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Bioinformatics Advance Access originally published online on May 10, 2005
Bioinformatics 2005 21(14):3181-3182; doi:10.1093/bioinformatics/bti470
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SCHIP: statistics for chromosome interphase positioning based on interchange data

Sergi Vives 1, Bradford Loucas 2, Mariel Vazquez 3, David J. Brenner 4, Rainer K. Sachs 3, Lynn Hlatky 5, Michael Cornforth 2 and Javier Arsuaga 6,*

1Departmento de Estadistica, Universidad de Barcelona Barcelona 08028, Spain
2Radiation Oncology Department, University of Texas Medical Branch Galveston, TX 77555, USA
3Mathematics Department, University of California, Berkeley CA 94720, USA
4Center for Radiological Research, Columbia University NY 10032, USA
5Dana Farber Cancer Institute, Harvard Medical School Boston, MA 02115, USA
6Balmain Lab, Cancer Research Institute, Comprehensive Cancer Center, University of California San Francisco, CA 94115, USA

*To whom correspondence should be addressed.

Motivation: The position of chromosomes in the interphase nucleus is believed to be associated with a number of biological processes. Here, we present a web-based application that helps analyze the relative position of chromosomes during interphase in human cells, based on observed radiogenic chromosome aberrations. The inputs of the program are a table of yields of pairwise chromosome interchanges and a proposed chromosome geometric cluster. Each can either be uploaded or selected from provided datasets. The main outputs are P-values for the proposed chromosome clusters. SCHIP is designed to be used by a number of scientific communities interested in nuclear architecture, including cancer and cell biologists, radiation biologists and mathematical/computational biologists.

Availability: http://cramer.stat.ub.es/schip

Contact:jarsuaga{at}cc.ucsf.edu

Supplementary information: http://cramer.stat.ub.es/schip/help.htm

Received on January 28, 2005; revised on April 12, 2005; accepted on April 25, 2005

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