Department of Computational Biology, St.Petersburg State Polytechnical University, 195251 St.Petersburg, Russia

BREReA - package for background removal, registration and averaging of quantitative gene expression data

This work is supported by NIH Grant RR07801 and RFBR grants 08-04-00712a, 09-04-001590-a

Description

BREReA package is designed to remove background from the one-dimensional patterns of segmentation gene expression in the early Drosophila embryo, to register them to reduce the variation in domain positions and to produce the reference data. The rationale behind this approach is the relative independence of segmentation gene expression from genes controlling the dorsoventral (D-V) patterning of the embryo. This allows us to consider the expression of segmentation genes in one dimension along the AP axis, which is a level of representation suitable for answering many important biological questions.

The key task, which BREReA performs, is the extraction of spatially localized characteristic features of expression patterns by means of spline approximation or fast redundant dyadic wavlet transform (FRDWT). To facilitate the feature extraction task we have developed an easy-to-use interactive graphical interface.

BREReA is a successor of GCPReg package.

1. Konstantin N. Kozlov, Ekaterina Myasnikova, Anastasia A. Samsonova, Svetlana Surkova, John Reinitz and Maria Samsonova (2009) GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly 3, 2,151-156.

2. K. Kozlov, E. Myasnikova, A.Pisarev, M. Samsonova and J. Reinitz (2002) A method for two-dimensional registration and construction of the two-dimensional atlas of gene expression patterns in situ. (2002) In Silico Biology, 2: 125-141, http://www.bioinfo.de/isb/2002/02/0011.

3. Ekaterina Myasnikova, Anastassia Samsonova, Konstantin Kozlov, Maria Samsonova, and John Reinitz. Registration of the expression patterns of Drosophila segmentation genes by two independent methods (2001). Bioinformatics, 17: 3-12.

Download BREReA (binary, x86_64)

Download BREReA manual (pdf)

Installation

Download BREReA and unpack the archive in your home directory, e.g to /your/home/QData.
Make sure that gnuplot and perl are installed on your workstation.

Running

Run BREReA with the command from the terminal:

[user@machine ~]$ /your/home/QData/bin/QData

Check here for latest RPMS and sources.

The tool is implemented with

gnuplot, gtk2+, Fedora Linux 11

Previous versions (here)