Models

Strength of functional signature correlates with effect size in autism

BACKGROUND: Disagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric genetics, creating a sharp divide between disease burdens attributed to common and rare variation, with study …

AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression

In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater replicability, typically measured in sample-sample correlations of gene expression levels. Through a re-analysis of ENCODE …

Positive and negative forms of replicability in gene network analysis

MOTIVATION: Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This has motivated a great deal of comparative evaluation and research into best practices. We explore the possibility …

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of RNA-seq expression data to determine factors affecting functional connectivity and topology in co-expression …

Measuring the wisdom of the crowds in network-based gene function inference

MOTIVATION: Network-based gene function inference methods have proliferated in recent years, but measurable progress remains elusive. We wished to better explore performance trends by controlling data and algorithm implementation, with a particular …

Conditions for the evolution of gene clusters in bacterial genomes

Genes encoding proteins in a common pathway are often found near each other along bacterial chromosomes. Several explanations have been proposed to account for the evolution of these structures. For instance, natural selection may directly favour …

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies

BACKGROUND: Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Here we assessed the ability of …