Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.
The R package ‘contamDE’ conducts differential expression (DE) analysis using high throughput next-generation RNA-seq read count data generated from contaminated tumor samples that are either matched or unmatched with normal samples, which estimates the proportion of pure tumor cells in each contaminated tumor sample, and provides tumor vs.
ALEXA is a microarray design platform for ‘alternative expression analysis’. This platform facilitates the design of gene expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites.