Biomedical subjects

Pinglang Wang

Publications and source records attributed to Pinglang Wang.

4 recordsLinked to original sources

PubMed2006

SNP Function Portal: a web database for exploring the function implication of SNP alleles.

MOTIVATION: Finding the potential functional significance of SNPs is a major bottleneck in understanding genome-wide SNP scanning results, as the related functional data are distributed across many different databases. The SNP Function Portal is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, the SNP Function Portal includes a powerful search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, our system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments. AVAILABILITY: http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/snpfunc.aspx.

Alleles↗

PubMed2005

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.

Genome-wide expression profiling is a powerful tool for implicating novel gene ensembles in cellular mechanisms of health and disease. The most popular platform for genome-wide expression profiling is the Affymetrix GeneChip. However, its selection of probes relied on earlier genome and transcriptome annotation which is significantly different from current knowledge. The resultant informatics problems have a profound impact on analysis and interpretation the data. Here, we address these critical issues and offer a solution. We identified several classes of problems at the individual probe level in the existing annotation, under the assumption that current genome and transcriptome databases are more accurate than those used for GeneChip design. We then reorganized probes on more than a dozen popular GeneChips into gene-, transcript- and exon-specific probe sets in light of up-to-date genome, cDNA/EST clustering and single nucleotide polymorphism information. Comparing analysis results between the original and the redefined probe sets reveals approximately 30-50% discrepancy in the genes previously identified as differentially expressed, regardless of analysis method. Our results demonstrate that the original Affymetrix probe set definitions are inaccurate, and many conclusions derived from past GeneChip analyses may be significantly flawed. It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions.

Alleles↗

PubMed2003

Synthesis and evaluation of dopamine and serotonin transporter inhibition by oxacyclic and carbacyclic analogues of methylphenidate.

Methylphenidate (Ritalin) binds stereoselectively and enantioselectively to the dopamine transporter (DAT) and inhibits dopamine reuptake with in vitro and in vivo potency similar to that of cocaine. Unlike cocaine, it manifests little, if any, tolerance or addiction liability. Since this compound has a substantial clinical history, it provides an excellent template from which to design potential medications for cocaine abuse. It has long been assumed that a nitrogen, such as exists in cocaine and methylphenidate, is essential for interaction with monoamine transporters. We previously demonstrated that an amine nitrogen in phenyltropane analogues of cocaine is not necessary for conferring high DAT binding affinity. We now report the synthesis of oxacyclic and carbacyclic analogues of methylphenidate, including the four enantiomerically pure isomers of 2-(3,4-dichlorophenyl)-2-(tetrahydropyran-2-yl)acetic acid methyl ester. The threo isomers are potent and selective inhibitors of the DAT. This is the first generalization of the principle that the presence of nitrogen is not a necessity for DAT inhibition.

Animals↗

PubMed2002

ProbeMatchDB--a web database for finding equivalent probes across microarray platforms and species.

SUMMARY: ProbeMatchDB is a web-based database designed to facilitate the search of EST/cDNA sequences or STS markers that can be used to represent the same gene across different microarray platforms and species. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms. AVAILABILITY: The database is accessible at http://brainarray.mhri.med.umich.edu/MARRAY/BC_ASP/brainarray.htm by clicking the 'Query ProbeMatchDB' link.

Animals↗