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Coexpression cluster:C2754

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Full id: C2754_temporal_duodenum_nonsmall_occipital_parietal_Nucleus_putamen



Phase1 CAGE Peaks

Hg19::chr3:79817111..79817121,-p11@ROBO1
Hg19::chr3:79817136..79817155,-p4@ROBO1
Hg19::chr3:79817162..79817175,-p6@ROBO1
Hg19::chr3:79817277..79817296,-p9@ROBO1


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


No GOStat results

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
central nervous system7.94e-4981
nervous system1.14e-4789
neural tube1.63e-4556
neural rod1.63e-4556
future spinal cord1.63e-4556
neural keel1.63e-4556
brain7.50e-4368
future brain7.50e-4368
regional part of nervous system1.96e-4153
regional part of brain1.96e-4153
neural plate2.88e-3682
presumptive neural plate2.88e-3682
neurectoderm1.55e-3586
regional part of forebrain1.94e-3541
forebrain1.94e-3541
anterior neural tube1.94e-3541
future forebrain1.94e-3541
brain grey matter1.64e-3134
gray matter1.64e-3134
cerebral hemisphere4.95e-3132
telencephalon6.67e-3134
pre-chordal neural plate3.10e-3061
regional part of telencephalon1.52e-2832
ecto-epithelium9.00e-27104
structure with developmental contribution from neural crest3.29e-26132
ectoderm-derived structure4.70e-26171
ectoderm4.70e-26171
presumptive ectoderm4.70e-26171
cerebral cortex5.97e-2425
pallium5.97e-2425
regional part of cerebral cortex3.36e-2322
organ system subdivision7.39e-23223
adult organism1.20e-20114
neocortex1.87e-2020
anatomical cluster5.64e-17373
posterior neural tube5.12e-1115
chordal neural plate5.12e-1115
multi-tissue structure4.61e-10342
tube4.97e-10192
intervertebral cartilage3.16e-095
symphysis3.16e-095
nonsynovial joint3.16e-095
fibrous joint3.16e-095
cartilaginous joint3.16e-095
developing mesenchymal condensation3.16e-095
pre-cartilage condensation3.16e-095
cartilaginous condensation3.16e-095
cartilage element3.16e-095
post-cranial axial skeletal system3.16e-095
vertebral column3.16e-095
intervertebral disk3.16e-095
intervertebral joint3.16e-095
brain vasculature3.55e-095
limbic system5.64e-095
neural nucleus6.01e-099
nucleus of brain6.01e-099
basal ganglion7.87e-099
nuclear complex of neuraxis7.87e-099
aggregate regional part of brain7.87e-099
collection of basal ganglia7.87e-099
cerebral subcortex7.87e-099
vasculature of organ1.31e-0811
temporal lobe2.20e-086
parietal lobe4.55e-085
cell layer6.31e-08309
epithelium1.10e-07306
segmental subdivision of hindbrain2.07e-0712
hindbrain2.07e-0712
presumptive hindbrain2.07e-0712
embryo2.66e-07592
brainstem3.64e-076
anatomical conduit4.91e-07240


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
USF1#739146.361499277207960.0006105011399140830.00508697371561249



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.