title: High-throughput protein analysis integrating bioinformatics and experimental assays.
abstract: The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins.
authors.affiliation: Division of Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany. c.delval@dkfz.de
authors.forename: Coral
authors.initials: C
authors.lastname: del Val
authors.forename: Alexander
authors.initials: A
authors.lastname: Mehrle
authors.forename: Mechthild
authors.initials: M
authors.lastname: Falkenhahn
authors.forename: Markus
authors.initials: M
authors.lastname: Seiler
authors.forename: Karl-Heinz
authors.initials: KH
authors.lastname: Glatting
authors.forename: Annemarie
authors.initials: A
authors.lastname: Poustka
authors.forename: Sandor
authors.initials: S
authors.lastname: Suhai
authors.forename: Stefan
authors.initials: S
authors.lastname: Wiemann
mesh_terms: D001331:Automation / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D020407:Internet; D016366:Open Reading Frames / Q000235:genetics; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D012984:Software
chemical_list: D018076:DNA, Complementary; D011506:Proteins