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Coexpression cluster:C3157

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Full id: C3157_cerebellum_smooth_ductus_occipital_bladder_brain_heart



Phase1 CAGE Peaks

Hg19::chr11:47546146..47546156,-p34@CELF1
Hg19::chr11:47546176..47546188,-p10@CELF1
Hg19::chr22:41763408..41763417,+p5@TEF


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:0003690double-stranded DNA binding0.0487681031437654
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0487681031437654
GO:0043566structure-specific DNA binding0.0487681031437654
GO:0045893positive regulation of transcription, DNA-dependent0.0487681031437654
GO:0003702RNA polymerase II transcription factor activity0.0487681031437654
GO:0045941positive regulation of transcription0.0487681031437654
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0487681031437654
GO:0016563transcription activator activity0.0487681031437654
GO:0031325positive regulation of cellular metabolic process0.0487681031437654
GO:0046983protein dimerization activity0.0487681031437654
GO:0009893positive regulation of metabolic process0.0487681031437654
GO:0006357regulation of transcription from RNA polymerase II promoter0.0487681031437654



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism7.79e-65114
neural tube5.46e-3056
neural rod5.46e-3056
future spinal cord5.46e-3056
neural keel5.46e-3056
regional part of nervous system1.01e-2953
regional part of brain1.01e-2953
brain5.96e-2568
future brain5.96e-2568
central nervous system8.97e-2581
telencephalon1.45e-2434
cerebral hemisphere8.06e-2432
regional part of forebrain9.55e-2441
forebrain9.55e-2441
anterior neural tube9.55e-2441
future forebrain9.55e-2441
regional part of cerebral cortex1.59e-2222
neocortex5.08e-2220
nervous system2.04e-2189
regional part of telencephalon3.60e-2132
neural plate6.47e-2182
presumptive neural plate6.47e-2182
brain grey matter1.15e-1934
gray matter1.15e-1934
neurectoderm1.51e-1986
cerebral cortex1.94e-1925
pallium1.94e-1925
structure with developmental contribution from neural crest6.76e-16132
pre-chordal neural plate1.53e-1561
ecto-epithelium1.01e-14104
organ system subdivision2.29e-11223
gyrus2.86e-116
ectoderm-derived structure5.10e-10171
ectoderm5.10e-10171
presumptive ectoderm5.10e-10171
temporal lobe2.98e-096
male genital duct1.28e-083
internal male genitalia1.28e-083
anatomical cluster2.35e-08373
anatomical conduit5.12e-08240
posterior neural tube1.83e-0715
chordal neural plate1.83e-0715
tube2.28e-07192
segmental subdivision of hindbrain3.41e-0712
hindbrain3.41e-0712
presumptive hindbrain3.41e-0712
organ7.13e-07503
multi-tissue structure7.42e-07342


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZNF263#1012738.221841637010680.001799043925565870.0108966159335484



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.