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Coexpression cluster:C558: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0008298!intracellular mRNA localization!0.0135990345038516!22794$GO:0000045!autophagic vacuole formation!0.0203943486750239!23192$GO:0016236!macroautophagy!0.0203943486750239!23192$GO:0006914!autophagy!0.0401466589318227!23192$GO:0033036!macromolecule localization!0.0401466589318227!22794;23192$GO:0006612!protein targeting to membrane!0.0407562844025515!23192
|gostat_on_coexpression_clusters=GO:0008298!intracellular mRNA localization!0.0135990345038516!22794$GO:0000045!autophagic vacuole formation!0.0203943486750239!23192$GO:0016236!macroautophagy!0.0203943486750239!23192$GO:0006914!autophagy!0.0401466589318227!23192$GO:0033036!macromolecule localization!0.0401466589318227!22794;23192$GO:0006612!protein targeting to membrane!0.0407562844025515!23192
|id=C558
|id=C558
|ontology_enrichment_celltype=CL:0000192!2.28e-10!42;CL:0000514!2.28e-10!42;CL:0000183!3.06e-10!59;CL:0000393!2.17e-09!60;CL:0000211!2.17e-09!60;CL:0000187!4.92e-09!54;CL:0000222!8.75e-09!119;CL:0000680!2.27e-08!57;CL:0000056!2.27e-08!57;CL:0000355!2.27e-08!57;CL:0000359!3.93e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!1.89e-11!312;UBERON:0000483!3.21e-11!309;UBERON:0002049!1.45e-10!79;UBERON:0007798!1.45e-10!79;UBERON:0004535!3.41e-10!110;UBERON:0001009!6.03e-10!113;UBERON:0000055!1.09e-08!69;UBERON:0000477!1.33e-08!286;UBERON:0004111!3.24e-08!241;UBERON:0000475!3.65e-08!365;UBERON:0002385!7.61e-08!63;UBERON:0001015!7.61e-08!63;UBERON:0000383!7.61e-08!63;UBERON:0004872!8.55e-08!84;UBERON:0001637!1.08e-07!42;UBERON:0003509!1.08e-07!42;UBERON:0004572!1.08e-07!42;UBERON:0001134!1.10e-07!61;UBERON:0002036!1.10e-07!61;UBERON:0003082!1.10e-07!61;UBERON:0000025!1.11e-07!194;UBERON:0000490!1.25e-07!138;UBERON:0001981!1.94e-07!60;UBERON:0007500!1.94e-07!60;UBERON:0004537!1.94e-07!60;UBERON:0006965!1.94e-07!60;UBERON:0003064!2.87e-07!37;UBERON:0005256!3.21e-07!143;UBERON:0004573!3.24e-07!33;UBERON:0004571!3.24e-07!33;UBERON:0004290!4.04e-07!70;UBERON:0000486!8.92e-07!82;UBERON:0000481!9.97e-07!347
}}
}}

Revision as of 14:54, 21 May 2012


Full id: C558_Mesenchymal_testis_Smooth_Endothelial_Placental_Tracheal_Hair



Phase1 CAGE Peaks

Hg19::chr11:120317216..120317220,+p@chr11:120317216..120317220
+
Hg19::chr11:500479..500483,-p@chr11:500479..500483
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Hg19::chr16:15128409..15128413,+p@chr16:15128409..15128413
+
Hg19::chr16:87400976..87400979,-p@chr16:87400976..87400979
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Hg19::chr17:38324198..38324204,+p7@CASC3
Hg19::chr17:79873312..79873316,-p@chr17:79873312..79873316
-
Hg19::chr18:77096710..77096715,+p@chr18:77096710..77096715
+
Hg19::chr19:2353015..2353053,+p@chr19:2353015..2353053
+
Hg19::chr1:156893889..156893893,+p@chr1:156893889..156893893
+
Hg19::chr20:44582326..44582328,-p@chr20:44582326..44582328
-
Hg19::chr22:19376002..19376007,-p@chr22:19376002..19376007
-
Hg19::chr22:24431967..24431972,+p@chr22:24431967..24431972
+
Hg19::chr2:242607635..242607639,+p7@ATG4B
Hg19::chr3:49070544..49070558,-p8@QRICH1
Hg19::chr3:52381988..52381993,+p@chr3:52381988..52381993
+
Hg19::chr9:131864675..131864680,-p@chr9:131864675..131864680
-


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:0008298intracellular mRNA localization0.0135990345038516
GO:0000045autophagic vacuole formation0.0203943486750239
GO:0016236macroautophagy0.0203943486750239
GO:0006914autophagy0.0401466589318227
GO:0033036macromolecule localization0.0401466589318227
GO:0006612protein targeting to membrane0.0407562844025515



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
cell layer1.89e-11312
epithelium3.21e-11309
vasculature1.45e-1079
vascular system1.45e-1079
cardiovascular system3.41e-10110
circulatory system6.03e-10113
vessel1.09e-0869
anatomical cluster1.33e-08286
anatomical conduit3.24e-08241
organism subdivision3.65e-08365
muscle tissue7.61e-0863
musculature7.61e-0863
musculature of body7.61e-0863
splanchnic layer of lateral plate mesoderm8.55e-0884
artery1.08e-0742
arterial blood vessel1.08e-0742
arterial system1.08e-0742
skeletal muscle tissue1.10e-0761
striated muscle tissue1.10e-0761
myotome1.10e-0761
tube1.11e-07194
unilaminar epithelium1.25e-07138
blood vessel1.94e-0760
epithelial tube open at both ends1.94e-0760
blood vasculature1.94e-0760
vascular cord1.94e-0760
intermediate mesoderm2.87e-0737
trunk mesenchyme3.21e-07143
systemic artery3.24e-0733
systemic arterial system3.24e-0733
dermomyotome4.04e-0770
multilaminar epithelium8.92e-0782
multi-tissue structure9.97e-07347


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.