Gene expression data have been archived as microarray and RNA-seq data in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, DNA DataBank of Japan started similar repository called Genomic Expression Archive (GEA)....
Kobayashi Y, Nojima Y, Sakamoto T, Iwabuchi K, Nakazato T, Bono H, Toyoda A, Fujiyama A, Kanost MR, Tabunoki H
Scientific Reports 9(1) 2170 Feb 2019 [Refereed]
Insects are well adapted to changing environmental conditions. They have unique systems for eliminating reactive oxygen species (ROS). Superoxide dismutase (SOD) is a key enzyme that plays a primary role in removing ROS. Bombyx mori is a lepidopte...
The possibility that anesthesia during cancer surgery may affect cancer recurrence, metastasis, and patient prognosis has become one of the most important topic of interest in cancer treatment. For example, the volatile anesthetic isoflurane was r...
Ichino F, Bono H, Nakazato T, Toyoda A, Fujiyama A, Iwabuchi K, Sato R, Tabunoki H
Drug Discoveries & Therapeutics 12(1) 7-15 Mar 2018 [Refereed]
Human intestinal absorption is estimated using a human colon carcinoma cell line (Caco-2) cells from human colorectal adenocarcinoma, intestinal perfusion, or a mammalian model. These current evaluation systems are limited in their ability to esti...
Piulats JM, Kondo J, Endo H, Ono H, Hagihara T, Okuyama H, Nishizawa Y, Tomita Y, Ohue M, Okita K, Oyama H, Bono H, Masuko T, Inoue M
Oncotarget 9 15968-15983 Mar 2018 [Refereed]
Individual and small clusters of cancer cells may detach from the edges of a main tumor and invade vessels, which can act as the origin of metastasis; however, the mechanism for this phenomenon is not well understood. Using cancer tissue-originate...
Hypoxia is an insufficient level of oxygen supply in the cell, and hypoxia-inducible factor is a central regulator of oxygen homeostasis. In order to elucidate functional insights in hypoxic response in data-driven way, we attempted meta-analysis ...
Nakamura H, Bono H, Hiyama K, Kawamoto T, Kato Y, Nakanishi T, Nishiyama M, Hiyama E, Hirohashi N, Sueoka E, Poellinger L, Tanimoto K
PLOS ONE 13(2) e0192136 Feb 2018 [Refereed]
Tumor hypoxia contributes to a biologically aggressive phenotype and therapeutic resistance. Recent studies have revealed that hypoxia reduces expression of several DNA damage recognition and repair (DRR) genes via both hypoxia-inducible factor (H...
Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and com...
Okamoto A, Sumi C, Tanaka H, Kusunoki M, Iwai T, Nishi K, Matsuo Y, Harada H, Takenaga K, Bono H, Hirota K
Scientific Reports 7 3816 Jun 2017 [Refereed]
The local anesthetic lidocaine induces cell death by altering reactive oxygen species (ROS) generation and mitochondrial electron transport chain function. Because hypoxia-inducible factor 1 (HIF-1) is involved in determining oxygen metabolism and...
Molecular Targeted Therapy of Lung Cancer 97-115 Jan 2017 [Invited]
Improvement of next-generation sequencing (NGS) has revealed novel driver genes and new therapeutic targets for cancer patients. We summarize here the history of NGS development, current situation of typical analysis pipeline utilizing NGS – espec...
Basement membranes support proliferation, survival, and differentiation of epithelial/parenchymal cells through interaction with cell membrane receptors. Laminins, which have a heterotrimeric structure, are the major class of basement membrane gly...
RefEx: Dataset for Reference Gene Expression
Hiromasa Ono, Hidemasa Bono
Practical Guide to Life Science Databases in press [Invited]
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