title: [Strategy of probe selection for studying mRNAs that participate in receptor-mediated apoptosis signaling].
abstract: Death receptors (DRs) and the participants of DR-mediated signaling are characterized by a large number of mRNA isoforms generated by alternative splicing. Due to their high labor intensity and high cost, conventional methods (RT-PCR and RT-PCR in real time) are ineffective when the simultaneous detection of a plurality of mRNA isoforms is needed. In this regard, the use of DNA biochips is has prospective applications in analyzing the expression of many genes simultaneously. In this paper, we suggest an optimal strategy of probes selection aimed at detecting the maximum number of mRNA splice variants generated by major participants of DR-signaling. The objects of the study were 185 genes that form 1134 mRNA isoforms. As a result, a biochip design was developed that enables the detection of 499 mRNA isoforms (44% of total mRNA splice variants). The proposed strategy combines a high degree of modularity, the use of modern high-performance computers, and broad opportunities for setting up the selection criteria in accordance with the objectives of the study.
authors.affiliation: Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, 603950 Russia.|solntsev.l.a@nniiem.ru.
authors.forename: L A
authors.initials: LA
authors.lastname: Solntsev
authors.affiliation: Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, 603950 Russia.
authors.forename: V D
authors.initials: VD
authors.lastname: Starikova
authors.affiliation: Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, 603950 Russia.
authors.forename: N A
authors.initials: NA
authors.lastname: Sakharnov
authors.affiliation: Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, 603950 Russia.
authors.forename: D I
authors.initials: DI
authors.lastname: Knyazev
authors.affiliation: Blokhina Scientific Research Institute of Epidemiology and Microbiology of Nizhny Novgorod, Nizhny Novgorod, 603950 Russia.|Nizhny Novgorod State Medical Academy, Nizhni Novgorod, 603005 Russia.
authors.forename: O V
authors.initials: OV
authors.lastname: Utkin
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D017209:Apoptosis / Q000235:genetics; D015342:DNA Probes / Q000737:chemistry / Q000378:metabolism*; D005091:Exons; D006801:Humans; D007438:Introns; D015335:Molecular Probes / Q000737:chemistry / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D053218:Receptors, Death Domain / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics
chemical_list: D015342:DNA Probes; D015335:Molecular Probes; D012322:RNA Precursors; D012333:RNA, Messenger; D053218:Receptors, Death Domain
keywords: DNA-microarray; algorithm Aho-Corasick; alternative splicing; apoptosis; death receptors; fetchGWI; mRNA