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Approaches to dimensionality reduction in proteomic biomarker studies

M. Hilario, A. Kalousis
2007 Briefings in Bioinformatics  
This article reviews dimensionality reduction methods that have been used in proteomic biomarker studies.  ...  A major data-analytical problem involved is the extremely high dimensionality (i.e. number of features or variables) of proteomic data, in particular when the sample size is small.  ...  The goal of this article is to review current approaches to DR in mass-spectra based proteomic biomarker identification; Table 1 gives a synoptic view of these different approaches.  ... 
doi:10.1093/bib/bbn005 pmid:18310106 fatcat:57agd2jsajgezlieq7hz4r26dm

Invited Commentary on "Potential Circulating Biomarkers for Abdominal Aortic Aneurysm Expansion and Rupture - a Systematic Review" by Urbonavicius et al

M.J. Bown, R.D. Sayers
2008 European Journal of Vascular and Endovascular Surgery  
such as dimension reduction techniques 8 and genetic algorithms. 9 If proteomic approaches are to be used in the future the need for bioinformatic support must be considered.  ...  In the future it is likely that research in this area will adopt dual approaches of descriptive proteomics studies and hypothesis based approaches.  ... 
doi:10.1016/j.ejvs.2008.06.007 fatcat:3564th2n3bbqnax7fygl7ye6mq

A data-mining approach to biomarker identification from protein profiles using discrete stationary wavelet transform

Hussain Montazery-Kordy, Mohammad Hossein Miran-Baygi, Mohammad Hassan Moradi
2008 Journal of Zhejiang University SCIENCE B  
As a dimensionality reduction procedure, the hard thresholding method was applied to reduce the number of wavelet coefficients.  ...  Conclusion: The results have shown that the new bioinformatic tool can be used in combination with the high-throughput proteomic data such as SELDI-TOF MS to find the potential biomarkers with high discriminative  ...  In our study, we have developed a data-mining approach based on discrete stationary wavelet transform (DSWT) and discriminant analysis to find highly accurate biomarkers from proteomic profiles.  ... 
doi:10.1631/jzus.b0820163 pmid:18988305 pmcid:PMC2579949 fatcat:erp6urbt5vg3nfeuqaueklxylm

Concept of Toxicoproteomics in Identifying Biomarkers of Toxicant Action

Yogeshwer Shukla
2012 Journal of Proteomics & Bioinformatics  
Additional modifications of MS/MS with closely integrated multi-dimensional separation schemes will continue to dominate proteomic analysis for identification and quantification and will result in following  ...  Other disparities on the LC-MS/MS method, closely linking LC separation to MS/MS instruments, have unified isotopic labelling approaches for protein quantitation and in-depth proteomic profiling of samples  ... 
doi:10.4172/jpb.100000e7 fatcat:mc7l7g6vobbgjjfzp4xoxxhwni


2013 Biocomputing 2014  
However, they face acute challenges from a data reproducibility standpoint, in that no two independent studies have been found to produce the same proteomic patterns.  ...  In this work, we propose a profile biomarker approach to overcome this problem from a machine-learning viewpoint by developing a novel derivative component analysis (DCA).  ...  Conclusions and Discussion In this study, we propose a profile biomarker diagnosis approach to overcome the data reproducibility issue in proteomics data and demonstrate its clinical level performances  ... 
doi:10.1142/9789814583220_0033 fatcat:dggtjeiri5allol7uyihiclq2y

A Parallel Approach to Identifying Biomarkers

KB Tomer
2003 Environmental Health Perspectives  
to identify biomarkers.  ...  Proteomics platforms appear particularly well suited for biomarker development in blood because the appearance of new polypeptides in the serum proteome may reveal early-stage disease and organ toxicity  ... 
doi:10.1289/ehp.111-1241639 pmid:12940285 pmcid:PMC1241639 fatcat:2a2hhibbizcrzepjf27hg2tmjm

Proteomics Approach and Techniques in Identification of Reliable Biomarkers for Diseases

Raed Abdullah Alharbi
2020 Saudi Journal of Biological Sciences  
So, different researches and studies that used proteomics approach to identify different biomarkers for different diseases were reviewed.  ...  Proteins are considered as a type of biomarkers based on their characteristics. Therefore, proteomics approach is one of the most promising approaches in this field.  ...  Acknowledgments The author would like to thank Deanship of Scientific Research at Majmaah University, Al Majmaah, 11952, Saudi Arabia for supporting this work under the Project Number R-1441-65.  ... 
doi:10.1016/j.sjbs.2020.01.020 pmid:32127776 pmcid:PMC7042613 fatcat:hlwg64varzbdznxqki4e4honfu

Proteomics strategies for target identification and biomarker discovery in cancer

Uros Rajcevic
2009 Frontiers in Bioscience  
Using fluorescent labels, two-dimensional differential in-gel electrophoresis (2D-DIGE) has been successfully applied to study mechanisms of tumor (10), biomarkers in plasma and serum (11) (12) (13)  ...  BIOMARKER DISCOVERY IN BIOFLUIDS Due to the complexity and large dynamic range of protein levels in biofluids, for large scale protein identification, multi-dimensional separationbased approaches at the  ... 
doi:10.2741/3452 pmid:19273274 fatcat:z3qcfxvchfd7pne6v7h5hqqeti

