Search results for "INFORMATICS"
showing 10 items of 2542 documents
Expanding the protein catalogue in the proteome reference map of human breast cancer cells
2006
In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a c…
Detection of renal cell carcinoma-associated markers via proteome- and other 'ome'-based analyses
2004
Proteome analysis has rapidly developed in the post-genome era and is now widely accepted as the complementary technology for genetic profiling. It has been shown to be a powerful tool for studying human diseases and for identifying novel prognostic, diagnostic and therapeutic markers. This review focuses on the identification of new biomarkers and therapeutic targets for renal cell carcinoma using different 'ome'-based technologies.
Design of proteome-based studies in combination with serology for the identification of biomarkers and novel targets
2002
Recently proteome analysis has rapidly developed in the post-genome era and is now widely accepted as a complementary technology to genetic profiling. The improvement in the technology of both two-dimensional electrophoresis (2-DE) analysis as well as protein identification has made proteomics a valuable and powerful tool to study human diseases. A combination of conventional proteome analysis with serology has been developed as a promising experimental approach for the discovery of serological markers in different malignancies. However, the design of proteome-based studies has to be carefully performed since there are a number of critical needs for systematic and reproducible proteome anal…
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome
2013
All participating laboratories are members of ProteoRed-ISCIII.-- et al.
"Omics" of HER2-positive breast cancer.
2013
HER2/neu amplification/overexpression is the only somatic mutation widely considered to be a marker of disease outcome and response to treatment in breast cancer. Pathologists have made large efforts to achieve accuracy in characterizing HER2/neu status. The introduction of transtuzumab contributed to development of additional measures to identify sensitive and resistant subclasses of HER2/neu-positive tumors. In this article, we describe the latest advances in HER2/neu status diagnostic assessment and the most relevant research emerging from ‘‘Omics’’ (genomics, epigenetics, transcriptomics, and proteomics) studies on HER2/neu-positive breast cancer. A large quantity of biomarkers from dif…
Correlation of Crystallin Expression and RGC Susceptibility in Experimental Glaucoma Rats of Different Ages.
2018
Glaucoma is one of the leading causes of blindness worldwide with age being an important risk factor. However, the pathogenesis remains poorly understood. Aim of this study was to focus on age-dependent molecular changes in an experimental animal model of glaucoma.Intraocular pressure was elevated in Sprague-Dawley rats aged 3, 14, and 47 weeks for a period of 7 weeks by episcleral vein cauterization. Ganglion cell loss was monitored by an immunohistochemical staining of the Brain-specific homeobox/POU (Pit-1, Oct-2, Unc-86) domain protein 3A positive cells in retinal flat-mounts and spectral-domain optical coherence tomography measuring the retinal nerve fiber layer thickness. Molecular pr…
CiliaCarta: An integrated and validated compendium of ciliary genes
2019
The cilium is an essential organelle at the surface of mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse…
Building high-quality assay libraries for targeted analysis of SWATH MS data
2015
Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identification. Quality and coverage of these libraries are therefore of crucial importance for the performance of the methods. Here we present a detailed protocol that has been successfully used to build high-quality, extensive reference libraries supporting targeted proteomics by SWATH MS. We describe each step of the process, including data acquisition by discovery proteomics, assertion of peptide-spectrum matches (PSMs), generation of consensus sp…
Feasibility of shotgun urinary proteomics for investigating prematurely born preschoolers (PBP)
2016
Background: Preterms and twins are at higher risk of respiratory morbidity later in life. Advances in proteomic approaches may allow the characterization of biomarkers involved in respiratory diseases (Mauri et al. Imm. Lett. 2014;162:2-10). Gel-free approach quantitatively identify differentially expressed proteins in relation to physiopathological conditions (Mauri&Dehò, Meth Enzymology 2008;447:99-117). This can improve the clinical reliability of the next generation of biomarkers to discriminate multiple phenotypes of childhood respiratory diseases. Aim: To assess the ability of gel-free proteomics for identifying specific protein profiles related to PBP. Methods: Urine samples were…
Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis
2022
6 p.-2 fig.-2 tab.