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Protein function prediction using the Protein Link EXplorer (PLEX).

Shailesh V Date¹, Edward M Marcotte

¹Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, 1 University Station, A4800, Austin, TX 78712-1064, USA.

Bioinformatics (Oxford, England)

|February 11, 2005

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The Protein Link EXplorer (PLEX) tool helps identify functionally linked genes and predict protein function by comparing phylogenetic profiles across many genomes. This aids in reconstructing cellular systems and pathways.

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

The Protein Link EXplorer (PLEX) is a web-based environment for analyzing protein function.
It facilitates the comparison of phylogenetic profiles for gene linkage analysis.

Purpose of the Study:

To introduce PLEX as a tool for identifying functionally linked genes.
To enable interactive prediction of protein function using comparative genomics.

Main Methods:

Construction and comparison of phylogenetic profiles for amino acid sequences.
Utilizing a database of ~350,000 predicted genes from 89 genomes.
Employing iterative searches, including chromosomal gene neighbors and Rosetta Stone linkages.

Main Results:

Related Experiment Videos

PLEX allows interactive identification of functionally linked genes.
Quantitative estimates of linkage confidence are provided.
Facilitates inference of gene function and reconstruction of cellular systems.

Conclusions:

PLEX is a valuable tool for functional genomics and systems biology.
It leverages comparative phylogenetic profiling for gene function prediction.
Enables researchers to explore gene linkages and cellular pathways effectively.