PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system

<p>Abstract</p> <p>Background</p> <p>In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results in an increasing amount of proteome data. This data must be archived and analysed using specialized bioinformatics tools.</p> <p>Description</p> <p>We herein describe "PARPs database," a data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics. PARPs database is a web-based tool whose features include experiment annotation, protein database searching, protein sequence management, as well as data-mining of the peptides and proteins identified.</p> <p>Conclusion</p> <p>Using this pipeline, we have successfully identified several interactions of biological significance between PARP-1 and other proteins, namely RFC-1, 2, 3, 4 and 5.</p

Nck2 promotes human melanoma cell proliferation, migration and invasion in vitro and primary melanoma-derived tumor growth in vivo

<p>Abstract</p> <p>Background</p> <p>Nck1 and Nck2 adaptor proteins are involved in signaling pathways mediating proliferation, cytoskeleton organization and integrated stress response. Overexpression of Nck1 in fibroblasts has been shown to be oncogenic. Through the years this concept has been challenged and the consensus is now that overexpression of either Nck cooperates with strong oncogenes to transform cells. Therefore, variations in Nck expression levels in transformed cells could endorse cancer progression.</p> <p>Methods</p> <p>Expression of Nck1 and Nck2 proteins in various cancer cell lines at different stages of progression were analyzed by western blots. We created human primary melanoma cell lines overexpressing GFP-Nck2 and investigated their ability to proliferate along with metastatic characteristics such as migration and invasion. By western blot analysis, we compared levels of proteins phosphorylated on tyrosine as well as cadherins and integrins in human melanoma cells overexpressing or not Nck2. Finally, in mice we assessed tumor growth rate of human melanoma cells expressing increasing levels of Nck2.</p> <p>Results</p> <p>We found that expression of Nck2 is consistently increased in various metastatic cancer cell lines compared with primary counterparts. Particularly, we observed significant higher levels of Nck2 protein and mRNA, as opposed to no change in Nck1, in human metastatic melanoma cell lines compared with non-metastatic melanoma and normal melanocytes. We demonstrated the involvement of Nck2 in proliferation, migration and invasion in human melanoma cells. Moreover, we discovered that Nck2 overexpression in human primary melanoma cells correlates with higher levels of proteins phosphorylated on tyrosine residues, assembly of Nck2-dependent pY-proteins-containing molecular complexes and downregulation of cadherins and integrins. Importantly, we uncovered that injection of Nck2-overexpressing human primary melanoma cells into mice increases melanoma-derived tumor growth rate.</p> <p>Conclusions</p> <p>Collectively, our data indicate that Nck2 effectively influences human melanoma phenotype progression. At the molecular level, we propose that Nck2 in human primary melanoma promotes the formation of molecular complexes regulating proliferation and actin cytoskeleton dynamics by modulating kinases or phosphatases activities that results in increased levels of proteins phosphorylated on tyrosine residues. This study provides new insights regarding cancer progression that could impact on the therapeutic strategies targeting cancer.</p

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-2

Sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-1

) In the Mass Spectrometry section the user defines the parameters of the mass spectrometer; IPxxx is the identification of immunoprecipitation experience. (C) The Protein Identification section summarizes protein identifications, including protein accession number, entrez gene accession, number of peptides identified and a protein summary function; (D) The Protein Card Layout contains links to a variety of external public sources; (E) The Protein-Protein Interaction Viewer allows the user to display protein-protein interactions from internal and external (publicly available) data sources. The full-scale schema is available on-line as supplemental Figure.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system-0

Sequence assignments using different search engines and protein identifications using different methods of inference; (D) the annotations and results are loaded automatically into PARPs database for viewing, annotation and analyses.<p><b>Copyright information:</b></p><p>Taken from "PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system"</p><p>http://www.biomedcentral.com/1471-2105/8/483</p><p>BMC Bioinformatics 2007;8():483-483.</p><p>Published online 19 Dec 2007</p><p>PMCID:PMC2266781.</p><p></p