title: Gene profiling and bioinformatics analyses reveal time course differential gene expression in surgically resected colorectal tissues.
abstract: It has previously been reported that gene profiles in surgically-resected colorectal cancer tissues are altered over time possibly due to the different tissue-acquisition methods and sample extraction timing that were used. However, the changes that occur are still not clearly understood. In the present study, time-dependent changes in gene expression profiling in colorectal surgical specimens were analyzed. Normal and tumor tissues at several time-points (0, 30, 60 and 120 min) were extracted, and RNA quality, microarray experiments, quantitative PCR and bioinformatics clustering were performed. Although RNA integrity was preserved 2 h after resection, inherent increased/decreased gene expression was observed from 30-120 min in approximately 10% of genes. Bioinformatics clustering could not distinguish case-by-case, probably due to gene profiling changes. Irregular changes in gene expression after surgical resection were found, which could be a crucial confounding factor for quantitative analyses.
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Aya
authors.initials: A
authors.lastname: Yamagishi
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Matsumoto
authors.affiliation: Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Watanabe
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Mizuguchi
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Hara
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Hayato
authors.initials: H
authors.lastname: Kan
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Yamada
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Michihiro
authors.initials: M
authors.lastname: Koizumi
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Seiichi
authors.initials: S
authors.lastname: Shinji
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Akihisa
authors.initials: A
authors.lastname: Matsuda
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Junpei
authors.initials: J
authors.lastname: Sasaki
authors.affiliation: Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Shimada
authors.affiliation: Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan.
authors.forename: Eiji
authors.initials: E
authors.lastname: Uchida
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D015179:Colorectal Neoplasms / Q000235:genetics*; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D012334:RNA, Neoplasm / Q000032:analysis / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors
chemical_list: D012334:RNA, Neoplasm