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Protocols

CellMiner specifications

Information


Unique identifier OMICS_10817
Name CellMiner
Restrictions to use None
Version 1.6.1
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Yves Pommier

Publications for CellMiner

CellMiner citations

 (13)
library_books

Characterizing Cancer Drug Response and Biological Correlates: A Geometric Network Approach

2018
Sci Rep
PMCID: 5913269
PMID: 29686393
DOI: 10.1038/s41598-018-24679-3

[…] ation resulting in a 50% reduction in the net protein increase during drug incubation as compared with the same increase in control cells,. Normalized (−log10) GI50 was retrieved using the R package rcellminer. This package complements the functionality of CellMiner by providing programmatic data access as well as analysis and visualization tool. By computing the Spearman’s correlation between the […]

call_split

Loss of function uORF mutations in human malignancies

2018
Sci Rep
PMCID: 5799362
PMID: 29402903
DOI: 10.1038/s41598-018-19201-8
call_split See protocol

[…] I) previously defined human tyrosine kinases, (II) previously validated proto-oncogenes and (III) genes identified manually as being post-transcriptionally overexpressed in cancer cell lines from the CellMiner database. We designed and established 367 customized PCR primer pairs (Supplementary Table ) to amplify 404 uORF initiation sites (including the uKozak context) as mapped by a previous genom […]

library_books

Global view of a drug sensitivity gene network

2017
Oncotarget
PMCID: 5790461
PMID: 29423044
DOI: 10.18632/oncotarget.23229

[…] ioinformatics technologies. The NCI-60 cell line panel and associated drug screens were used to pioneer the approach of linking drug sensitivity to genomic data []. Meanwhile, with the development of CellMiner, rapid data retrieval of genomic data along with activity reports for ∼20,000 chemical compounds across the NCI-60 was allowed []. Hence, we can acquire genomic data related to drug sensitiv […]

library_books

Identifying drug pathway association pairs based on L1L2,1 integrative penalized matrix decomposition

2017
Oncotarget
PMCID: 5564627
PMID: 28624800
DOI: 10.18632/oncotarget.18254

[…] ociation using gene expression and drug sensitivity data. In literature [], the authors apply this method on the NCI-60 data set. The gene expression and drug sensitivity data are downloaded from the CellMiner database [] (http://discover.nci.nih.gov/cellminer). The iFad method is effective in identifying paired drug-pathway associations. Since this method uses the Markov Chain Monte Carlo (MCMC) […]

library_books

Using Pharmacogenomic Databases for Discovering Patient Target Genes and Small Molecule Candidates to Cancer Therapy

2016
Front Pharmacol
PMCID: 5040751
PMID: 27746730
DOI: 10.3389/fphar.2016.00312

[…] CellMiner is a web-based suite of bioinformatics tools designed to explore the drug activity in the NCI-60 cell lines (). The database is continually updated and maintained by Center for Molecular The […]

library_books

SOX5 is involved in balanced MITF regulation in human melanoma cells

2016
BMC Med Genomics
PMCID: 4772287
PMID: 26927636
DOI: 10.1186/s12920-016-0170-0

[…] el), which comprises 60 cancer cell lines from nine different cancer types (breast, central nervous system, colon, kidney, leukemia, lung, melanoma, ovary and prostate). The data were downloaded from CellMiner and based on an integration of five different microarray platforms (5-Platform, Affymetrix HG-U95, HG-U133, HG-U133 Plus 2.0, GH Exon 1.0 ST, and Agilent WHG) yielding a z-score for each gen […]

Citations

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CellMiner institution(s)
Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA; Systems Research and Applications Corp., Fairfax, VA, USA; HiThru Analytics LLC, Laurel, MD, USA; Developmental Therapeutics Program, DCTD, NCI, NIH, Bethesda, MD, USA

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