Bioinformatics Gene Expression and Transcriptome Analysis

Analytical and Computational Tools

• NIH Center for Human Immunology, Autoimmunity and Inflammation
• Cycas: RT-PCR Data Normalization Tool
  An RT-PCR data normalization tool that processes RT-PCR data and primer information to make annotation files, and analyzes the data.
• Gene Pattern (iGene Pattern)
• Human Immunology Project Consortium
  It capitalizes on recent advances in immune profiling methods to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s).
• Pathogen Portal RNA-Seq Pipeline (BRC)
• Seqbias
  Graphical per-position bias correction of quantitative sequence abundance in RNA-Seq experiments.
• TM4
  
  • Microarray Data Analysis System (MIDAS)
    MIDAS, a Java application, provides users an intuitive interface to design analysis protocols combining one or more normalization and filtering steps.
  • Microarray Data Manager (MADAM)
    MADAM guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses.
  • Multiexperiment Viewer (MeV)
  • TIGR Spotfinder
    This was designed for rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.

Databases and Data Sets

• ImmPORT Gene Lists
• Miminal Information About a Microarray Experiment (MIAME) Database
  The database is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.
• Influenza Microarray Data Sets
• Influenza Research Database
• Systems Approach to Immunology/Computational Core
  The Computational Core aggregates and integrates data from consortium Cores; constructs pipelines for automated data processing; disseminates consortium data to the scientific community.
• Systems Virology Agilent Microarray
• VectorBase Gene Expression
  VectorBase maintains a repository for all published and about-to-be-published microarray experiments pertaining to invertebrate vector species.

Visualization and Modeling Tools

• NIH Center for Human Immunology, Autoimmunity and Inflammation
• Gene Pattern (iGene Pattern)
• Single Nucleotide Polymorphism (SNP) Explorer
  Analysis and visualization of hyper-igm/cvid re-sequencing microarray data.
• TM4
  
  • Multiexperiment Viewer (MeV)
  • TIGR Spotfinder
    This was designed for rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.

Contact Information

For more information on Bioinformatics Gene Expression and Transcriptome Analysis, email:
Bioinformatics and Computational Sciences Branch