Related Experiment Video
Updated: Jun 22, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
GoGene: gene annotation in the fast lane
Conrad Plake1, Loic Royer, Rainer Winnenburg
1Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany. conrad.plake@biotec.tu-dresden.de
Nucleic Acids Research
|May 26, 2009
Summary
GoGene enhances gene discovery by integrating manual Gene Ontology annotations with text mining of biomedical literature. This approach expands gene information beyond function and location, offering comprehensive, literature-backed data for 10 model organisms.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- High-throughput screening generates vast gene datasets requiring comprehensive annotation.
- Existing Gene Ontology annotations are limited to gene process, function, and location, and do not cover all genes.
- A need exists for broader, literature-supported gene information beyond curated ontologies.
Purpose of the Study:
- To develop GoGene, a system that complements manual gene annotations with high-throughput text mining.
- To expand gene information to include diseases, compounds, techniques, and mutations.
- To provide the most current and complete gene facts, ranked by novelty and importance.
Main Methods:
- Text mining of over 18 million PubMed entries to extract gene-term co-occurrences.
- Integration of high-throughput text mining with existing Gene Ontology annotations.
- Development of a searchable database (GoGene) covering 10 model organisms.
Main Results:
- GoGene contains over 4 million associations between genes and biomedical terms.
- The database covers genes beyond process, function, and location, including diseases, compounds, techniques, and mutations.
- Search functionalities include keywords, gene lists, sequences, PubMed, EntrezGene, and BLAST, with literature evidence provided.
Conclusions:
- GoGene addresses limitations of manual annotations by incorporating text mining for comprehensive gene information.
- The system provides transparent, literature-supported gene associations, enhancing gene discovery and research.
- GoGene offers a valuable, up-to-date resource for exploring gene functions and relationships in model organisms.
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
02:05Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
01:57Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
02:02Genomics
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...