Tools and software

CattleGeneAtlas

We analysed 723 (156 newly generated and 567 existing) RNA-seq datasets to build the most comprehensive gene atlas in cattle to date, which included 91 tissues and cell types from 447 individuals. We summarized the sample information, their NCBI accession numbers, and expression (FPKM) of 24,616 Ensembl genes (based on UMD3.1). Through integrative analyses of this gene atlas with large-scale genome-wide association studies, we detected relevant tissues/cell types and candidate genes for 45 economically important traits in cattle (in press). This cattle gene atlas will serve as a primary source for biological interpretation and functional validation of GWAS findings, studies of adaptive evolution and population genetics, as well as genomic improvement in cattle.

The website allows the user to search for the expression of genes of interest based on Ensembl gene ID or gene symbol, and plot them according to tissue types. It also allows the user to link genes of interest to phenome-wide association analysis (pheWAS) results in humans by querying the GeneATLAS website. The annotation of orthologues genes between human and cattle was from Ensembl version 94. Keeping with the lab motto of open science, the full results can be downloaded freely. But, please, if you use the data, cite us.

http://cattlegeneatlas.roslin.ed.ac.uk/

GeneATLAS

GeneATLAS is a large database of associations between hundreds of traits and millions of variants using the UK Biobank cohort.

The associations have been computed using 452,264 UK Biobank White British individuals. To avoid having to remove a large number of related individuals present on the study, the associations have been computed using Mixed Linear Models in the UK’s national supercomputer called ARCHER using DISSECT. The objective of the current database is to benefit the research community by making a searchable atlas of genetic associations that help researchers to query associations results in an easy way, without the need to incur in the high computational costs required to analyse the UK Biobank large cohort.

http://geneatlas.roslin.ed.ac.uk/

DISSECT

DISSECT is a freely available software, which is able to exploit the distributed-memory parallel computational architectures of compute clusters, to perform a wide range of genomic and epidemiologic analyses. These type of analyses can currently only be carried out on reduced sample sizes or under restricted conditions. 

http://www.dissect.ed.ac.uk

REACTA

Developed under a collaborative project between EPCC and The Roslin Institute between 2011 and 2014, Regional Heritability Advanced Complex Trait Analysis (REACTA) is a modified version of GCTA with improved computational performance, support for Graphics Processing Units (GPUs), and additional features. REACTA was formerly known as ACTA. The purpose of REACTA is to quantify the contribution of genetic variation to phenotypic variation for complex traits, including performing regional heritability analyses.

https://www.epcc.ed.ac.uk/projects-portfolio/reacta