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Coexpression cluster:C2494

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Full id: C2494_brain_neuroblastoma_duodenum_occipital_temporal_parietal_small



Phase1 CAGE Peaks

Hg19::chr19:4474846..4474881,+p@chr19:4474846..4474881
+
Hg19::chr20:42875935..42875966,+p1@GDAP1L1
Hg19::chr6:3228944..3228955,+p2@uc003mvi.1
Hg19::chr6:33388013..33388053,+p4@SYNGAP1


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
nervous system1.17e-5789
central nervous system8.00e-5581
neurectoderm2.68e-4686
neural tube1.02e-4556
neural rod1.02e-4556
future spinal cord1.02e-4556
neural keel1.02e-4556
neural plate2.62e-4582
presumptive neural plate2.62e-4582
regional part of nervous system2.35e-4353
regional part of brain2.35e-4353
brain6.38e-4368
future brain6.38e-4368
ectoderm-derived structure5.52e-41171
ectoderm5.52e-41171
presumptive ectoderm5.52e-41171
pre-chordal neural plate1.20e-3561
regional part of forebrain2.19e-3441
forebrain2.19e-3441
anterior neural tube2.19e-3441
future forebrain2.19e-3441
ecto-epithelium4.42e-34104
structure with developmental contribution from neural crest9.43e-31132
telencephalon1.23e-2934
brain grey matter1.86e-2934
gray matter1.86e-2934
cerebral hemisphere1.96e-2832
regional part of telencephalon5.36e-2832
organ system subdivision3.83e-27223
cerebral cortex5.28e-2325
pallium5.28e-2325
regional part of cerebral cortex3.34e-2122
neocortex1.88e-1920
adult organism1.97e-19114
anatomical cluster8.86e-18373
multi-tissue structure1.80e-12342
posterior neural tube3.70e-1215
chordal neural plate3.70e-1215
organ part3.17e-11218
segmental subdivision of hindbrain5.53e-1012
hindbrain5.53e-1012
presumptive hindbrain5.53e-1012
embryo9.58e-10592
segmental subdivision of nervous system6.96e-0913
epithelium1.17e-08306
cell layer2.77e-08309
basal ganglion3.15e-089
nuclear complex of neuraxis3.15e-089
aggregate regional part of brain3.15e-089
collection of basal ganglia3.15e-089
cerebral subcortex3.15e-089
multi-cellular organism3.95e-08656
neural nucleus6.93e-089
nucleus of brain6.93e-089
regional part of metencephalon7.76e-089
metencephalon7.76e-089
future metencephalon7.76e-089
developing anatomical structure7.89e-08581
tube1.02e-07192
germ layer1.36e-07560
germ layer / neural crest1.36e-07560
embryonic tissue1.36e-07560
presumptive structure1.36e-07560
germ layer / neural crest derived structure1.36e-07560
epiblast (generic)1.36e-07560
embryonic structure1.53e-07564
temporal lobe1.66e-076


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.