Biomedical subjects

Cathy Wu

Publications and source records attributed to Cathy Wu.

5 recordsLinked to original sources

PubMed2006

Quantitative assessment of dictionary-based protein named entity tagging.

OBJECTIVE: Natural language processing (NLP) approaches have been explored to manage and mine information recorded in biological literature. A critical step for biological literature mining is biological named entity tagging (BNET) that identifies names mentioned in text and normalizes them with entries in biological databases. The aim of this study was to provide quantitative assessment of the complexity of BNET on protein entities through BioThesaurus, a thesaurus of gene/protein names for UniProt knowledgebase (UniProtKB) entries that was acquired using online resources. METHODS: We evaluated the complexity through several perspectives: ambiguity (i.e., the number of genes/proteins represented by one name), synonymy (i.e., the number of names associated with the same gene/protein), and coverage (i.e., the percentage of gene/protein names in text included in the thesaurus). We also normalized names in BioThesaurus and measures were obtained twice, once before normalization and once after. RESULTS: The current version of BioThesaurus has over 2.6 million names or 2.1 million normalized names covering more than 1.8 million UniProtKB entries. The average synonymy is 3.53 (2.86 after normalization), ambiguity is 2.31 before normalization and 2.32 after, while the coverage is 94.0% based on the BioCreAtive data set comprising MEDLINE abstracts containing genes/proteins. CONCLUSION: The study indicated that names for genes/proteins are highly ambiguous and there are usually multiple names for the same gene or protein. It also demonstrated that most gene/protein names appearing in text can be found in BioThesaurus.

Dictionaries as Topic↗

PubMed2006

Proteomic and bioinformatic characterization of the biogenesis and function of melanosomes.

Melanin, which is responsible for virtually all visible skin, hair, and eye pigmentation in humans, is synthesized, deposited, and distributed in subcellular organelles termed melanosomes. A comprehensive determination of the protein composition of this organelle has been obstructed by the melanin present. Here, we report a novel method of removing melanin that includes in-solution digestion and immobilized metal affinity chromatography (IMAC). Together with in-gel digestion, this method has allowed us to characterize melanosome proteomes at various developmental stages by tandem mass spectrometry. Comparative profiling and functional characterization of the melanosome proteomes identified approximately 1500 proteins in melanosomes of all stages, with approximately 600 in any given stage. These proteins include 16 homologous to mouse coat color genes and many associated with human pigmentary diseases. Approximately 100 proteins shared by melanosomes from pigmented and nonpigmented melanocytes define the essential melanosome proteome. Proteins validated by confirming their intracellular localization include PEDF (pigment-epithelium derived factor) and SLC24A5 (sodium/potassium/calcium exchanger 5, NCKX5). The sharing of proteins between melanosomes and other lysosome-related organelles suggests a common evolutionary origin. This work represents a model for the study of the biogenesis of lysosome-related organelles.

Animals↗

PubMed2005

BioThesaurus: a web-based thesaurus of protein and gene names.

UNLABELLED: BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase. Currently covering more than two million proteins, BioThesaurus consists of over 2.8 million names extracted from multiple molecular biological databases according to the database cross-references in iProClass. The BioThesaurus web site allows the retrieval of synonymous names of given protein entries and the identification of protein entries sharing the same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus

Animals↗

PubMed2004

Update on genome completion and annotations: Protein Information Resource.

The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt--the Universal Protein Resource--which now unifies the PIR, Swiss-Prot and TrEMBL databases. The PIRSF (SuperFamily) classification system is central to the PIR/UniProt functional annotation of proteins, providing classifications of whole proteins into a network structure to reflect their evolutionary relationships. Data integration and associative studies of protein family, function and structure are supported by the iProClass database, which offers value-added descriptions of all UniProt proteins with highly informative links to more than 50 other databases. The PIR system allows consistent, rich and accurate protein annotation for all investigators.

Animals↗

PubMedDate not supplied

Gene and protein profiling of the response of MA-10 Leydig tumor cells to human chorionic gonadotropin.

Activation of the steroidogenic machinery by peptide hormones involves a number of steps for transmitting signals from the plasma membrane to mitochondria in a spatially and temporally coordinated manner. Although key proteins mediating the hormonal signal have been identified, recent data suggest that the pathway might involve more complex protein-protein and protein-lipid interactions. Genomic and proteomic methods of analysis, namely the Affymetrix Murine Genome U74A v2 GeneChip and the BD PowerBlot Western Array, were used to identify human chorionic gonadotropin (hCG)-induced changes in mRNA and protein of MA-10 Leydig tumor cells that parallel the increase seen in progesterone synthesis. To analyze the massive amount of data that was generated, a comprehensive protein information matrix summarizing the features of each gene or protein, including its known properties, as well as annotations derived by homology-based functional inference, was developed. Of the genes examined by Affymetrix array, approximately 79 were differentially expressed and of gene products examined by PowerBlot, 9 were differentially expressed (above twofold). Changes in the expression of selected transcripts of interest were confirmed using real-time quantitative polymerase chain reaction and immunoblot analyses. Collectively, these results indicate that hormonal regulation of steroidogenesis is a complex phenomenon, involving proteins that participate in various known and novel pathways, which are implicated in transmitting signals from the plasma membrane to mitochondria and nucleus.

Blotting, Western↗