Combinatorial chemistry & high throughput screening
Jan 1, 2017
BACKGROUND: The cell cycle-regulated genes express periodically with the cell cycle stages, and the identification and study of these genes can provide a deep understanding of the cell cycle process. Large false positives and low overlaps are big pro...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence vari...
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Jan 1, 2017
Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signa...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The GO captures many aspects of functional annotations, but there are other alternative complementary sources of protein function information. For example, enzyme functional annotations are described in a range of resources from the Enzyme Commission...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Evidence and Conclusion Ontology (ECO) is a community resource for describing the various types of evidence that are generated during the course of a scientific study and which are typically used to support assertions made by researchers. ECO des...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The specificity of knowledge that Gene Ontology (GO) annotations currently can represent is still restricted by the legacy format of the GO annotation file, a format intentionally designed for simplicity to keep the barriers to entry low and thus enc...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
Contemporary techniques in biology produce readouts for large numbers of genes simultaneously, the typical example being differential gene expression measurements. Moreover, those genes are often richly annotated using GO terms that describe gene fun...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its s...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2017
The Gene Ontology Consortium (GOC) produces a wealth of resources widely used throughout the scientific community. In this chapter, we discuss the different ways in which researchers can access the resources of the GOC. We here share details about th...