Cellminer is a web application that provides molecular profile data and query tools for the nci 60 and additional cell types. The nci60 human tumor cell lines screen has served the global cancer research community for 20 years. For that analysis, we present here two new nci60 transcript profile data sets a based on affymetrix hgu95 and hgu3a chips. Mutation profiles of over 1,000 cell lines used in cancer research. The nci60 database includes drug sensitivity data from more than 50. However, a critical missing component of previous analyses has been the inability to place the massive amounts of omic data in the context of functional protein signaling networks, which often contain many of the drug targets for new targeted therapeutics. Advances in the understanding of cancer cell biology and response to drug treatment have benefited from new molecular technologies and methods for integrating information from multiple sources. Nci60 growth inhibition data nci dtp data nci wiki. More broadly, it provides a template to use in providing such functionality for other molecular profile data generated by academic institutions, public projects, or the private sector. The nci60 cell line panel screen includes 60 human tumor cell lines derived. Nov 26, 2019 2d versions of nci open database compounds as of october 1999, with biological test data added. Oct 24, 2017 the nci 60 human tumour cell lines screen is an initiative started by the national institutes of health nih in the late 1980s, focusing on the development of 59 human tumour cell lines for use. These cell lines have undergone extensive study, including response to treatment with over 100,000 chemical compounds.
The nci60 panel is the national cancer institutes s collection of 60 human cancerous cell lines. Quantitative proteome landscape of the nci60 cancer cell. The cell line list included in the altogen96 panel contains a majority of the same cell lines used in the nci60 human cancer cell line screen panel and are well characterized in regards to their genotype and phenotype, including databases available to download rna expression data, protein expression data, epigenetics and dna sequencing. The nci60 cell lines used by ncis human tumor cell lines screen as described on the website of the developmental therapeutics program. Predictive models for each drug are individually created by combining two data sources. Here we describe a proteomic data resource for the nci60 cell lines generated by pressure cycling technology and swath mass spectrometry. The length of the arrow is proportional to the divergence between the data sets. Nci60 cell line genomic reference data set enabling translational oncology through application of the nci60 cell lines. For other bioinformatic tools and database resources from gbg go to the. Integrating global gene expression and radiation survival. The project was published online in cancer research 20.
Cellminer is a relational database tool for storing,querying, integrating, and downloading molecular profile data on the nci 60 and other cancer cell types. The nci transcriptional pharmacodynamics workbench. These tissues of origin were selected because they are hard to treat, and include lung cancer, melanoma, ovarian cancer, renal cancer, colon cancer and others, yves pommier, chief of the laboratory of molecular pharmacology at the national cancer institute, told bioit world. The nci60 cancer cell line panel is a group of 60 human cancer cell lines used by the national. A database and query tool designed for the cancer research community to facilitate integration of the molecular datasets generated by the genomic and parmacology facility and its collaborators on the nci60 cellminercdb.
Hi i am trying to see if there is any publically available rnaseq data for nci60 cell lines. I have not found a perticular website where i can download the nci 60. Cellminer cross database cdb is the first web application to allow translational researchers to conduct analyses across all major cancer cell line pharmacogenomic data sources from ncidtp nci60, sanger gdsc, and broad cclectrp. Cellminer is a web application that provides molecular profile data and query tools for the nci60 and additional cell types. The nci60 cell line set is likely the most molecularly profiled set of human tumor cell lines in the world.
The nci tpw integrates cell line sensitivity data for 15 clinically relevant anticancer agents with both basaltranscript levels and agentinduced transcriptional changes for 12,704 genes at three time points across the nci60 panel. I want to purchase the sf539 and snb75 glioma cell lines from the nci60 collection but they are not available from atc. The nci60 cell lines were derived from cancers from nine tissues of origin. Small noncoding rna transcriptome of the nci60 cell line. Cellminer users can visit the database website for access to a number of information streams, including nci60 analysis tools for automation of several commonlydone analyses, dataset metadata, queries for genomic and drug data, cell line metadata, and mutation data a list of mutations found in 24 known human cancer genes. It provides matched molecular and drug activity profiling data. Molecular profiles and drug response for the nci60 cell lines.
Where can i find a complete list of oncogenes and ts for. Genomes released of nci60 cancer cell lines bioit world. However,what confuses me is that where can i download the nci 60 data. The line is available with the following restrictions.
The nci60 cell lines are well characterized reference standards used in cancer research. Cellminer cross database cdb is the first web application to allow translational researchers to conduct analyses across all major cancer cell line. A relational database and query tool for the nci60 cancer cell lines. July 17, 20 on monday, researchers released the largest database of cancerrelated genetic variationsthe genomes of the 60 cancer cell lines represented by the nci60 list. Predicting in vitro drug sensitivity using random forests. The cellosaurus identifier is a combination of the cell line name variant chosen by cellosaurus, with the cellosaurus accession id, the latter written as rrid. Additional lines evaluated for use in the screen and currently available are listed separately at the bottom of the page. Repositioning of the anthelmintic drug mebendazole for the. Implementation of the nci60 human tumor cell line panel. Karyotypic complexity of the nci60 drugscreening panel. The national cancer institute developmental therapeutics program. What i forget to say is data on the drugcell line result and the copy number on the nci 60. The nci60 human tumor cell line panel is an invaluable resource for. Nci60 human cancer cell line screen nci60 human tumor.
