title: ProfileDB: a resource for proteomics and cross-omics biomarker discovery.
abstract: The increasing size and complexity of high-throughput datasets pose a growing challenge for researchers. Often very different (cross-omics) techniques with individual data analysis pipelines are employed making a unified biomarker discovery strategy and a direct comparison of different experiments difficult and time consuming. Here we present the comprehensive web-based application ProfileDB. The application is designed to integrate data from different high-throughput 'omics' data types (Transcriptomics, Proteomics, Metabolomics) with clinical parameters and prior knowledge on pathways and ontologies. Beyond data storage, ProfileDB provides a set of dedicated tools for study inspection and data visualization. The user can gain insights into a complex experiment with just a few mouse clicks. We will demonstrate the application by presenting typical use cases for the identification of proteomics biomarkers. All presented analyses can be reproduced using the public ProfileDB web server. The ProfileDB application is available by standard browser (Firefox 18+, Internet Explorer Version 9+) technology via http://profileDB.-microdiscovery.de/ (login and pass-word: profileDB). The installation contains several public datasets including different cross-'omics' experiments. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
authors.affiliation: MicroDiscovery GmbH, Marienburger Str. 1, D-10405 Berlin, Germany.
authors.forename: Chris
authors.initials: C
authors.lastname: Bauer
authors.affiliation: MicroDiscovery GmbH, Marienburger Str. 1, D-10405 Berlin, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Glintschert
authors.affiliation: MicroDiscovery GmbH, Marienburger Str. 1, D-10405 Berlin, Germany. Electronic address: johannes.schuchhardt@microdiscovery.de.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schuchhardt
mesh_terms: D000818:Animals; D014408:Biomarkers, Tumor / Q000032:analysis*; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D005260:Female; D006801:Humans; D055432:Metabolomics; D051379:Mice; D009363:Neoplasm Proteins / Q000032:analysis*; D040901:Proteomics; D012984:Software; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins
keywords: Cross-omics; Data analysis; Database