iPath™ - Online functional genomics and proteomics research tool

In the post genome era, abundant information regarding the function of genes and proteins involved in the development of multiple diseases is becoming available at an ever increasing pace.

Genes and proteins involved in normal and diseased biological states can behave quite differently both at the molecular as well as the cellular level.

As a direct consequence, there is an increasing demand for means to understand these data in their biological context. In particular, pathway content is proving to be particularly useful in the interpretation of various types of experimental data, from high throughput expression analysis or identification of genes involved in regulation of cellular functions to identification of potential drug targets. For example, after statistical analysis of gene/protein expression microarray data, a long list of differentially expressed genes/proteins can be identified and patterns may emerge implicating involvement in specific biological pathways. At present, this downstream analysis requires extensive in-house bioinformatics expertise as well as access to a number of public and third party databases of proteomics pathways.

Also, scientists worldwide require access to such pathway information for proper planning of their experiments. Research projects often extend across numerous applications including for example cellular in-vitro and in-vivo assays, gene/protein characterization and expression, gene silencing, protein localization, protein-protein interaction. Therefore, complex experiments now need to be designed and interpreted at the systems biology level and a strong need is emerging for finding quickly and efficiently optimal products for specific research applications. As researchers tackle more complex and higher-throughput experiments by using an increasing number of methodologies, technology platforms, instruments and bioinformatics tools, it becomes harder for them to determine appropriate reagents for their needs.

What is iPath™?
In an effort to offer its customers fully integrated biological solutions, Invitrogen has developed iPath™, a comprehensive online resource for gene- and protein-based scientific research. iPath™ is a user-friendly, highly educational bioinformatics tool for the exploration of biological pathways, investigation of gene/protein function and selection of appropriate Invitrogen products for specific research needs. iPath™ provides easy access to 225 human cell signaling and metabolic pathways covering over 2,700 distinct genes/proteins, public sequence/experimental data resources and about 11,000 gene- an protein-related Invitrogen products.

Invitrogen has licensed from GeneGo the 225 maps of human biological pathways (mostly signaling pathways) used to create iPath™. GeneGo’s scientists have spent years combing peer-reviewed journal articles to put together these comprehensive maps, which have been constructed based on a highly sophisticated procedures that employ natural language processing, artificial intelligence and manual scientific curation.

Invitrogen’s R&D BioInformatics scientists have deconvoluted the relationship between various gene names/symbols, various types of IDs, synonyms, protein complexes, and normalized all of them to a specific set of reference sequence IDs. Then based on this information, we have identified corresponding reagents that map to each given gene/protein on a pathway.

Invitrogen has created an easy-to-use web interface where worldwide customers can search and browse the content of the 225 maps and easily identify specific pathways relevant to their research. Gene and protein content associated to our iPath™ maps can be searched for using a wide variety of criteria including keyword, gene/protein Accession Number, Gene Symbol, Gene ID, UniGene ID, SwissProt ID, UniProt ID, Ensembl ID, InterPro ID, OMIM ID, Affymetrix probe set ID, Agilent probe ID, GE Amersham probe ID, and Invitrogen catalog number. For example, scientists can upload their protein or DNA expression microarray gene/proteins IDs (even in a batch search mode) and map them to relevant proteomics pathways.

Pathway related data is presented in an easy-to-use format with additional information just a click away. Along the way, customers will have available at their fingertips extensive bioinformatics information and resources including access to public databases such as NCBI (National Center for Biotechnology Information), PubMed references, transcript maps, Microarray, SAGE (Serial Analysis of Gene Expression) and Virtual Northern experimental data from The Cancer Genome Anatomy Project, etc. Pathways developed by KEGG (Kyoto Encyclopedia of Genes and Genomes) are also accessible from iPath™, covering an additional 2020 genes/proteins mostly involved in metabolic processes.

Also, easily accessible through iPath™ are Invitrogen’s proprietary bioinformatics tools for biomolecule design such as BLOCK-iT™ RNAi Designer (winner of the 2004 Frost & Sullivan Excellence in Research Award), D-LUX™ Designer for Q-PCR primers, PeptideSelect™ Designer for designing peptides from a protein target sequence.

A rich selection of about 11,000 optimal Invitrogen products that match a particular genes or proteins of interest is also easily available. Products featured on iPath™ include Stealth Select and validated Stealth RNAi molecules, Ultimate ORF and MGC clones, certified LUX and LUX Select Q-PCR primers, proteins (kinases & phosphatases), antibodies, biochemical assays. Unlike a standard catalog, iPath™ takes advantage of Invitrogen’s global e-commerce system to provide technologies and reagents in the context of the real biological question that a customer is asking. This way, iPath™ also offers the convenience of purchasing directly online all products featured on iPath™ as well as any of the other Invitrogen products in a single shopping cart.

Future Plans
Invitrogen plans to further enlarge the content of the system in collaboration with GeneGo and the agreement could actually increase the potential market for GeneGo's products, especially within the academic sector. Researchers could use iPath as a gateway to pathway analysis and may eventually purchase a more sophisticated application like MetaCore that they wouldn't have even been aware of otherwise.

Also, Invitrogen plans to expand its offering of free application-based BioInformatics tools beyond pathways. In particular, our company plans to utilize a similar framework into areas of biological research protocols and workflows as well as search. Using a very simple interface, all Invitrogen‘s gene/protein based reagents and technologies will be matched to a specific nucleotide/aminoacid sequence, allowing our product content to be fully searchable and quickly accessible.