Stephanopoulos:ALSYSTA

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ALSYSTA - Systems Analysis Software for Win98, ME, 2k, NT & XP.

Outline:

ALSYSTA is a software suite that includes a series of tools for the analysis of different aspects of biological systems, such as the expression phenotype and the metabolic flux profiles of cells, as well as various tools to search web based databases.

The "Projection" moiety uses either Principal Component Analysis (PCA) - with various filtering tools, or Fisher Discriminant Analysis (FDA), to project gene expression data into a reduced dimensional space. This enables one to find patterns and structure in the expression phenotype which can be used either to reduce the gene set into fewer discriminatory gene, or facilitate further analysis.

With the "Metabolic Analysis" moiety it is possible to draw a reaction network, with detailed carbon transition information, and automatically generate a stoichiometry matrix from the drawing itself, which can then be passed on to external programs for tracer experiment simulation and analysis.

Downloads:

Supporting Papers:

  1. Hwang D, Schmitt WA, Stephanopoulos G, and Stephanopoulos G. Determination of minimum sample size and discriminatory expression patterns in microarray data. Bioinformatics. 2002 Sep;18(9):1184-93. PubMed ID:12217910 | HubMed [66]
  2. Stephanopoulos G, Hwang D, Schmitt WA, Misra J, and Stephanopoulos G. Mapping physiological states from microarray expression measurements. Bioinformatics. 2002 Aug;18(8):1054-63. PubMed ID:12176828 | HubMed [65]
  3. Misra J, Schmitt W, Hwang D, Hsiao LL, Gullans S, Stephanopoulos G, and Stephanopoulos G. Interactive exploration of microarray gene expression patterns in a reduced dimensional space. Genome Res. 2002 Jul;12(7):1112-20. DOI:10.1101/gr.225302 | PubMed ID:12097349 | HubMed [64]
All Medline abstracts: PubMed | HubMed


Sample Data Sets:

  • PCA Analysis: Jatin Misra et. al. Paper:Expression measurements of 6972 genes made from 40 normal human tissue samples using Affymetrix GeneChips; from Brigham & Women's Hospital, Boston - Tab-delimited text file


  • FDA Analysis and Cross Validations: Gr. Stephanopoulos et. al.; and Daehee Hwang et. al. Papers:Expression measurements of 7070 human genes measured in samples from patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) (Golub et al., 1999). The ALL samples are further subdivided into B-lineage ALL and T-lineage ALL classes - Tab-delimited text file format ; Test case for classification (single microarray experiment) - text file.



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