Proteomic Strategies in the Search of New Biomarkers in Atherothrombosis

José Tuñón, José Luis Martín-Ventura, Luis Miguel Blanco-Colio, Óscar Lorenzo, Juan Antonio López, Jesús Egido
2010 Journal of the American College of Cardiology  
For such approaches, it is not necessary to study the published data to select potential biomarkers.  ...  Novel proteomic approaches make it possible to compare the expression of hundreds of proteins in several samples in a single experiment.  ...  Proteomic approaches combine 2-dimensional electrophoresis (2DE) and mass spectrometry (MS), allowing hundreds of proteins in a given sample tissue to be assayed simultaneously (3) (Fig. 1) .  ... 
doi:10.1016/j.jacc.2010.01.036 pmid:20447523 fatcat:w4736722jbeshmcelfem4sxeom

Integrated Chemometrics and Statistics to Drive Successful Proteomics Biomarker Discovery

Anouk Suppers, Alain van Gool, Hans Wessels
2018 Proteomes  
In this review, we focus on the biomarker selection process and critically discuss the chemometrical and statistical decisions made in proteomics biomarker discovery to increase to selection of high value  ...  Here we review multiple chemometrical and statistical methods for their value in proteomics-based biomarker discovery and propose to include key components in scientific documentation.  ...  Acknowledgments: The authors wish to thank Dirk J. Lefeber and Monique van Scherpenzeel for fruitful discussions and valuable suggestions.  ... 
doi:10.3390/proteomes6020020 pmid:29701723 pmcid:PMC6027525 fatcat:vseoqjteardtxmu7rhgdkbl6xi

Cancer Biomarker Discovery: Speed-bumps and Tire Shredders

Michael A. Tainsky, Michael A. Tainsky
2010 Cancer Biomarkers  
The ease of obtaining such high dimensional data and the throughput of these approaches to discover cancer-specific changes in various molecular moieties belie the difficulties in the full development  ...  One only needs to look at the standard approaches to biomarker discovery to identify specimens as the major barrier to arriving at sensitive and specific biomarker panels for each clinical application.  ...  The ease of obtaining such high dimensional data and the throughput of these approaches to discover cancer-specific changes in various molecular moieties belie the difficulties in the full development  ... 
doi:10.3233/cbm-2009-0147 pmid:20938083 fatcat:hww5uuybi5fxxflqgdmdnrgrca

Proteomic Profiling of Pancreatic Cancer for Biomarker Discovery

Ru Chen, Sheng Pan, Teresa A. Brentnall, Ruedi Aebersold
2005 Molecular & Cellular Proteomics  
In recent years, there has been a substantial interest in applying proteomics technologies to identify protein biomarkers for early detection of cancer.  ...  In this article, we discuss recent progress and challenges for applying quantitative proteomics technologies for biomarker discovery in pancreatic cancer.  ...  With recent progress in 2-DE and MS, several groups have started to employ a proteomics approach to study pancreatic juice.  ... 
doi:10.1074/mcp.r500004-mcp200 pmid:15684406 fatcat:suube6tkybdttebqyatp3kmghq

Proteomics of the Salivary Fluid [chapter]

Goran Mitulović
2019 Salivary Glands - New Approaches in Diagnostics and Treatment  
So far, more than 3000 proteins have been identified in different studies and more is to come with new instrumentation and methods available.  ...  Following the sequencing of the human genome, the mapping of the human proteome is the next task to being completed in order to gain knowledge on how proteins are involved in disease genesis, growth, therapy  ...  An important finding of the study was achieved in the prediabetic saliva: Salivary biomarkers of established Diabetes Mellitus were identified by proteomic profiling to be also differentially abundant  ... 
doi:10.5772/intechopen.72309 fatcat:svqjsjapzfa75itkp3ndg5p6uu

Clinical proteomics and OMICS clues useful in translational medicine research

Elena López, Luis Madero, Juan López-Pascual, Martin Latterich
2012 Proteome Science  
Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage.  ...  Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems  ...  study design when performing studies involving clinical samples in biomarker studies.  ... 
doi:10.1186/1477-5956-10-35 pmid:22642823 pmcid:PMC3536680 fatcat:qigbjg5yqfgd3bzsj53bocrewe

Proteomic technology for biomarker profiling in cancer: an update

Moulay A. Alaoui-Jamali, Ying-jie Xu
2006 Journal of Zhejiang University SCIENCE B  
This review is to update the current research efforts in high-resolution proteomic technology for discovery and monitoring cancer biomarkers.  ...  Clearly, there is urgent need to unravel novel biomarkers for early detection. Most of the functional information of the cancer-associated genes resides in the proteome.  ...  Therefore, studying the cancer proteome is the logical starting point for identifying diagnostic biomarkers and therapeutic targets for cancer.  ... 
doi:10.1631/jzus.2006.b0411 pmid:16625706 pmcid:PMC1473998 fatcat:lo6w5gr3preanieoa6r3jnlhj4
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