Related Experiment Video
Updated: Jun 13, 2026
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
PhenoFam-gene set enrichment analysis through protein structural information.
Maciej Paszkowski-Rogacz1, Mikolaj Slabicki, M Teresa Pisabarro
1Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr, 108, 01307 Dresden, Germany. paszkows@mpi-cbg.de
BMC Bioinformatics
|May 19, 2010
Summary
PhenoFam is a new web tool that combines gene set enrichment analysis (GSEA) with protein structural information to help researchers understand large biological datasets and discover gene functions.
Area of Science:
- Genomics
- Proteomics
- Bioinformatics
Background:
- High-throughput biological studies generate massive datasets requiring advanced analysis tools.
- Gene set enrichment analysis (GSEA) and protein structural investigation are powerful methods for data interpretation.
- A unified tool for combining these approaches in high-throughput data analysis was lacking.
Purpose of the Study:
- To develop a user-friendly, web-based application named PhenoFam.
- To integrate gene set enrichment analysis with protein structural and functional domain information.
- To facilitate the functional annotation of genes from high-throughput data.
Main Methods:
- PhenoFam utilizes Ensembl databases to link user identifiers with InterPro protein domain features.
- It performs GSEA using protein domain families as annotation terms.
- The tool analyzes complete high-throughput study results without pre-filtering.
Main Results:
- PhenoFam successfully identified a novel function of plexins with RasGAP domains from an RNA interference screen.
- Analysis of breast cancer gene expression profiles revealed a connection between PX domain-containing proteins and carcinoma.
- The tool demonstrated its utility in uncovering functional insights from large-scale biological data.
Conclusions:
- PhenoFam offers an accessible web interface for GSEA using high-throughput data and protein structural information.
- The application aids in the functional annotation of genes.
- It addresses the need for integrated tools in analyzing complex biological datasets.
More Related Videos
09:10A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
09:16A Spin-Tip Enrichment Strategy for Simultaneous Analysis of N-Glycopeptides and Phosphopeptides from Human Pancreatic Tissues
Published on: May 4, 2022
Related Concept Videos
01:27C4 Pathway and CAM
Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...
C4 Pathway
The C4 pathway is used by plants such as...
02:15Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
01:56Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
01:56Structural Protein Function
Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to form...
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,...
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,...