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Recent Posts
- New gene page, new Bgee interface
- Confirming that autism and epilepsy genes are expressed in specific brain areas
- Gene expression enrichment tests are sensitive enough to detect where your background data came from #TopAnat
- When fold-enrichment is more informative than p-values: #TopAnat analysis of autism genes from GWAS
- #TopAnat where are genes significant in a breast cancer GWAS expressed?
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- RT @neXtProt_news: #SWAT4HCLS Wondering what data is in neXtProt, how it is modeled in RDF and which SPARQL predicates to use to query the… 2 days ago
- poke @ISBSIB @OMABrowser @uniprot @uberanat @neXtProt_news 5 days ago
- We have a subset of our SQL database, which has explicit expression information. We want to change the name because… twitter.com/i/web/status/1… 5 days ago
- RT @neXtProt_news: Slides on Using SPARQL to explore human protein data in neXtProt and beyond are here bit.ly/2qOeLgC https://t.c… 3 weeks ago
- RT @ISBSIB: ... joint queries applied to SIB #bioinformatics Resources @OMABrowser @Bgeedb and @uniprot-KB/@SIB_SwissProt ➡️ leveraging bio… 3 weeks ago
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Category Archives: topanat
New gene page, new Bgee interface
Yesterday we have released a major update of our web interface: The download functionality remains the same, as does the data (processing for the next release is just starting with the new Ensembl release – we love Ensembl). It’s just easier … Continue reading
Posted in bgee update, presentation, topanat, usability
Tagged gene page, statistics, web interface
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Confirming that autism and epilepsy genes are expressed in specific brain areas
Recently we presented on this blog a quick-and-dirty analysis of genes with the keyword “autism” from the GWAS Catalog at EBI. But recently, Jabbari and Nürnberg have published a more thorough study of autism and epilepsy candidate genes: Jabbari and … Continue reading
Gene expression enrichment tests are sensitive enough to detect where your background data came from #TopAnat
When you invent such a cool toy as TopAnat, you play with it. And then sometimes, you’re afraid that you might have broken it. But then, maybe it’s more robust than you expected. This is such a story. One lab … Continue reading
When fold-enrichment is more informative than p-values: #TopAnat analysis of autism genes from GWAS
In a recent post on this blog we saw how to analyze results from a breast cancer GWAS. In that case, we did not have very strong expectations of tissue-specificity for the genes; it was more of an exploratory analysis. … Continue reading
#TopAnat where are genes significant in a breast cancer GWAS expressed?
Genome Wide Association Studies (GWAS) report many significant SNPs, which may be associated to many genes. How can we make sense of them? One way is to compute enrichment of the resulting gene list for properties of interest. For example … Continue reading
The contribution of #RNAseq, #microarrays, in situ hybridization and ESTs to #TopAnat gene enrichment signal
In Bgee, we integrate gene expression data from RNA-seq, Affymetrix microarrays, ESTs and in situ hybridization data. It is natural to think that with RNA-seq being so powerful, we should not bother with other sources of information. Yet we still have … Continue reading
Posted in RNA-Seq, topanat
Tagged ESTs, in situ hybridization, Microarray, RNA-Seq, statistics
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What makes #TopAnat special relative to classical #GeneOntology enrichment?
In bioinformatics and genomics, we are all familiar with GO (Gene Ontology) enrichment test. You take a gene list, paste it into a tool such as Gorilla, PANTHER, or others, and obtain a list of terms which are enriched in … Continue reading
Posted in topanat
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