Related Experiment Video
Updated: Aug 12, 2026
08:09
Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways
1Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019, USA.
F1000Research
|May 28, 2019
Summary
We created the Gene Annotation Easy Viewer (GAEV) to simplify gene function and pathway analysis using KEGG data. This tool aids in annotating genomes for non-model organisms and metagenomics research.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Accurate gene annotation is crucial for understanding biological functions and pathways.
- Existing tools may lack user-friendliness or integration with comprehensive databases like KEGG.
- Non-model organisms and metagenomic data present unique challenges for genome annotation.
Purpose of the Study:
- To develop an accessible tool, Gene Annotation Easy Viewer (GAEV), for integrating and visualizing gene annotation data.
- To simplify the process of understanding gene function, orthologs, and pathway involvement.
- To facilitate genome annotation for non-model species and metagenomics.
Main Methods:
- Integration of gene annotation data from the KEGG Automatic Annotation Server.
- Development of a user-friendly interface presenting gene name, KO number, ortholog information, and pathway mapping.
- Implementation of direct links to KEGG pathway maps for interactive exploration.
Main Results:
- GAEV generates easy-to-read tables summarizing key gene annotation information.
- Users can visualize gene product interactions within molecular pathways via KEGG map links.
- Successful demonstration of GAEV utility through annotation of the *Daphnia pulex* genome.
Conclusions:
- GAEV provides a gene-centered view of function and pathways, enhancing annotation efficiency.
- The tool significantly facilitates genome annotation for non-model species and metagenomics.
- GAEV offers an accessible solution for researchers without extensive command-line experience.
Related Concept Videos
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...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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.
01:09Epistasis Analysis
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
02:26Protein Networks
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
01:11IP3/DAG Signaling Pathway
Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and produces two-second...