207385848
GO:0005863striated muscle thick filament0.0291932207385848
GO:0032501multicellular organismal process0.0351270622408377
GO:0005859muscle myosin complex0.0374187747719306
GO:0016460myosin II complex0.0374187747719306
GO:0050381unspecific monooxygenase activity0.0374187747719306
GO:0030424axon0.0459438181410297
GO:0051216cartilage development0.0459438181410297
GO:0006941striated muscle contraction0.0459438181410297



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><br>


Cell Type
Ontology termp-valuen
CD14-positive, CD16-negative classical monocyte6.71e-0942
classical monocyte1.26e-0845
Uber Anatomy
Ontology termp-valuen
adult organism2.65e-26115
neural tube1.16e-0857
neural rod1.16e-0857
future spinal cord1.16e-0857
neural keel1.16e-0857
central nervous system5.34e-0882
regional part of brain4.84e-0759
regional part of nervous system6.88e-0794
nervous system6.88e-0794


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.