BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles
By Frederik Otzen Bagger, Savvas Kinalis, N. Rapin. 2018
205 citations recorded by the source corpus.
Abstract BloodSpot is a gene-centric database of mRNA expression of haematopoietic cells. The web-based interface to the database includes three concomitant levels of visualization for a gene query; foremost is the expression across hematopoietic cell types, second is analysis of survival of Acute Myeloid Leukaemia patients based on gene expression, and lastly, the expression visualized in an interactive developmental tree. With the introduction of single cell data we have now also included an unbiased dimensionality reduction method to show gene expression over the continuum of haematopoiesis. The webserver includes a few select analysis functionalities, like Student's t-test, identification of correlating genes and lookup of whole genetic signatures, with the aim of making generation and testing of hypotheses quick and intuitive. The visualizations have been updated to accommodate new datatypes and the database has been largely expanded with RNA-sequencing datasets, both purified in bulk and at single cell resolution, increasing the number of single samples more than 10 fold, while keeping simplicity in presentation. The database should be of interest for any researcher within leukaemia, haematopoiesis, cellular development, or stem cells. The database is freely available at www.bloodspot.eu
Subfields: Cancer Research, Hematology, Molecular Biology, Computational Biology & Bioinformatics
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Citations in the corpus
- UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction (2018, methodology): “Based upon preliminary releases of a soware implementation, UMAP has already found widespread use in the elds of bioinformatics [4, 15, 37, 2, 36, 13], materials science [27, 19], and machine learning [8, 20, 17, 38] among others.”