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Coexpression cluster:C3418: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0004016!adenylate cyclase activity!0.00524549629106322!196883$GO:0006171!cAMP biosynthetic process!0.00524549629106322!196883$GO:0046058!cAMP metabolic process!0.00524549629106322!196883$GO:0016849!phosphorus-oxygen lyase activity!0.00524549629106322!196883$GO:0009975!cyclase activity!0.00524549629106322!196883$GO:0009190!cyclic nucleotide biosynthetic process!0.00529848110208407!196883$GO:0009187!cyclic nucleotide metabolic process!0.00567694403794722!196883$GO:0009165!nucleotide biosynthetic process!0.0245496291063228!196883$GO:0016829!lyase activity!0.0245496291063228!196883$GO:0009117!nucleotide metabolic process!0.0265164895154298!196883$GO:0055086!nucleobase, nucleoside and nucleotide metabolic process!0.0265164895154298!196883$GO:0000287!magnesium ion binding!0.0296052631578947!196883
|gostat_on_coexpression_clusters=GO:0004016!adenylate cyclase activity!0.00524549629106322!196883$GO:0006171!cAMP biosynthetic process!0.00524549629106322!196883$GO:0046058!cAMP metabolic process!0.00524549629106322!196883$GO:0016849!phosphorus-oxygen lyase activity!0.00524549629106322!196883$GO:0009975!cyclase activity!0.00524549629106322!196883$GO:0009190!cyclic nucleotide biosynthetic process!0.00529848110208407!196883$GO:0009187!cyclic nucleotide metabolic process!0.00567694403794722!196883$GO:0009165!nucleotide biosynthetic process!0.0245496291063228!196883$GO:0016829!lyase activity!0.0245496291063228!196883$GO:0009117!nucleotide metabolic process!0.0265164895154298!196883$GO:0055086!nucleobase, nucleoside and nucleotide metabolic process!0.0265164895154298!196883$GO:0000287!magnesium ion binding!0.0296052631578947!196883
|id=C3418
|id=C3418
|ontology_enrichment_celltype=CL:0002139!2.27e-16!24;CL:0000115!7.82e-15!35;CL:0000071!2.13e-12!18;CL:0002546!2.13e-12!18;CL:0002078!2.48e-11!44;CL:1000413!2.82e-07!9
|ontology_enrichment_celltype=CL:0002139!1.49e-19!24;CL:0000115!4.78e-18!36;CL:0002078!1.43e-14!45;CL:0000071!2.19e-14!18;CL:0002546!2.19e-14!18;CL:0000213!6.84e-08!58;CL:0000215!6.84e-08!58;CL:1000413!8.32e-08!9;CL:0005020!9.34e-07!6;CL:0002138!9.34e-07!6;CL:0005022!9.34e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.65e-35!115;UBERON:0004111!2.21e-20!241;UBERON:0000477!1.46e-17!286;UBERON:0000025!1.11e-16!194;UBERON:0001049!7.00e-15!57;UBERON:0005068!7.00e-15!57;UBERON:0006241!7.00e-15!57;UBERON:0007135!7.00e-15!57;UBERON:0000483!1.60e-14!309;UBERON:0000119!3.33e-14!312;UBERON:0002616!6.83e-14!59;UBERON:0000468!1.77e-13!659;UBERON:0003080!6.18e-13!42;UBERON:0001986!2.13e-12!18;UBERON:0004638!2.13e-12!18;UBERON:0004852!2.13e-12!18;UBERON:0002780!2.17e-12!41;UBERON:0001890!2.17e-12!41;UBERON:0006240!2.17e-12!41;UBERON:0005743!9.50e-12!86;UBERON:0000467!1.08e-11!625;UBERON:0003075!1.59e-11!86;UBERON:0007284!1.59e-11!86;UBERON:0001017!1.67e-11!82;UBERON:0000480!1.76e-11!626;UBERON:0002346!1.79e-11!90;UBERON:0000475!2.26e-11!365;UBERON:0000955!4.90e-11!69;UBERON:0006238!4.90e-11!69;UBERON:0002020!6.17e-11!34;UBERON:0003528!6.17e-11!34;UBERON:0001893!8.99e-11!34;UBERON:0000073!1.00e-10!94;UBERON:0001016!1.00e-10!94;UBERON:0002791!1.85e-10!33;UBERON:0001869!3.74e-10!32;UBERON:0000055!7.94e-10!69;UBERON:0000153!1.73e-09!129;UBERON:0007811!1.73e-09!129;UBERON:0000033!3.94e-09!123;UBERON:0000487!4.15e-09!22;UBERON:0006914!4.38e-09!25;UBERON:0002049!5.29e-09!79;UBERON:0007798!5.29e-09!79;UBERON:0000924!5.47e-09!173;UBERON:0006601!5.47e-09!173;UBERON:0004121!6.80e-09!169;UBERON:0002619!7.42e-09!22;UBERON:0000481!1.02e-08!347;UBERON:0004872!2.44e-08!84;UBERON:0003056!2.79e-08!61;UBERON:0001950!3.21e-08!20;UBERON:0001981!5.45e-08!60;UBERON:0007500!5.45e-08!60;UBERON:0004537!5.45e-08!60;UBERON:0006965!5.45e-08!60;UBERON:0000956!1.13e-07!25;UBERON:0000203!1.13e-07!25;UBERON:0000064!1.55e-07!219;UBERON:0003914!2.27e-07!118;UBERON:0003103!2.79e-07!69;UBERON:0003915!2.82e-07!9;UBERON:0004700!2.82e-07!9;UBERON:0001917!2.82e-07!9;UBERON:0000922!2.98e-07!612;UBERON:0001009!3.68e-07!113
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35
}}
}}

