Abstract
Proteins are the principal mediators of the functions in the cell; therefore, any abnormal variations on their abundance levels may reflect the presence of pathological processes. In this sense, many researchers rely on the functional interpretation of protein lists generated by quantitative proteomics experiments to analyze, for instance, these variations in the context of diseases´ molecular basis and drug discovery. Since no analytical strategy or bioinformatics tool by itself is capable of extract all the information covered by a single experiment; herein we seek to provide the biologists with four groups of different but complementary bioinformatics tools for the functional interpretation of quantitative proteomics results. To this end we will review the basic concepts of a set of different bioinformatics approaches and we will give examples of freely available tools for each one of these approaches.
Keywords: Bioinformatics, biological network analysis, candidate gene prioritization, comparative proteomics, data interpretation, enrichment analysis, text mining.
Current Topics in Medicinal Chemistry
Title:Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results
Volume: 14 Issue: 3
Author(s): Teresa Nunez Villavicencio-Diaz, Arielis Rodriguez-Ulloa, Osmany Guirola-Cruz and Yasset Perez-Riverol
Affiliation:
Keywords: Bioinformatics, biological network analysis, candidate gene prioritization, comparative proteomics, data interpretation, enrichment analysis, text mining.
Abstract: Proteins are the principal mediators of the functions in the cell; therefore, any abnormal variations on their abundance levels may reflect the presence of pathological processes. In this sense, many researchers rely on the functional interpretation of protein lists generated by quantitative proteomics experiments to analyze, for instance, these variations in the context of diseases´ molecular basis and drug discovery. Since no analytical strategy or bioinformatics tool by itself is capable of extract all the information covered by a single experiment; herein we seek to provide the biologists with four groups of different but complementary bioinformatics tools for the functional interpretation of quantitative proteomics results. To this end we will review the basic concepts of a set of different bioinformatics approaches and we will give examples of freely available tools for each one of these approaches.
Export Options
About this article
Cite this article as:
Villavicencio-Diaz Nunez Teresa, Rodriguez-Ulloa Arielis, Guirola-Cruz Osmany and Perez-Riverol Yasset, Bioinformatics Tools for the Functional Interpretation of Quantitative Proteomics Results, Current Topics in Medicinal Chemistry 2014; 14 (3) . https://dx.doi.org/10.2174/1568026613666131204105110
DOI https://dx.doi.org/10.2174/1568026613666131204105110 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
Call for Papers in Thematic Issues
Medicinal Chemistry Advancement in Life-Threatening Diseases
The current issue will highlight concise reports that specify ground-breaking insights, including the novel discovery of drug targets and their action mechanism or drugs of novel classes. These are projected to encourage medicinal chemistry future efforts to address the most challenging medical needs. The current issue highlights further efforts to ...read more
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
Pharmacokinetic Profiles of Anticancer Herbal Medicines in Humans and the Clinical Implications
Current Medicinal Chemistry Editorial [Hot Topic: Oncohematology: From Bench to Bedside (Guest Editor: Vincenzo De Feo)]
Mini-Reviews in Medicinal Chemistry Therapeutic Application of Natural Medicine Monomers in Cancer Treatment
Current Medicinal Chemistry Biomolecules of Human Female Fertility - Potential Therapeutic Targets for Pharmaceutical Design
Current Pharmaceutical Design Anti-Cancer Drugs of Today and Tomorrow: Are we Close to Making the Turn from Treating to Curing Cancer?
Current Pharmaceutical Design Recent Developments of Magnetic Nanoparticles for Theranostics of Brain Tumor
Current Drug Metabolism Alpha-Emitters for Immuno-Therapy: A Review of Recent Developments from Chemistry to Clinics
Current Topics in Medicinal Chemistry CD95 Signaling in Cancer Treatment
Current Pharmaceutical Design Stable Indomethacin Dispersions in Water from Drug, Ethanol, Cationic Lipid and Carboxymethyl-Cellulose
Pharmaceutical Nanotechnology CD147 Promotes Melanoma Progression Through Hypoxia-Induced MMP2 Activation
Current Molecular Medicine Involvement of Cannabinoids in Cellular Proliferation
Mini-Reviews in Medicinal Chemistry Targeted Cancer Therapy; Nanotechnology Approaches for Overcoming Drug Resistance
Current Medicinal Chemistry The Beneficial Effects of Sulfur-containing Amino Acids on Cisplatininduced Cardiotoxicity and Neurotoxicity in Rodents
Current Medicinal Chemistry Exploring siRNA Umpired Nanogels: A Tale of Barrier Combating Carrier
Current Pharmaceutical Design Invariant Natural Killer T Cell-Based Therapy of Autoimmune Diseases
Current Immunology Reviews (Discontinued) Role of CNS Transporters in the Pharmacotherapy of HIV-1 Associated Neurological Disorders
Current Pharmaceutical Design Recent Progress in the Development of Synthetic Hybrids of Natural or Unnatural Bioactive Compounds for Medicinal Chemistry
Mini-Reviews in Medicinal Chemistry Patent Selections
Recent Patents on Biomarkers The Apoptosis Mechanism of Epirubicin Combined with BCG on Human Bladder Cancer Cells
Anti-Cancer Agents in Medicinal Chemistry State of Art and Recent Developments of Anti-Cancer Strategies Based on TRAIL
Recent Patents on Anti-Cancer Drug Discovery