Gene Expression-Based Cross Species Tissue Mapping

Cross-species queries of large gene expression databases

MOTIVATION Expression databases, including the Gene Expression Omnibus and ArrayExpress, have experienced significant growth over the past decade and now hold hundreds of thousands of arrays from multiple species. Since most drugs are initially tested on model organisms, the ability to compare expression experiments across species may help identify pathways that are activated in a similar way i...

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences....

Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression

An important research problem in computational biology is the identification of expression programs, sets of co-activated genes orchestrating physiological processes, and the characterization of the functional breadth of these programs. The use of mammalian expression data compendia for discovery of such programs presents several challenges, including: 1) cellular inhomogeneity within samples, ...

A Cross-Species Gene Expression Marker-Based Genetic Map and QTL Analysis in Bambara Groundnut

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources develop...

symbiosis revealed through cross - species eQTL mapping