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Coexpression cluster:C750

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Full id: C750_Smooth_Mesenchymal_Fibroblast_Hepatic_Chondrocyte_Lens_tenocyte



Phase1 CAGE Peaks

Hg19::chr12:6937564..6937585,+p1@LEPREL2
Hg19::chr17:39968182..39968244,-p1@LEPREL4
Hg19::chr17:39968926..39968976,+p2@FKBP10
Hg19::chr17:39969232..39969265,+p1@FKBP10
Hg19::chr19:50031252..50031285,+p1@RCN3
Hg19::chr19:50031567..50031632,+p2@RCN3
Hg19::chr1:11994715..11994833,+p1@PLOD1
Hg19::chr1:12014885..12014920,+p@chr1:12014885..12014920
+
Hg19::chr1:43232649..43232715,-p1@LEPRE1
Hg19::chr7:150929550..150929619,+p1@CHPF2
Hg19::chrX:51636712..51636759,+p1@MAGED1


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:0031418L-ascorbic acid binding6.16739262198812e-07
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors2.05166582405436e-06
GO:0019797procollagen-proline 3-dioxygenase activity2.05166582405436e-06
GO:0031544peptidyl-proline 3-dioxygenase activity2.05166582405436e-06
GO:0005783endoplasmic reticulum2.05166582405436e-06
GO:0051213dioxygenase activity4.09714468760063e-06
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen4.09714468760063e-06
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen4.09714468760063e-06
GO:0019798procollagen-proline dioxygenase activity5.67381898068508e-06
GO:0031543peptidyl-proline dioxygenase activity7.14845068613665e-06
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen3.27411397309372e-05
GO:0019842vitamin binding7.96121713291799e-05
GO:0005788endoplasmic reticulum lumen0.00052552777865081
GO:0005506iron ion binding0.000584123997613624
GO:0044432endoplasmic reticulum part0.000601781767003522
GO:0005737cytoplasm0.000932935717654791
GO:0046946hydroxylysine metabolic process0.00128537226735743
GO:0046947hydroxylysine biosynthetic process0.00128537226735743
GO:0044444cytoplasmic part0.00165350468860902
GO:0008475procollagen-lysine 5-dioxygenase activity0.00346999433782819
GO:0008285negative regulation of cell proliferation0.00401542118850137
GO:0043169cation binding0.00767490924381294
GO:0046872metal ion binding0.00938806226834687
GO:0016491oxidoreductase activity0.00938806226834687
GO:0043167ion binding0.00938806226834687
GO:0030867rough endoplasmic reticulum membrane0.00978140308676731
GO:0050680negative regulation of epithelial cell proliferation0.0102746571907546
GO:0042127regulation of cell proliferation0.0128654976873371
GO:0009067aspartate family amino acid biosynthetic process0.0130046817132735
GO:0005791rough endoplasmic reticulum0.0130046817132735
GO:0044424intracellular part0.0130046817132735
GO:0009066aspartate family amino acid metabolic process0.0202044284172302
GO:0050678regulation of epithelial cell proliferation0.0208221240785165
GO:0043231intracellular membrane-bound organelle0.0208221240785165
GO:0043227membrane-bound organelle0.0208221240785165
GO:0050673epithelial cell proliferation0.0211587578541618
GO:0008283cell proliferation0.0240554820540468
GO:0005622intracellular0.0245856893432835
GO:0001666response to hypoxia0.028377623610498
GO:0019538protein metabolic process0.0322888692633528
GO:0031974membrane-enclosed lumen0.0353706228375008
GO:0043233organelle lumen0.0353706228375008
GO:0043229intracellular organelle0.0420348181285098
GO:0043226organelle0.0420348181285098
GO:0008652amino acid biosynthetic process0.0429255537871426
GO:0048523negative regulation of cellular process0.0433668328287759
GO:0003755peptidyl-prolyl cis-trans isomerase activity0.0433668328287759
GO:0016859cis-trans isomerase activity0.0433668328287759
GO:0048519negative regulation of biological process0.0433668328287759
GO:0043170macromolecule metabolic process0.0433668328287759



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.