While ncih660 has the appearance and many of the properties of small cell carcinoma, there are also differences. Cellminer is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the nci60 and other cancer cell types. Analysis for gene expression data of the nci 60 cancer cell. Dark background indicates cell lines that are not associated with any microarrays. This is a list of the 60 human cancer cell lines used in the screen and maintained at ncifrederick. National cancer institute to screen 100,000 compounds plus natural products since 1990 710. Mutation analysis of 24 known cancer genes in the nci60 cell. National cancer institute university of virginia clinical trials in vivo studies d a t a b a s e t m olecular targets 150 specific database a targets activity patterns 60 cell lines 68k pds 4,000,000 numbers inventory 300,000 cmpds 60cell line screen 68,000 cmpds the nci cancer drug discovery development pipeline mrna expression. The nci60 is a panel of 60 human cancer cell lines used by the developmental therapeutics program dtp of the u. The nci60 have been molecularly and pharmacologically characterized with unparalleled depth and coverage, offering a prime in vitro model to further our understanding of cancer biology and cellular responses to anticancer agents. Is there such data available and if yes when can i can download the raw data for these if possible. National cancer institute to screen over 100,000 chemical compounds and natural products since 1990. Drug sensitivity prediction by cpg island methylation.
The nci60, a panel of 60 diverse human cancer cell lines used by the developmental therapeutics program of the u. Database and query tool for the nci60 cancer cell lines. We developed the diaexpert software to curate and visualize the swath data, leading to reproducible detection of over 3,100 swissprot proteotypic proteins and systematic quantification of pathway activities. The screen was implemented in fully operational form in 1990 and utilizes 60 different human tumor cell lines to identify and characterize novel compounds with growth inhibition or. Correlation of expression profiles between micrornas and. Cell lines in the in vitro screen nci60 human tumor cell lines.
More broadly, it provides a template to use in providing such functionality for other molecular profile data generated by academic institutions, public projects, or the private. Please note the links for more information on the snb19, u251, nci adrres, and mdamb435 cell lines. Microrna expression profiles for the nci60 cancer cell. The global correlation between the data matrices was 0. The nci60 human cancer cell line panel contains 60 lines from nine different tissue types. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Where can i find a complete list of oncogenes and ts for nci60 cell lines. With the increasing availability of mrna and mirna expression data, it might be possible to assess functional targets using the fact that a mirna might downregulate its target mrnas.
Systems analysis of the nci60 cancer cell lines by. A description of the nci 60 assay and calculations can be found here. I tried to browse for datasets but can only find microarray data for these cell lines. This panel has been used as a key tool to develop and screen anticancer drugs. This project was intended to screen thousands of pharmacological compounds for anticancer activity, thus replacing earlier cumbersome en vivo models. Analysis for gene expression data of the nci 60 cancer. Global proteome analysis of the nci60 cell line panel. A description of the nci60 assay and calculations can be found here.
In this work we computed the correlation of expression profiles between mirnas and target mrnas using the nci60 expression data. At this moment, the nci60 cells constitute the most extensively and diversely characterized cell panel anywhere, and several databases have been generated based on these cell lines, such as drug activity database for 30,000 chemically defined. To cite the tool, the primary literature references are shankavaram, bmc genomic, 2009 and reinhold, cancer res, 2012. Cellminer is a webaccessible relational database tool that organizes, navigates, and integrates multiple types of molecular profile data on the nci60 cell line panel at the t dna, rna, protein, and smallmolecule levels. I want to purchase the sf539 and snb75 glioma cell lines from the nci 60 collection but they are not available from atc. Neither the cell line nor products derived from it may be sold or used for commercial purposes. Quantitative proteome landscape of the nci60 cancer cell lines. A web application that facilitates comprehensive proteome analysis of the nci60 cell line panel. Implementation of the nci60 human tumor cell line panel to screen 2260 cancer drug combinations to generate 3 million data points used to populate a large matrix of antineoplastic agent combinations almanac database. The nci60, a panel of 60 diverse human cancer cell lines used by the developmental therapeutics. To confirm cell line identity and exclude possible culture contamination, all cell lines used in this study were typed for hla class i which cross referenced to previous high resolution sequence based typing of nci60 or other cell lines. Other intermediate scale sequencing projects have also been carried out across some of the cell lines within the set cancer cell line encyclopaedia ccle 5,6 and sequencing of the nci60 set by the nci 7 and comparison of the data across these studies identified a large degree of overlap between the different datasets. To evaluate the utility of transcript profiling for prediction of protein expression levels, we compared profiles across the nci60 cancer cell panel, which represents nine tissues of origin. Data from the nci 60 cell line panel revealed only modest correlation between mbz and abz, indicating differences in mechanism of action.
These data are publicly available from the dtp human tumor cell line screen andor the dtp aids antiviral screen. Comprehensive transcriptomic analysis of cell lines as. Found the population mean and sigma for the expression of each of the genes across all the 60 cancer cell lines 3. The nci60 human tumour cell lines screen is an initiative started by the national institutes of health nih in the late 1980s, focusing on the. The nci60 cell lines were assembled by the national cancer institute as an in vitro anticancer drug screen, which went into operation in 1990. The people involved in the stanford nci60 cancer microarray project. Analyzing the nci60 cancer cell lines using data obtained. This is a list of the 60 human cancer cell lines used in the screen and maintained at nci frederick. The nci60 human tumor cell lines screen has served the global cancer research. Jun 26, 2018 full release of endpoints calculated from concentration curves. Please note the links for more information on the snb19, u251, nciadrres, and mdamb435 cell lines.
The nci has established a panel of cell lines nci60 and used it to screen compounds for anticancer activity over the last decades 1. Ncih716 cells were one of several colorectal cancer cell lines originally described in 1987 park et al. Nci60 human tumor cell line screen service altogen labs. Permissivity of the nci60 cancer cell lines to oncolytic. Plot the cut in the dendrogram that yielded the 4 clusters. The nci60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. Microrna expression profiles for the nci60 cancer cell panel. Affymetrix 125k snp array data from the sellers lab nature 436, 117122 2005. Affymetrix, santa clara, ca and one new protein profile data set based on.
Every cell line in the nci60 panel had karyotypic abnormalities, but there were notable individual variations among the cell lines in the level of karyotypic complexity. The nci60 panel of human tumor cell lines has been used in cancer research for almost. This particular cell line was developed from cells harvested in ascites fluid of a 33year old caucasian male with colorectal cancer. Systems analysis of the nci60 cancer cell lines by alignment. We developed the diaexpert software to curate and visualize the. Nov 18, 2015 data is provided as an excel file listing copy number of each chromosomal band for each cell line. Nov 22, 2019 the nci60 human cancer cell line panel contains 60 lines from nine different tissue types. Found the sample mean and estimated sigma for each gene, cancer cell line. Computer scientist with expertise in software and database development, genomic data analysis and visualization, software for clinical trial management, and computational and systems biology.
Full release of endpoints calculated from concentration curves. The base medium for this cell line is atcc formulated rpmi1640 medium. I am working on nci 60 database for data mining purpose. The nci almanac database therefore constitutes a valuable resource. I am wondering if such a listdatabase is available for cancer in general or cell lines in nci60. The nci 60 human tumor cell lines screen has served the global cancer research community for 20 years. Nci60 cancer cell lines introduction to nci60 human cancer cell lines the late 1980s saw the development and creation of the national cancer institute nci 60 human tumor cell line anticancer drug discovery project. The panel comprises 60 human cancer cell lines representing nine tissue of origin types. We defined the complexity of the karyotype based on the basis of three factors. Ncih660 expresses elevated levels of ldopa carboxylase and bombesinlike immunoreactivity.
Transcript and protein expression profiles of the nci60. What i forget to say is data on the drug cell line result and the copy number on the nci 60. An automated comparison against a database of more than 88,000 pure compounds and more than 34,000. This was further supported when gene expression signatures were compared in the cmap database. Colors represent the nine nci60 cell line classes as in figure 1.
I am working on nci60 database for data mining purpose. In the 1980s, the national cancer institute nci selected 60 cell lines representing nine tumor types breast, central nervous system, colon, leukemia, lung, melanoma, ovarian, prostate, and renal and established the nci60 panel of cancer cell lines as a tool for in vitro drug screening. Cellminer is a webaccessible relational database tool that organizes, navigates, and integrates multiple types of molecular profile data on the nci 60 cell line panel at the t dna, rna, protein. Patterns of growth inhibition across the nci60 cell lines are similar for. Hi i am trying to see if there is any publically available rnaseq data for nci 60 cell lines. Implementation of the nci60 human tumor cell line panel to. Abz ranked very low when mbz was used as the query signature. Html table with samples plain html table image gallery simply count hits entire db nsc number file cactvs hitlist records alchemy cactvs binary cerius cml compass ctx gaussian input jcampcs molconnz molfile pdb smd 4 sdfile smiles sybyl2 vrml 2. The nci60, a panel of 60 diverse human cancer cell lines, has been used by the national cancer institute to screen 100,000 chemical compounds and natural product extracts for anticancer activity. Developmental therapeutics program link to analysis tools for exploring the drug sensitivity database, the gene expression database, and other drug targets measured by the dtp. Breast cancer cell lines are spread out over 3 clusters. The nci60 have been molecularly and pharmacologically characterized with unparalleled depth and coverage, offering a prime in vitro model to further our understanding of cancer biology and cellular responses to anticancer agents monks et al. The screen was implemented in fully operational form in 1990 and utilizes 60 different human tumor cell lines to identify and characterize novel compounds with growth inhibition or killing of tumor cell lines. Cellminer currently focuses on two cancer cell line sets, the nci60 and the du145rc.