PathwayWorld is a dedicated free online resource to guide researchers towords exploring and analysing experimental data in the context of biological pathways.
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Editor's Note:
> Background
The sequencing of the human genome has inspired the development of several high-throughput techniques that help us analyze the expression changes in large number of genes and proteins simultaneously. Hierarchy of molecular events that can be represented as biological pathways probably connects the genes and proteins that show synchronous alterations in expression. Constructing interaction networks between these co-regulated genes and proteins could provide deeper insights into the molecular mechanisms of the complex biological processes and is a natural preference for downstream analysis in gene expression studies.
> Motivation
In order to assist researchers to analyze and explore their genomic data in the context of biological pathways, we have created a unique open-source web based resource - Pathway-World. This pathway portal hosts thousands of hypothetical molecular interaction maps. Each map represents the hierarchy of molecular interactions between genes changing expression in a given experiment.
> Maps
A first-cut analysis of all available microarray datasets has been performed using automation of Strand’s proprietary data mining platform, AVADIS™. We have converted thousands of these gene lists into biologically relevant interaction maps. Each map is a collection of genes depicted as nodes and their molecular interactions as edges. The depicted interactions between the genes are derived from Strand’s proprietary molecular interactions database. This database contains information on N molecular interactions between proteins that have been extracted primarily from published scientific literature using Natural Language Processing (NLP). A second source of molecular interactions data is found under the International Molecular Exchange consortium (IMEX) which forms a repository of high throughput physical interactions experiments.
Strand Life Sciences’ Pathway-World is an innovative resource for life scientists and clinical researchers. The key feature that distinguishes pathways contained in Pathway-World is that each network represents a testable hypothesis where every gene in a given pathway can now be a guide to exploring the mechanistic context of the expression results. Genes differentially expressed in several different experiments can converge various biological conditions, thus providing novel molecular understanding of diseases.
> Contrast
In addition, Pathway-World presents the genomic community with a forum for discussions and exchange of ideas, sharing data and also highlights seminal publications in the field.
