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Coexpression cluster:C2830

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Full id: C2830_mature_Hepatocyte_mesenchymal_liver_pleomorphic_pancreas_chorionic



Phase1 CAGE Peaks

Hg19::chr5:78365455..78365489,+p3@BHMT2
Hg19::chr5:78365536..78365543,+p4@BHMT2
Hg19::chr5:78365545..78365572,+p2@BHMT2
Hg19::chr7:150038704..150038758,-p1@RARRES2


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:0047150betaine-homocysteine S-methyltransferase activity0.00185441379597977
GO:0008898homocysteine S-methyltransferase activity0.00185441379597977
GO:0008172S-methyltransferase activity0.00271948664090565
GO:0001523retinoid metabolic process0.00271948664090565
GO:0016101diterpenoid metabolic process0.00271948664090565
GO:0006721terpenoid metabolic process0.0028841766369992
GO:0006720isoprenoid metabolic process0.00794257461958667
GO:0019748secondary metabolic process0.00818429998071893
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0117988707879793
GO:0008168methyltransferase activity0.0311175964910053
GO:0016741transferase activity, transferring one-carbon groups0.0311175964910053



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
fat cell5.01e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.05e-29115
multi-tissue structure9.27e-18347
organism subdivision2.80e-17365
neurectoderm1.53e-1690
neural plate3.91e-1686
presumptive neural plate3.91e-1686
regional part of nervous system7.06e-1694
nervous system7.06e-1694
neural tube2.21e-1457
neural rod2.21e-1457
future spinal cord2.21e-1457
neural keel2.21e-1457
central nervous system2.36e-1482
regional part of brain8.65e-1459
multi-cellular organism1.75e-13659
anatomical cluster8.36e-13286
brain1.52e-1169
future brain1.52e-1169
pre-chordal neural plate1.93e-1161
cell layer2.66e-11312
epithelium2.94e-11309
ectoderm5.82e-11173
presumptive ectoderm5.82e-11173
ectoderm-derived structure1.58e-10169
anterior neural tube2.11e-1042
head7.00e-10123
anterior region of body7.32e-10129
craniocervical region7.32e-10129
regional part of forebrain7.56e-1041
forebrain7.56e-1041
future forebrain7.56e-1041
liver1.23e-0919
digestive gland1.23e-0919
liver bud1.23e-0919
organ2.65e-09511
anatomical conduit2.83e-09241
embryo3.60e-09612
organ part5.78e-09219
abdominal segment of trunk5.83e-0961
abdomen5.83e-0961
tube6.51e-09194
anatomical system2.10e-08625
anatomical group3.11e-08626
trunk mesenchyme3.87e-08143
embryonic structure1.05e-07605
developing anatomical structure1.05e-07605
gray matter1.21e-0734
brain grey matter1.21e-0734
primordium1.39e-07168
telencephalon1.61e-0734
germ layer1.84e-07604
embryonic tissue1.84e-07604
presumptive structure1.84e-07604
epiblast (generic)1.84e-07604
digestive tract diverticulum1.97e-0723
regional part of telencephalon2.27e-0733
endocrine gland2.55e-0735
trunk2.66e-07216
immune organ3.57e-0726
hepatic diverticulum5.18e-0722
liver primordium5.18e-0722
tissue6.34e-07787
cerebral hemisphere7.74e-0732
Disease
Ontology termp-valuen
ovarian cancer7.59e-0714


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.