title: Evaluation of differentially expressed genes by a combination of cDNA array and RAP-PCR using the AtlasImage 2.0 software.
abstract: Evaluation of genes regulated differentially is essential for the development of therapeutic approaches in multifactorial diseases. To characterize gene expression profiles in multifactorial inflammatory and malignant diseases such as rheumatoid arthritis (RA) or colon adenoma (CA), RNA arbitrarily primed PCR (RAP-PCR) combined with cDNA array hybridization were performed and evaluated using an array-specific software.RNA of synovial fibroblasts from patients with RA and osteoarthritis (OA), and laser microdissected normal and colon adenoma tissue was used. RAP-PCR reactions were hybridized to cDNA array membranes. Arrays were analyzed by phosphor imaging, and the AtlasImage 2.0 software with different normalization settings. The AtlasImage 2.0 software was a useful tool to evaluate differentially expressed genes. However, software settings were needed to be optimized for every experimental approach and should be used without changes for all experiments. To compare RA vs. OA synovial fibroblasts and normal vs. CA expression patterns, global normalization using the sum method is recommended.
authors.affiliation: Department of Internal Medicine I, University Hospital Regensburg, D-93042, Regensburg, Germany.
authors.forename: Elena
authors.initials: E
authors.lastname: Neumann
authors.forename: Sandra
authors.initials: S
authors.lastname: Lechner
authors.forename: Ingo H
authors.initials: IH
authors.lastname: Tarner
authors.forename: Joachim
authors.initials: J
authors.lastname: Grifka
authors.forename: Steffen
authors.initials: S
authors.lastname: Gay
authors.forename: Josef
authors.initials: J
authors.lastname: Rüschoff
authors.forename: Birgit
authors.initials: B
authors.lastname: Renke
authors.forename: Jürgen
authors.initials: J
authors.lastname: Schölmerich
authors.forename: Frank
authors.initials: F
authors.lastname: Kullmann
authors.forename: Ulf
authors.initials: U
authors.lastname: Müller-Ladner
mesh_terms: D001168:Arthritis / Q000235:genetics / Q000378:metabolism*; D001172:Arthritis, Rheumatoid / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D003110:Colonic Neoplasms / Q000235:genetics / Q000378:metabolism*; D005347:Fibroblasts / Q000378:metabolism / Q000473:pathology; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010003:Osteoarthritis / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012984:Software; D013583:Synovial Membrane / Q000473:pathology