Biomedical subjects

Kenneth R Williams

Publications and source records attributed to Kenneth R Williams.

4 recordsLinked to original sources

PubMed2006

Isotope-coded affinity tags for protein quantification.

An important goal in proteomics is to compare the relative amounts of different proteins in biological samples and to try to correlate these differences with changes in physiological state. The isotopecoded affinity tag technique pioneered in Aebersold's laboratory takes advantage of differential tagging of cysteine residues in proteins with stable isotopes to significantly reduce the complexity of peptide mixtures and increase the number of sequences that are identified in a single tandem mass spectrometry experiment. In this approach, two samples are isotopically labeled (one heavy, one light) through a reactive group that specifically binds to cysteine residues; the samples are combined, separated with chromatography, and analyzed by mass spectrometry. The results are then database searched and a list of hundreds of proteins and their heavy:light ratio is obtained.

Avidin↗

PubMed2006

MALDI-MS data analysis for disease biomarker discovery.

In this chapter, we address the issue of matrix-assisted laser desorption/ionization mass spectrometry (MS) data analysis for disease biomarker discovery. We first give a general framework of MS data analysis, then focus on several key steps. After that, we show some application examples using an ovarian sera cancer dataset. Finally, we discuss the limitations of current approaches and possible future research directions.

Animals↗

PubMed2004

Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas.

Affymetrix and spotted oligonucleotide microarrays were used to assess global differential gene expression comparing normal human melanocytes with six independent melanoma cell strains from advanced lesions. The data, validated at the protein level for selected genes, confirmed the overexpression in melanoma cells relative to normal melanocytes of several genes in the growth factor/receptor family that confer growth advantage and metastasis. In addition, novel pathways and patterns of associated expression in melanoma cells not reported before emerged, including the following: (a) activation of the NOTCH pathway; (b) increased Twist expression and altered expression of additional transcriptional regulators implicated in embryonic development and epidermal/mesenchymal transition; (c) coordinated activation of cancer/testis antigens; (d) coordinated down-regulation of several immune modulation genes, in particular in the IFN pathways; (e) down-regulation of several genes implicated in membrane trafficking events; and (f) down-regulation of growth suppressors, such as the Prader-Willi gene NECDIN, whose function was confirmed by overexpression of ectopic Flag-necdin. Validation of differential expression using melanoma tissue microarrays showed that reduced ubiquitin COOH-terminal esterase L1 in primary melanoma is associated with worse outcome and that increased expression of the basic helix-loop-helix protein Twist is associated with worse outcome. Some differentially expressed genes reside on chromosomal regions displaying common loss or gain in melanomas or are known to be regulated by CpG promoter methylation. These results provide a comprehensive view of changes in advanced melanoma relative to normal melanocytes and reveal new targets that can be used in assessing prognosis, staging, and therapy of melanoma patients.

Animals↗

PubMed2004

KARMA: a web server application for comparing and annotating heterogeneous microarray platforms.

We have developed a universal web server application (KARMA) that allows comparison and annotation of user-defined pairs of microarray platforms based on diverse types of genome annotation data (across different species) collected from multiple sources. The application is an effective tool for diverse microarray platforms, including arrays that are provided by (i) the Keck Microarray Resource at Yale, (ii) commercially available Affymetrix GeneChips and spotted arrays and (iii) custom arrays made by individual academics. The tool provides a web interface that allows users to input pairs of test files that represent diverse array platforms for either single or multiple species. The program dynamically identifies analogous DNA fragments spotted or synthesized on multiple microarray platforms based on the following types of information: (i) NCBI-Unigene identifiers, if the platforms being compared are within the same species or (ii) NCBI-Homologene data, if they are cross-species. The single-species comparison is implemented based on set operations: intersection, union and difference. Other forms of retrievable annotation data, including LocusLink, SwissProt and Gene Ontology (GO), are collected from multiple remote sites and stored in an integrated fashion using an Oracle database. The KARMA database, which is updated periodically, is available on line at the following URL: http://ymd.med.yale.edu/karma/cgi-bin/karma.pl.

Gene Expression Profiling↗