DNA MIcroarray-Assisted Modeling of Metabolic and Regulatory Networks With Applications to Bio-Defense
Abstract
During the course of the project four software tools for BioSPICE were developed. These include Network Component Analysis (NCA), GeneScreen, 1cDNA, and MIcroArray Experimental Spice (MIAMESpice). NCA uses available connectivity information between genes and transcriptional factors and gene expression level time course data (obtainable through DNA microarray experiments) to estimate parameters and infer a gene transcriptional network through a Matlab analysis routine. GeneScreen processes gene expression data with a collection of computational statistic routines to extract significant gene association patterns. 1cDNA estimates confidence intervals for messenger RNA, mRNA expression levels in microarray experiments, including elimination of extreme outliers, quality filtering, normalization of the log10 signal intensity ratios, and assessment of expression levels. MIAMESpice packages raw and normalized data files from a set of related microarray experiments, saving all associated data from an experiment (or set of experiments) into one archive file. Users can also enter experimental annotations, array design information, and array design files.
Document Details
- Document Type
- Technical Report
- Publication Date
- Sep 01, 2006
- Accession Number
- ADA457394
Entities
People
- James C Liao
- Vwani Roychawdhury
Organizations
- University of California Regents