Data

• Schizosaccharomyces pombe

The orginal data sets with missing values, described in the article of Rustici et al.⁽¹⁾, can be downloaded from the website of the Sanger Institute.

• Imputed data sets

The rows with more than 25% missing entries have been filtered out from each original expression matrix and any other missing expression entries have been imputed with the DTWimpute⁽²⁾ algorithm. The DTWimputed data sets can be downloaded from here.

• Transformed data sets

The data standardization algorithm has been applied to each imputed matrix. For each gene profile a varying number of neighboring gene profiles (R=0.2) has been identified and further used to calculate its standardized expression profile. The standardized data sets can be downloaded from here.

Software

The executable of the data standardization algorithm can be downloaded from here.

• Usage options:

GTETransformer <matrix> <R> <outfile>

<matrix> = matrix to be standardized

<R> = global radius (use R between 0.1 and 0.4)

<outFile> = file to receive the standardized matrix

 

---

(1) Rustici,G., Mata, J., Kivinen, K., Lio, P., Penkett, C. J., Burns, G., Hayles, J., Brazma, A., Nurse, P., Bähler, J. (2004) Periodic gene expression program of the fission yeast cell cycle, Nature Genetics, 36, 809-817.

(2) Tsiporkova,E. and Boeva,V. Two-pass imputation algorithm for missing value estimation in gene expression time series. Journal of Bioinformatics and Computational Biology, 5 5 (October 2007) 1005-1022.