Revision as of 15:05, 19 October 2012


Full id: C3418_Endothelial_Renal_heart_lung_Chondrocyte_spleen_penis



Phase1 CAGE Peaks

Hg19::chr14:24804269..24804292,-p1@ADCY4
Hg19::chr14:24804295..24804306,-p2@ADCY4
Hg19::chr19:8408139..8408153,-p1@KANK3


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:0004016adenylate cyclase activity0.00524549629106322
GO:0006171cAMP biosynthetic process0.00524549629106322
GO:0046058cAMP metabolic process0.00524549629106322
GO:0016849phosphorus-oxygen lyase activity0.00524549629106322
GO:0009975cyclase activity0.00524549629106322
GO:0009190cyclic nucleotide biosynthetic process0.00529848110208407
GO:0009187cyclic nucleotide metabolic process0.00567694403794722
GO:0009165nucleotide biosynthetic process0.0245496291063228
GO:0016829lyase activity0.0245496291063228
GO:0009117nucleotide metabolic process0.0265164895154298
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.0265164895154298
GO:0000287magnesium ion binding0.0296052631578947



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>

Uber Anatomy
Ontology termp-valuen
adult organism7.62e-45114
anatomical conduit2.84e-24240
anatomical cluster1.27e-22373
neural tube1.04e-2056
neural rod1.04e-2056
future spinal cord1.04e-2056
neural keel1.04e-2056
regional part of nervous system3.13e-1953
regional part of brain3.13e-1953
tube4.17e-19192
regional part of forebrain4.97e-1741
forebrain4.97e-1741
anterior neural tube4.97e-1741
future forebrain4.97e-1741
neural plate1.04e-1682
presumptive neural plate1.04e-1682
brain2.48e-1668
future brain2.48e-1668
neurectoderm4.60e-1686
brain grey matter8.98e-1634
gray matter8.98e-1634
cell layer1.28e-15309
epithelium1.45e-15306
structure with developmental contribution from neural crest1.49e-15132
telencephalon1.59e-1534
central nervous system2.65e-1581
regional part of telencephalon1.01e-1432
cerebral hemisphere1.35e-1432
blood vessel endothelium2.19e-1418
endothelium2.19e-1418
cardiovascular system endothelium2.19e-1418
multi-cellular organism2.37e-13656
nervous system4.33e-1389
multi-tissue structure5.34e-13342
ecto-epithelium1.28e-12104
regional part of cerebral cortex2.24e-1222
pre-chordal neural plate8.47e-1261
anatomical system1.31e-11624
anatomical group1.79e-11625
neocortex2.42e-1120
cerebral cortex8.05e-1125
pallium8.05e-1125
squamous epithelium1.84e-1025
simple squamous epithelium2.46e-1022
organ part9.75e-10218
organ system subdivision1.81e-09223
vessel2.92e-0968
ectoderm-derived structure3.60e-09171
ectoderm3.60e-09171
presumptive ectoderm3.60e-09171
vasculature1.70e-0878
vascular system1.70e-0878
splanchnic layer of lateral plate mesoderm4.25e-0883
endothelial tube8.32e-089
arterial system endothelium8.32e-089
endothelium of artery8.32e-089
embryo3.07e-07592
circulatory system3.78e-07112
epithelial tube open at both ends3.93e-0759
blood vessel3.93e-0759
blood vasculature3.93e-0759
vascular cord3.93e-0759
embryonic structure4.44e-07564
developing anatomical structure9.30e-07581


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.

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