elNetMolDataNCI60: NCI60 Molecular Data

In rcellminer: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Description

Z-scores of values for a variety of assays conducted on the NCI-60 to facilitate comparison. Z-scores calculated over the 60 cell lines for the given feature.

Details

A list containing various assay values:

• cop Copy number values; Described in Pubmed ID: 24670534

• exp Expression values; Obtained from "RNA: 5 Platform Gene Transcript" http://discover.nci.nih.gov/cellminer/loadDownload.do; Missing values imputed using the R package "impute"

• mut Mutation values; Deleterious mutations obtained from TODO

• mir MicroRNA values; Obtained from "RNA: Agilent Human microRNA (V2)" http://discover.nci.nih.gov/cellminer/loadDownload.do

• pro Reverse protein lysate array values; Obtain from "Protein: Lysate Array" http://discover.nci.nih.gov/cellminer/loadDownload.do

• mda NCI-60 metadata.

  • CNV_GAIN Proportion of genome copy number gains; Described in Pubmed ID: 24670534

  • CNV_LOSS Proportion of genome copy number losses; Described in Pubmed ID: 24670534

  • CNV_TOTAL Sum of CNV_GAIN and CNV_LOSS

  • P53_BIN Binary TP53 profile curated by William Reinhold

  • MSI_OGAN_BIN Binary microsatellite instability (MSI) profile curated by Ogan Abaan using COSMIC data; Obtained from Supplementary Table 1 - Ogan Whole Exome Sequencing (WES) paper in Cancer Res.

  • EPITHELIAL Epithelial by tissue of origin - pattern extracted from the CellMiner cell line metadata http://discover.nci.nih.gov/cellminer/celllineMetadata.do

  • EPITHELIAL_KURT Kurt Kohn curation for epithelial-like cell lines based on molecular parameters described in Pubmed ID: 24940735

  • DELETERIOUS Total deleterious variants from WES dataset; Fabricio Sousa curation

  • MISSENSE Total missense variants from WES dataset; Fabricio Sousa curation

  • SILENT Total silent variants from WES dataset; Fabricio Sousa curation

  • TOTAL_AA Total amino acid changing variants from WES dataset; Fabricio Sousa curation

  • CELL-CELL Cell-to-cell adhesion curated by William Reinhold

  • DOUBLINGTIME The doubling time pattern was extracted from the CellMiner cell line metadata http://discover.nci.nih.gov/cellminer/celllineMetadata.do

Author(s)

Vinodh Rajapakse vinodh.rajapakse AT nih.gov

References

http://discover.nci.nih.gov/cellminer

rcellminer documentation built on Nov. 26, 2020, 2:02 a.m.