Cross Chip Probe Matching Tool: A Tool For Linking Probes From Microarrays Within And Across Species
Advisory Committee Chair
Gary Grimes
Advisory Committee Members
Grier Page
Murat Tanik
Document Type
Thesis
Date of Award
2006
Degree Name by School
Master of Science in Electrical Engineering (MSEE) School of Engineering
Abstract
raditionally, but not exclusively, a microarray experiment is conducted on a single type of microarray. However, different labs often use different chip types, and new versions of chips may be developed. Comparing experiments can be problematic in such cases, as it is not always clear which probe sets correspond to the same gene across experiments. The goal of this research was to develop a tool that allows investigators to identify probe sets that correspond to the gene within and across species. The Cross Chip Probe Matching Tool (CCPMT) makes use of the probe sequences for all features on arrays from corporate literature, white papers, and corresponding documentation. Probes were assigned to a particular gene by using the Basic Local Alignment Search Tool (BLAST) developed at the National Center for Biotechnology Information (NCBI). The sequence alignment was achieved using database resources from The Arabidopsis Information Resource (TAIR), microarray vendor sequences, and The Institute for Genomic Research (TIGR) gene indices. For CCPMT the identification of the orthologous genes across species was performed by evaluating Eukaryotic Gene Orthologs (EGO) defined by TIGR. CCPMT allows investigators to combine data across multiple chip types and make better multi propositional inferences, as well as aiding in the meta-analysis of experiments.
Recommended Citation
Ghanekar, Ruchi, "Cross Chip Probe Matching Tool: A Tool For Linking Probes From Microarrays Within And Across Species" (2006). All ETDs from UAB. 3576.
https://digitalcommons.library.uab.edu/etd-collection/3576
