Pathway Analysis

All biological components in the human body (from genes and proteins to organs) work together, and their aim is to allow for normal growth and to sustain health. This is made possible with the use of a biological network of pathways which allow genes, molecules and cells to communicate with each other in a very intricate way. The study of biological pathways is a new field which is rapidly growing, but there are still many pathways that have not yet been discovered. Further research is also required in order to discover how these pathways are integrated in the human body. It is also vital to learn how damages to these pathways may lead to a disease and what can be done in order to repair these pathways or at least to prevent them from being damaged in the first place.

MedicWave's aim is to provide researchers with novel analytical tools that will help to better understand the metabolic components and networks within a cell (metabolome). We focus on developing bioinformatics tools that can measure local concentrations of components (i.e. amino acids, carbohydrates, and other metabolites) within a cell in order to detect metabolic differences between normal and diseased cells. We believe that with the help of Pathway Analysis it will be possible to create biological models which can be used to detect the presence of a disease within the human body at an early stage. Such information will be crucial in biomedical research aimed for more precise diagnosis, prevention, and treatment of a wide assortment of known diseases.

From Reductionism to Systems Biology

High-throughput Proteomics data analysis has started to undergo a phase transition from Reductionism to Systems Biology. The Systems Biology approach, known as Pathway Analysis (PA), is rapidly gaining strength in Proteomics. Within a few years time most proteomics researchers will be routinely employing PA.

The future of medicine lies in personalized diagnostics, in which patient´s personal data help stratify the disease, select optimal therapy and monitor its progress. Personalized approach requires more than just genotyping, as genotype is roughly constant over lifetime. Personalized diagnostics requires short- and middle-term molecular information in form of quantitative proteome and metabolome LC/MS measurements.

The Pathway Search Engine (PSE)

The Pathway Search Engine (PSE) is a software tool that converts the top-proteome (metabolome) data from LC/MS measurements into a list of up- and down-regulated signaling (metabolic) pathways. The pathway information is easily understood in terms of such biological processes as cell death (apoptosis), proliferation, inflammation, etc. Biomarkers are thus searched not among molecules but among pathways or pathway patterns. All pathways are the same for all humans. Thus pathway biomarkers will also be common, although the identities and concentrations of molecules measured by LC/MS are person-dependent.

Publications concerning Pathway Analysis

  • "Identification of dominant signaling pathways from proteomics expression data", Roman A. Zubarev, Michael L. Nielsen, Eva M. Fung, Mikhail M. Savitski, Olga Kel-Margoulis, Edgar Wingender, Alexander Kel, JOURNAL OF PROTEOMICS 71 (2008) 89–96

PathProt

Pathway Analysis is a Systems Biology approach which is rapidly gaining strength in Proteomics.

PathProt-III 2010

PathProt-III will occur on the 15-17th of October 2010.

PathProt-II 2009

On the 14-16th of October 2009, MedicWave attended the second Pathway Analysis conference (PathProt-II) which took place in Oeiras, Portugal. The meeting focused on toxicity and safety problems in what concerns their possible assessment via pathways and networks.

PathProt-I 2008

On the 8-10th of November 2008, MedicWave attended the first Pathway Analysis conference (PathProt-I) which took place in Oeiras, Portugal. The meeting exceeded all expectations, both in terms of enthusiastic participation (85 participants) as well as the breadth and depth of the problems discussed.

PathProt-I: A dedicated forum for Pathway Analysis-related research.