Meta cohort with 28000 bulk gene expression profiles

 Meta cohorts can be very interesting to get a quick comprehensive overview of the gene expression pattern for your gene of interest.

Here a meta cohort that has been around for some time, but still provides valuable information at a single glance. The integration of a harmonised Affymetrix cohort of nearly 28.000 bulk profiles. Using the 'sample maps' feature in the free open online R2 platform ( https://r2.amc.nl ), you can use data driven representations, such as UMAP, tSNE, PCA etc for exploration. Or make use of a wealth of other features available in the versatile data science tool, intended for biomedical researchers.






Comments

Post a Comment

Popular posts from this blog

Plotting updates for the open online R2platform. The data science platform for biomedical researchers

Image
  Ploting updates for the R2platform We have been working hard to bring you the latest update in the R2 genomics analysis and visualization platform ( https://r2.amc.nl ); the goto web-tool for biomedical researchers to test their hypotheses on public omics data, without the need for bioinformatics or coding expertise. In the latest update, we have made substantial changes to many of the plots that can be produced within R2. Many of the adaptable parameters have now become interactive and are placed under the 'gears' icon. The 'gears' icon Let's have a look at a gene within one of the many resources that are publicly available in R2. We will look at the GATA3 gene in an integrated resouce where samples from both GTEx as well as the TCGA have been integrated and 'batch corrected' to get an immersive view of expression in normal as well as cancer samples. We first select our resource of interest by clicking on 'select a data set'. and then find the ...
Read more

Create a visual Fisher's Exact plot in a few simple clicks in the R2 Genomics Analysis & Visualization platform

Image
Create a visual Fisher's Exact plot in a few simple clicks in the R2 Genomics Analysis & Visualization platform ( https://r2.amc.nl ). The data science platform that has been completely designed with the biomedical researcher in mind. This means that no coding or bioinformatics expertise is needed to operate the R2platform. Everything can be assessed by dropdown menu's and interlinked interactive visualizations. Just see the whole process in action in the illustration below. The Fisher's Exact test is often used to demonstrate whether the proportions of 2 different categorical variables are equal to the expectation. A significant p-value then informs you that this is unlikely (when used as a 2-sided test). Within R2, we added a visual element to such a test, where you can see the different groups in the contingency table as separate dots. These dots, are linked to actual samples in the data set, and can thus also be decorated using their meta data (color by a grouping v...
Read more

Compare polyA and ribo depletion mRNA head to head in nearly 300 matched samples in the R2 Genomics Analysis & Visualization platform

Image
The RNA atlas that is hosted in the R2 Platform ( https://r2.amc.nl ) is a great 300 samples reseource where all of the samples have been analysed on polyA isolation, ribo depletion as well as small RNA sequencing. As such it is an invaluable resource that can also be used to investigate the effects of the different isolation methods. You can use the 'two-set view' to analyze andvisualize 2 resources head-to-head h For example check out the expression of a Histone gene (that lacks a poly A tail), where you can clearly see that the poly A isolation lacks the aility to assess the expression of such genes.  Or visualize the profiles in the landscape views in the embedded genome browser of R2. Just a couple of simple things that R2 can be of great value with a few mouse clicks. Visit  https://r2.amc.nl  and explore this, or one of the hundreds of other public resources from the comfort of your web browser
Read more