Proteome Database (LMPD)

Introduction

11/04/08: The LIPID MAPS Proteome Database (LMPD) of lipid-related proteins and genes has recently been revised extensively.

In this latest release, the list of mouse proteins was checked to remove obsolete UniProt accessions and associated data. The database was then updated with current UniProt accessions and Entrez gene ID's corresponding to those proteins. Secondly, the most recent releases of the NCBI Refseq and Uniprot databases were searched for proteins with validated lipid-associated functions, and these were merged with the existing mouse protein list. Finally, the entire list of protein sequences was curated manually to remove records of dubious quality either from a sequence or a functional standpoint.

The database of human lipid-related proteins has undergone a complete overhaul. The NCBI HomoloGene database of homologs was used to find the human orthologous sequences corresponding to the curated mouse proteins described above. Approximately 95% of our set of lipid-related mouse proteins had human orthologs listed in HomoloGene. As was done for the mouse proteins, this list was then supplemented with data from recent releases of the NCBI Refseq and Uniprot databases whose gene/protein annotations, Gene Ontology annotations or KEGG pathway descriptions gave a reliable indication of a lipid-associated function.

In summary, the new release of LMPD contains approximately 1200 lipid-related proteins for each of Homo sapiens and Mus musculus. Exact numbers of genes and proteins are expected to change slightly as part of our ongoing curation efforts. We welcome comments and suggestions from the public with regard to the accuracy and completeness of the LMPD.

Statistics

Number of proteins/genes*

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