Category Archives: topanat

New gene page, new Bgee interface

Posted on March 11, 2016 by bgeedb

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 , , | 1 Comment

Confirming that autism and epilepsy genes are expressed in specific brain areas

Posted on March 7, 2016 by bgeedb

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 →

Posted in topanat, using bgee | Tagged , , , | 1 Comment

Gene expression enrichment tests are sensitive enough to detect where your background data came from #TopAnat

Posted on March 2, 2016 by bgeedb

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 →

Posted in RNA-Seq, topanat | Tagged , , , | 1 Comment

When fold-enrichment is more informative than p-values: #TopAnat analysis of autism genes from GWAS

Posted on February 29, 2016 by bgeedb

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 →

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#TopAnat where are genes significant in a breast cancer GWAS expressed?

Posted on February 26, 2016 by bgeedb

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 →

Posted in topanat, using bgee | Tagged , , , | 1 Comment

The contribution of #RNAseq, #microarrays, in situ hybridization and ESTs to #TopAnat gene enrichment signal

Posted on February 26, 2016 by bgeedb

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 →

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What makes #TopAnat special relative to classical #GeneOntology enrichment?

Posted on February 25, 2016 by bgeedb

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 →

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#TopAnat: GO-like enrichment of anatomical terms mapped to genes by expression patterns

Posted on November 24, 2015 by bgeedb

Update: This was the first blogpost on TopAnat. There are now quite a few more, under the tag TopAnat. We are glad to roll out the first public beta version of our new tool, TopAnat: http://bgee.org/?page=top_anat TopAnat uses the classical … Continue reading →

Posted in bgee update, ontology, topanat | 1 Comment