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Open AccessJournal ArticleDOI

Gene Ontology: tool for the unification of biology

TLDR
The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Abstract
Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.

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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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limma powers differential expression analyses for RNA-sequencing and microarray studies

TL;DR: The philosophy and design of the limma package is reviewed, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.
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WGCNA: an R package for weighted correlation network analysis.

TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

TL;DR: The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
References
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Journal ArticleDOI

Myb-related Schizosaccharomyces pombe cdc5p is structurally and functionally conserved in eukaryotes.

TL;DR: It is demonstrated that Cef1p is not involved in transcriptional activation of a class of G2/M-regulated genes typified by SWI5, and results suggest that Cdc5 family members participate in a novel pathway to regulate G 2/M progression.
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DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams

TL;DR: The authors at DDBJ process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams, which is so large that it alone exceeds the total amount submitted in the preceding 10 years.
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Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure.

TL;DR: Comparison of proteins from complete eukaryotic proteomes will be an extremely powerful way to learn more about a particular protein's structure, its function, and its relationships with other proteins.
Journal ArticleDOI

GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements

TL;DR: The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse designed as an open-ended system that can integrate different types of expression data.
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