What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins

Abstract

The genomic era has enabled research projects that use approaches including genome-scale screens, microarray analysis, next-generation sequencing, and mass spectrometry-based proteomics to discover genes and proteins involved in biological processes. Such methods generate data sets of gene, transcript, or protein hits that researchers wish to explore to understand their properties and functions and thus their possible roles in biological systems of interest. Recent years have seen a profusion of Internet-based resources to aid this process. This review takes the viewpoint of the curious biologist wishing to explore the properties of protein-coding genes and their products, identified using genome-based technologies. Ten key questions are asked about each hit, addressing functions, phenotypes, expression, evolutionary conservation, disease association, protein structure, interactors, posttranslational modifications, and inhibitors. Answers are provided by presenting the latest publicly available resources, together with methods for hit-specific and data set-wide information retrieval, suited to any genome-based analytical technique and experimental species. The utility of these resources is demonstrated for 20 factors regulating cell proliferation. Results obtained using some of these are discussed in more depth using the p53 tumor suppressor as an example. This flexible and universally applicable approach for characterizing experimental hits helps researchers to maximize the potential of their projects for biological discovery.

FIGURE 1:

Generalized workflow for the analysis of DNA, RNA, or protein samples and questions about the hits identified. Nucleic acid or protein samples isolated from the biological material of interest are processed, then analyzed by various methods. Raw analytical data are then matched to entries in public databases, generating a results table listing the genes, transcripts, or proteins (hits) identified. For each of these hits, 10 questions relating to their features, functions, and other properties are shown (blue boxes). Each question is addressed by a section in the text, plus one or more supplemental tables containing examples of hyperlinks to entries in online resources.

FIGURE 2:

Approaches for obtaining functional information about experimentally identified gene, transcript, or protein hits. Freely available software tools can be used to obtain information about features and functions of genes, transcripts, or proteins in a results table from multiple sources. Generation of an interaction network shows at a glance the nature of any previously reported interactions between members of a set of hits, each of which can be explored using the resources indicated. Making a hyperlinked results table allows one-click access from each hit directly to relevant pages from a wide range of resources. Creating an annotated results table containing controlled-vocabulary terms or keywords from a range of sources allows hits to be classified and sorted on the basis of these terms. Step-by-step protocols for performing these analyses are presented in the Supplemental Materials.