Sat, 26 Jul 2008 06:37:01 BST CiteULike: jyuh's Antonov http://www.citeulike.org/user/jyuh/author/Antonov CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/jyuh/article/2782593 <i>Nucleic acids research (6 May 2008)</i><br /><br />ProfCom is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of 'complex functions'. A 'Complex function' is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. ProfCom provides a user friendly dialog-driven web page submission available for several model organisms and supports most available gene identifiers. In addition, the web service interface allows the submission of any kind of annotation data. ProfCom is freely available at http://webclu.bio.wzw.tum.de/profcom/. ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Alexey V Antonov Thorsten Schmidt Yu Wang Hans W Mewes Nucleic acids research (6 May 2008) 2008-05-10T08:46:46-00:00 2008 Nucleic acids research 1362-4962 no-tag http://www.citeulike.org/user/jyuh/article/2742269 <i>BMC medical genomics, Vol. 1 (2008)</i><br /><br />ABSTRACT: BACKGROUND: Molecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge. RESULTS: We present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97. CONCLUSION: We developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor. Expression profiling with RNA from formalin-fixed, paraffin-embedded material. A Oberli V Popovici M Delorenzi A Baltzer J Antonov S Matthey S Aebi HJ Altermatt R Jaggi doi:10.1186/1755-8794-1-9 BMC medical genomics, Vol. 1 (2008) 2008-05-01T09:50:20-00:00 2008 BMC medical genomics 1755-8794 1 no-tag