BrainImageR: spatiotemporal gene set analysis referencing the human brain

Bioinformatics
Sara B LinkerFred H Gage

Abstract

Neuronal analyses such as transcriptomics, epigenetics and genome-wide association studies must be assessed in the context of the human brain to generate biologically meaningful inferences. It is often difficult to access primary human brain tissue; therefore, approximations are made using alternative sources such as peripheral tissues or in vitro-derived neurons. Gene sets from these studies are then assessed for their association with the post-mortem human brain. However, most analyses of post-mortem datasets are achieved by building new computational tools each time in-house, which can cause discrepancies from study to study. The field is in need of a user-friendly tool to examine spatiotemporal expression with respect to the postmortem brain. Such a tool will be of use in the molecular interrogation of neurological and psychiatric disorders, with direct advantages for the disease-modeling and human genetics communities. We have developed brainImageR, an R package that calculates both the spatial and temporal association of a dataset with post-mortem human brain. BrainImageR identifies anatomical regions enriched for candidate gene set expression. It further predicts the developmental time point of the sample, a task that ha...Continue Reading

References

Sep 13, 2003·Journal of Biomedical Informatics·Stephan Dreiseitl, Lucila Ohno-Machado
Sep 22, 2012·Nature·Michael J HawrylyczAllan R Jones
Apr 4, 2014·Nature·Jeremy A MillerEd S Lein
Jun 11, 2015·Proceedings of the National Academy of Sciences of the United States of America·Spyros DarmanisStephen R Quake
Sep 24, 2015·Proceedings of the National Academy of Sciences of the United States of America·Michael P SchwartzJames A Thomson
Dec 9, 2015·Proceedings of the National Academy of Sciences of the United States of America·J Gray CampBarbara Treutlein
Dec 17, 2016·Journal of Neurovirology·Richard Lathe, Juergen G Haas

❮ Previous
Next ❯

Citations

Nov 27, 2019·Cold Spring Harbor Perspectives in Biology·Krishna C VadodariaFred H Gage
Aug 15, 2020·Human Molecular Genetics·George Andrew S InglisAndrew Escayg
Jun 20, 2019·Frontiers in Immunology·Luke W BonhamJennifer S Yokoyama

❮ Previous
Next ❯

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.