Screening for genes determining the sensitivity to anticancer drugs using open database
Students will learn how to use the cancer cell line database (CellMinerCDB, TCGA, depmap, cbioportal, NLC mapper, NCBI, Human Protein Atlas, clinicaltrial.gov and others). Through these analyses, students will learn how anti-cancer agents act, and about DNA repair.
※CellMinerCDB enables exploration and analysis of cancer cell line pharmacogenomic data across different sources.
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CellMinerCDB： https://discover.nci.nih.gov/rsconnect/cellminercdb/
CellMinerCDB enables exploration and analysis of cancer cell line pharmacogenomic data across different sources.
TCGA (The Cancer Genome Atlas)： https://portal.gdc.cancer.gov
Database of cancer tissue analyses and the patient prognosis.
Depmap： https://depmap.org/portal/
The analysis tool of cancer cell line pharmacogenomic data across different sources. The essentiality of each gene is validated by gene knockdown or gene knockout.
cBioportal： https://www.cbioportal.org
The cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. The goal of cBioPortal is to significantly lower the barriers between complex genomic data and cancer researchers by providing rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects, and therefore to empower researchers to translate these rich data sets into biologic insights and clinical applications.
NLC mapper: https://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi
Nuclear location signal analysis tool developed by a Kieo IAB team.
NCBI: https://www.ncbi.nlm.nih.gov
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.
Human Protein Atlas: https://www.proteinatlas.org
The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.
The Human Protein Atlas consists of ten separate sections, each focusing on a particular aspect of the genome-wide analysis of the human proteins.
clincaltrials.gov: https://www.clinicaltrials.gov
ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world.