ChromSorter PC: a database of chromosomal regions associated with human prostate cancer.
BACKGROUND
Our increasing use of genetic and genomic strategies to understand human prostate cancer means that we need access to simplified and integrated information present in the associated biomedical literature. In particular, microarray gene expression studies and associated genetic mapping studies in prostate cancer would benefit from a generalized understanding of the prior work associated with this disease. This would allow us to focus subsequent laboratory studies to genomic regions already related to prostate cancer by other scientific methods. We have developed a database of prostate cancer related chromosomal information from the existing biomedical literature. The input material was based on a broad literature search with subsequent hand annotation of information relevant to prostate cancer.


METHODS
The database was then analyzed for identifiable trends in the whole scale literature. We have used this database, named ChromSorter PC, to present graphical summaries of chromosomal regions associated with prostate cancer broken down by age, ethnicity and experimental method. In addition we have placed the database information on the human genome using the Generic Genome Browser tool that allows the visualization of the data with respect to user generated datasets.


CONCLUSIONS
We have used this database as an additional dataset for the filtering of genes identified through genetics and genomics studies as warranting follow-up validation studies. We would like to make this dataset publicly available for use by other groups. Using the Genome Browser allows for the graphical analysis of the associated data http://www.prostategenomics.org/datamining/chrom-sorter_pc.html. Additional material from the database can be obtained by contacting the authors (mdatta@mcw.edu).
Etim
Ann
A
Department of Pathology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. aetim@mcw.edu
Zhou
Guohui
G
Wen
Xinyu
X
Liu
Hang
H
Ruotti
Victor
V
Twigger
Simon
S
Jin
Weihong
W
Matysiak
Brian
B
Mathis
Jedidiah
J
Tonellato
Peter J
PJ
Datta
Milton W
MW
D000367:Age Factors; D000368:Aged; D002877:Chromosomes, Human; D003196:Computer Graphics; D030541:Databases, Genetic; D006801:Humans; D008297:Male; D008875:Middle Aged; D011471:Prostatic Neoplasms / Q000208:ethnology / Q000235:genetics*