A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis | Zendy

Mary E. Edgerton | Zendy; Ronald C. Taylor | Zendy; John Powell | Zendy; Lawrence Hunter | Zendy; Richard Simon | Zendy; Edison T. Liu | Zendy

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A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis

Author(s) -

Mary E. Edgerton,

Ronald C. Taylor,

John Powell,

Lawrence Hunter,

Richard Simon,

Edison T. Liu

Publication year - 2002

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/18.5.774

Subject(s) - biology , perl , computational biology , carcinogenesis , gene , human genome , ensembl , set (abstract data type) , genetics , genome , computer science , genomics , world wide web , programming language

One of the challenges to the effective utilization of cDNA microarray analysis in mouse models of oncogenesis is the choice of a critical set of probes that are informative for human disease. Given the thousands of genes with a potential role in human oncogenesis and the hundreds of thousands of mouse sequences available for use as probes, selection of an informative set of mouse probes can be an overwhelming task. We have developed a web based sequence mining tool using DataBase Independent (DBI) Perl to annotate publicly available sequences. The Mouse Oncochip Design Tool uses the Mouse Genome Database (MGD) developed and maintained by the Jackson Laboratories for mouse DNA sequences. There are over 380 000 sequences in their database. The output list has been ordered to present the genes more likely to be informative in a mouse model of human cancer using a candidate set of oncogenes to order the list. Mouse sequences that represent genes that are homologous with a member of a human oncogene set are listed first. In addition it provides a set of links for information on clone source gene function.

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