Abstract
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity.
Highlights
A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation
The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data
The GeneWeaver software system (Baker et al 2012) contains a database and a suite of tools to enable dissemination, integration, analysis, and discovery from heterogeneous data derived through functional genomics experimentation and biological data curation (Fig. 1)
Summary
There is a growing need to find consensus among large collections of diverse biological data to relate molecular mechanisms to disease and to understand the relations among diverse disease characteristics, models, and mechanisms through their underlying biology. The outcomes of functional experiments consist of a set of genomic features, often genes or transcripts, but increasingly other entities such as allelic variants, methylation sites, small non-coding RNA, and an expanding variety of new biomolecular endpoints Each of these is associated with a biological or behavioral assay, which is in turn associated with a disease-related construct. A system of users, groups, and projects allows for persistent storage or user selections, progressive reanalysis, and result sharing Most of these sources and GeneWeaver’s current tool suite operate on lists of genes and their association scores (p value, q-value, correlation coefficient, etc.), an upcoming release will support storage of gene–gene relations to provide for the direct comparison of biological networks. The structure and contents of the GeneWeaver system have been previously described (Baker et al 2012), as have the methods for identifier alignment (Jay 2012) and
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