title: Comparison of gene expression profiles produced by CAGE, illumina microarray and real time RT-PCR.
abstract: Several technologies are currently used for gene expression profiling, such as Real Time RT-PCR, microarray and CAGE (Cap Analysis of Gene Expression). CAGE is a recently developed method for constructing transcriptome maps and it has been successfully applied to analyzing gene expressions in diverse biological studies. The principle of CAGE has been developed to address specific issues such as determination of transcriptional starting sites, the study of promoter regions and identification of new transcripts. Here, we present both quantitative and qualitative comparisons among three major gene expression quantification techniques, namely: CAGE, illumina microarray and Real Time RT-PCR, by showing that the quantitative values of each method are not interchangeable, however, each of them has unique characteristics which render all of them essential and complementary. Understanding the advantages and disadvantages of each technology will be useful in selecting the most appropriate technique for a determined purpose.
authors.affiliation: Computational Science Research Program, RIKEN, Wako, Saitama, Japan. andrefujita@riken.jp.
authors.forename: André
authors.initials: A
authors.lastname: Fujita
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Seiya
authors.initials: S
authors.lastname: Imoto
authors.forename: Ayumu
authors.initials: A
authors.lastname: Saito
authors.forename: Emi
authors.initials: E
authors.lastname: Ikeda
authors.forename: Teppei
authors.initials: T
authors.lastname: Shimamura
authors.forename: Rui
authors.initials: R
authors.lastname: Yamaguchi
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling / Q000295:instrumentation / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012044:Regression Analysis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger