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Gene Ontology: tool for the unification of biology

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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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Journal ArticleDOI

A module map showing conditional activity of expression modules in cancer.

TL;DR: It is suggested that there is a single mechanism for both primary tumor proliferation and metastasis to bone, and multiple research directions for diagnostic, prognostic and therapeutic studies are presented.
Journal ArticleDOI

The ConsensusPathDB interaction database: 2013 update

TL;DR: ConsensusPathDB has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases, and has re-implemented the graph visualization feature of Consensus pathDB using the Cytoscape.js library.
Book ChapterDOI

Amino‐Acid Properties and Consequences of Substitutions

TL;DR: Since the earliest protein sequences and structures were determined, it has been clear that the positioning and properties of amino acids are key to understanding many biological processes, and the first-determined protein structure, haemoglobin, provided a molecular explanation for the genetic disease sickle cell anaemia.
Posted ContentDOI

TBtools - an integrative toolkit developed for interactive analyses of big biological data

TL;DR: TBtools (a Toolkit for Biologists integrating various biological data handling tools), a stand-alone software with a user-friendly interface designed to meet the increasing demand for big-data analyses, ranging from bulk sequence processing to interactive data visualization.
References
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Journal ArticleDOI

Cluster analysis and display of genome-wide expression patterns

TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI

The Pfam protein families database

TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI

The genome sequence of Drosophila melanogaster

Mark Raymond Adams, +194 more
- 24 Mar 2000 - 
TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Journal ArticleDOI

Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization

TL;DR: A comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle is created, and it is found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins.
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