HSLS Update

HSLS Biological Pathway Analysis Resources

Research in biological sciences is moving from single gene or protein-focused investigation to biological systems-based research. Advances in high-throughput (HT) technologies such as microarrays and protein arrays -- the major driving force for this change -- are producing large-scale data sets of genes or proteins. 

The biological significance of these 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 the large data sets of genes or proteins with knowledge drawn from the published literature. The number of articles andjournals published is increasing at a notable rate, so much so that it has become impossible to manually analyze the HT results set. To help biologists  with this challenging task, databases of gene or protein information culled from published literature are being created by either:
•  Text mining algorithms (e.g., natural language processing (NLP)) technologies, or
•  Expert human curation.

Researchers routinely use NLP and human-curated databases for HT data analysis. Some prefer NLP driven tools, which promise broader coverage of published knowledge due to their automated scientific fact-extraction feature. Others prefer human-curated databases for their high level of quality control.

HSLS Provides Tools for HT Results Analysis

HSLS is pleased to offer access to three HT results analysis software products. These are Ingenuity Pathways Analysis from Ingenuity Systems Inc., PathwayArchitect from Stratagene, and PathwayStudio from Ariadne Genomics.  While Ingenuity offers a high quality expert-curated datasource, both Stratagene and Ariadne deliver NLP driven databases. Researchers can easily find the biological significance of their HT expression data sets by using these tools to:
•  Identify biological interactions among genes of interest from the published literature and link to the supporting sentences in the matching journal article citations (for articles available online through PubMed);
•  Connect two molecules by the shortest possible path;
•  Import a list of genes and arrange them into a pathway;
•  Import expression results and display as a heat map, as well as a pathway map;
•  Find common upstream and downstream regulators of a gene;
•  Display array results according to subcellular localization.

Each tool has its own strengths and weaknesses, and noteworthy features are listed below.

Ingenuity Pathways Analysis (IPA) 3.1 is a Web-based software
application that enables biologists to identify the biological mechanisms, pathways and functions most relevant to their HT expression experimental datasets or genes of interest. For examples of IPA use in a wide range of research applications and peer-reviewed articles see <www.ingenuity.com/solutions/ssolutions.html>.

System requirements and a link for registration to download IPA are at <www.hsls.pitt.edu/guides/genetics/ipa/>.

PathwayArchitect helps you to interpret experiment results in the context of pathways, gene regulation networks, and protein interaction maps. Using curated and automatically created databases, PathwayArchitect identifies relationships among genes, small molecules, cell objects and processes; builds networks; and creates publication-quality pathway diagrams.

The HSLS license for Pathway Architect will support five simultaneous users. Link to system requirements and register to download at <www.hsls.pitt.edu/guides/genetics/pathwayarchitect/index_html>.

PathwayStudio (formerly known as  PathwayAssist) helps to interpret experimental HT expression results in the context of pathways, gene regulation networks and protein interaction maps. You can interpret microarray and proteomics data, classify and prioritize proteins, draw pathway diagrams, export, import, and filter data, and automatically update your pathways with newly published facts. The software includes ResNet, a proprietary database of more than one million  functional  relationships automatically extracted from scientific literature.

HSLS has three distributable static licenses for PathwayStudio. Link to system requirements and register to download at: <www.hsls.pitt.edu/guides/genetics/pathwaystudio>.

HSLS offers hands-on workshops and group or individual consultations
for  these  resources.  See <www. hsls.pitt.edu/guides/genetics/> or contact Ansuman Chattopadhyay at ansuman@pitt.edu or 412-648-1297.

--Ansuman Chattopadhyay