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SPACE: an algorithm to predict and quantify alternatively spliced isoforms using microarrays

Miguel A Anton1 email, Dorleta Gorostiaga1 email, Elizabeth Guruceaga1 email, Victor Segura1 email, Pedro Carmona-Saez2 email, Alberto Pascual-Montano3 email, Ruben Pio4,5 email, Luis M Montuenga4,6 email and Angel Rubio1 email

1CEIT and TECNUN, University of Navarra, San Sebastián, Spain

2Integromics SL, Madrid, Spain

3Computer Architecture Department, Facultad de Ciencias Físicas, Universidad Complutense de Madrid, Madrid 28040, Spain

4Center for Applied Medical Research, University of Navarra, Pamplona, Spain

5Department of Biochemistry, University of Navarra, Pamplona, Spain

6Department of Histology and Pathology, University of Navarra, Pamplona, Spain

author email corresponding author email

Genome Biology 2008, 9:R46doi:10.1186/gb-2008-9-2-r46

Published: 29 February 2008

Subject areas: Bioinformatics, Molecular biology, Genome studies


Additional files

Additional data file 1:

Figures S1-S8 show the structure of all genes and transcripts, as well as probe positions, that have been used to make the synthetic data in the simulations for the eight selected genes with SPACE algorithm. Figure S9 shows an example of the affinity, property and concentration matrices according to Wang et al.'s model. Figure S10 shows the results of applying SPACE algorithm to six arrays with two isoforms of CASP2 gene (synthetic data). Three of these simulated arrays had one concentration ratio and the other three the opposite ratio. Figures S11-S22 show the results obtained in the simulations done for 100 random genes selected from the human genome (synthetic data).

Format: PDF Size: 299KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

This zipped file includes the Matlab data files (.mat) for the three genes in Johnson et al.'s study and the code for the algorithms to predict number of transcripts, concentrations and structure. A convenient demo script file (demojohnson.m) is included to show how to use the functions.

Format: ZIP Size: 22KB Download file


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