• Are you engaged in basic science or translational research?
• Do your experiments include microarray expression, proteomics profiles, SNP/haplotype and mutation maps, or siRNA knockouts?
• Does your data include huge lists of genes or protein IDs?

Research in biological sciences has moved from primarily single gene-focused to biological systems-based experimentation. Advances in high-throughput (HT) technologies (e.g., protein or microarrays) are producing large-scale protein/gene data sets. The biological significance of these complex data sets can be uncovered by exploring biological pathways, functions, and molecular interactions associated with the genes or proteins derived from HT expression experiments. This requires systematic comparison of these large data sets with knowledge drawn from the published literature. The number of articles and journals published is increasing at an exponential rate, so much so that it is impossible to manually analyze the HT experimental results set. To help researchers with this challenging task, powerful systems biology tools commonly known as pathway analysis software have been developed. These tools search databases of gene or protein information culled from published literature.

The Molecular Biology Information Service at HSLS is pleased to offer access to major leading commercial pathway analysis packages. The list includes Ingenuity Pathways Analysis (IPA) from Ingenuity Systems, MetaCore from GeneGo, Inc., and PathwayArchitect from Stratagene.

IPA enables biologists and bioinformaticians to identify the biological mechanisms, pathways, and functions most relevant to their experimental datasets or genes of interest.

MetaCore is an integrated software suite for functional analysis of experimental data covering microarray & SAGE gene expression, SNPs & CGH arrays, proteomic, metabolomics, pathway analysis, yeast 2 hybrid, and other custom interactions.

PathwayArchitect uses curated and automatically created databases to identify relationships among genes, small molecules, cell objects, & processes, build networks, and create pathway diagrams suitable for publication.

Exploring your data with all three software packages serves to reinforce and provide confidence in your results. These tools can be used as complementary resources to:

  • discover biological and chemical information relevant to your research
  • explore context by building customized pathways, overlaying drug, biomarker and toxicity information, and computing cellular and molecular function
  • identify biological interactions among genes of interest from the published literature and link to the supporting sentences in the matching journal article citations
  • connect two molecules by the shortest possible path
  • import a list of genes and arrange them into a pathway
  • find common upstream and downstream regulators of a group of genes
  • display array results according to subcellular localization

To access these resources visit www.hsls.pitt.edu/guides/genetics/licensed_tools.

The HSLS Molecular Biology Information Service offers access information, hands-on workshops, and group or individual consultations for these resources. For more information, visit www.hsls.pitt.edu/guides/genetics or contact Ansuman Chattopadhyay (ansuman@pitt.edu, 412-648-1297) or Carrie Iwema (iwema@pitt.edu; 412-383-6887).

~ Ansuman Chattopadhyay and Carrie Iwema

Posted in the 2008 Issue