A tool-kit for cDNA microarray and promoter analysis | Zendy

Nigam H. Shah | Zendy; David King | Zendy; Prachi Shah | Zendy; Nina V. Fedoroff | Zendy

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A tool-kit for cDNA microarray and promoter analysis

Author(s) -

Nigam H. Shah,

David King,

Prachi Shah,

Nina V. Fedoroff

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg253

Subject(s) - computer science , normalization (sociology) , expediting , computational biology , standardization , promoter , set (abstract data type) , microarray analysis techniques , data mining , biology , information retrieval , genetics , gene , gene expression , programming language , engineering , systems engineering , sociology , anthropology , operating system

We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. It allows combining of result files into comprehensive data sets, evaluation of the quality of both technical and biological replicates and row and/or column standardization of data matrices. The second set supports mapping ESTs in the genome, identifying the corresponding genes and recovering their promoters, analyzing promoters for transcription factor binding sites, and visual representation of the results. The programs are designed primarily for Arabidopsis thaliana researchers, but can be adapted readily for other model systems. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/

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