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Bioinformatics Advance Access published online on May 10, 2005
Bioinformatics, 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@oupjournals.org
Received January 28, 2005
Revised April 12, 2005
Accepted April 25, 2005

Applications note

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*

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

* To whom correspondence should be addressed.
Javier Arsuaga, E-mail: jarsuaga{at}cc.ucsf.edu


  Abstract

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 data sets. 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.

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


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