Development and its application of the "virtual dissection" method using gene expression profiles of clinical specimens
Project/Area Number |
18K06198
|
Research Category |
Grant-in-Aid for Scientific Research (C)
|
Allocation Type | Multi-year Fund |
Section | 一般 |
Review Section |
Basic Section 43060:System genome science-related
|
Research Institution | Juntendo University |
Principal Investigator |
Mogushi Kaoru 順天堂大学, 大学院医学研究科, 非常勤講師 (60569292)
|
Co-Investigator(Kenkyū-buntansha) |
島田 周 東京医科歯科大学, 大学院医歯学総合研究科, 助教 (20609705)
|
Project Period (FY) |
2018-04-01 – 2022-03-31
|
Project Status |
Completed (Fiscal Year 2021)
|
Budget Amount *help |
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2020: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2018: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
|
Keywords | バイオインフォマティクス / 仮想ダイセクション法 / 教師なし学習 / 遺伝子発現解析 / 仮想ダイセクション / 臨床検体 / 遺伝子発現情報 |
Outline of Final Research Achievements |
In this research, we designed a novel algorithm to estimate ratios of cells in a tissue by deconvolution of bulk expression profiles into each type of cells including normal, inflammatory, and / or tumor cells. The expression profiles of those mixture of cells were obtained from public databases and were used to investigate the reference expression patterns of major types of cells in several cancers including hepatocellular carcinoma, lung cancer, and breast cancer. Furthermore, we aimed to develop a system to provide the estimated ratio of cells from given expression profiles.
|
Academic Significance and Societal Importance of the Research Achievements |
近年ではシングルセル解析技術の進展がめざましく、本研究でゴールとした細胞集団の同定や比率推定などが実験的に可能になりつつある。しかしながらシングルセル解析にはバルク解析よりコストが掛かることや、すでに公開データベースに蓄積された臨床検体のバルクRNA-seqデータやマイクロアレイによる発現プロファイルの再解析により既存検体の細胞集団の推定が可能になることで、シングルセル解析で得られる情報と相補的に活用できることが期待される。
|
Report
(5 results)
Research Products
(15 results)
-
-
-
-
[Journal Article] Tau aggregation and seeding analyses of two novel MAPT variants found in patients with motor neuron disease and progressive parkinsonism.2019
Author(s)
Nakayama S, Shimonaka S, Elahi M, Nishioka K, Oji Y, Matsumoto SE, Li Y, Yoshino H, Mogushi K, Hatano T, Sato T, Ikura T, Ito N, Motoi Y, Hattori N.
-
Journal Title
Neurobiology of Aging
Volume: 19
Pages: 240.e13-240.e22
DOI
Related Report
Peer Reviewed
-
[Journal Article] Estrogen receptor-positive ductal carcinoma in situ frequently overexpresses HER2 protein without gene amplification.2019
Author(s)
Horimoto Y, Terao T, Tsutsumi Y, Tanabe M, Mogushi K, Hlaing MT, Sasaki R, Saeki H, Okazaki M, Sonoue H, Arakawa A, Saito M.
-
Journal Title
Am J Surg Pathol
Volume: 43(9)
Issue: 9
Pages: 1221-1228
DOI
Related Report
Peer Reviewed / Open Access
-
-
-
[Journal Article] Stromal fibroblasts induce metastatic tumor cell clusters via epithelial-mesenchymal plasticity.2019
Author(s)
Matsumura Y, Ito Y, Mezawa Y, Sulidan K, Daigo Y, Hiraga T, Mogushi K, Wali N, Suzuki H, Itoh T, Miyagi Y, Yokose T, Shimizu S, Takano A, Terao Y, Saeki H, Ozawa M, Abe M, Takeda S, Okumura K, Habu S, Hino O, Takeda K, Hamada M, Orimo A.
-
Journal Title
Life Sci Alliance
Volume: 2(4):e201900425.
Issue: 4
Pages: 1-24
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
-
[Journal Article] Comprehensive molecular characterization of liver cancer and inheritance of the phenotypic traits during tumor recurrence.2019
Author(s)
Shimada S, Mogushi K, Akiyama Y, Furuyama T, Watanabe S, Ogura T, Ogawa K, Ono H, Mitsunori Y, Ban D, Kudo A, Arii S, Tanabe M, Wands JR, Tanaka S.
-
Journal Title
EBioMedicine
Volume: 40
Pages: 457-470
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
-
-
[Journal Article] Tumor Sidedness and Enriched Gene Groups for Efficacy of First-line Cetuximab Treatment in Metastatic Colorectal Cancer.2018
Author(s)
Sunakawa Y, Mogushi K, Lenz HJ, Zhang W, Tsuji A, Takahashi T, Denda T, Shimada K, Kochi M, Nakamura M, Kotaka M, Segawa Y, Tanioka H, Negoro Y, Moran M, Astrow SH, Hsiang J, Stephens C, Fujii M, Ichikawa W.
-
Journal Title
Mol Cancer Ther.
Volume: 17
Issue: 12
Pages: 2788-2795
DOI
Related Report
Peer Reviewed / Int'l Joint Research
-
[Journal Article] KCTD12 is negatively regulated by Kit in gastrointestinal stromal tumors.2018
Author(s)
Suehara Y, Akaike K, Mukaihara K, Kurisaki-Arakawa A, Kubota D, Okubo T, Mitomi H, Mitani K, Takahashi M, Toda-Ishii M1, Kim Y, Tanabe Y, Takagi T, Hayashi T, Mogushi K, Kaneko K, Yao T, Saito T.
-
Journal Title
Oncotarget
Volume: 9(43)
Issue: 43
Pages: 27016-27026
DOI
Related Report
Peer Reviewed / Open Access
-
-
-