Computer scientist with expertise in software and database development, genomic data analysis and visualization, software for clinical trial management, and computational and systems biology. Affymetrix, santa clara, ca and one new protein profile data set based on. Where can i find a complete list of oncogenes and ts for nci60 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. This is a list of the 60 human cancer cell lines used in the screen and maintained at nci frederick. Full release of endpoints calculated from concentration curves. A web application that facilitates comprehensive proteome analysis of the nci60 cell line panel. Cellminer data analytics app could help with cancer research. 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 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.
We defined the complexity of the karyotype based on the basis of three factors. The line is available with the following restrictions. 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. The nci60 cell lines are well characterized reference standards used in cancer research. We developed the diaexpert software to curate and visualize the. 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. Plot the cut in the dendrogram that yielded the 4 clusters. What i forget to say is data on the drug cell line result and the copy number on the nci 60. Implementation of the nci60 human tumor cell line panel. 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. Patterns of growth inhibition across the nci60 cell lines are similar for. I have not found a perticular website where i can download the nci 60. This project was intended to screen thousands of pharmacological compounds for anticancer activity, thus replacing earlier cumbersome en vivo models.
Dark background indicates cell lines that are not associated with any microarrays. 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. 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. While ncih660 has the appearance and many of the properties of small cell carcinoma, there are also differences. Found the sample mean and estimated sigma for each gene, cancer cell line. The nci60 human tumor cell line panel is an invaluable resource for. Affymetrix 125k snp array data from the sellers lab nature 436, 117122 2005. The nci60 cell lines were derived from cancers from nine tissues of origin. The nci60 is a panel of 60 human cancer cell lines used by the developmental therapeutics program dtp of the u. The nci 60 human tumor cell lines screen has served the global cancer research community for 20 years.
The global correlation between the data matrices was 0. 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. Additional lines evaluated for use in the screen and currently available are listed separately at the bottom of the page. Where can i find a complete list of oncogenes and ts for. This was further supported when gene expression signatures were compared in the cmap database. Drug sensitivity prediction by cpg island methylation. Cellminer is a relational database tool for storing,querying, integrating, and downloading molecular profile data on the nci60 and other cancer cell types. 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. For other bioinformatic tools and database resources from gbg go to the. 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.
Nci60 growth inhibition data nci dtp data nci wiki. This panel has been used as a key tool to develop and screen anticancer drugs. Mutation analysis of 24 known cancer genes in the nci60 cell. I am working on nci 60 database for data mining purpose.
Predicting in vitro drug sensitivity using random forests. Nci60 cell line genomic reference data set enabling translational oncology through application of the nci60 cell lines. Karyotypic complexity of the nci60 drugscreening panel. This particular cell line was developed from cells harvested in ascites fluid of a 33year old caucasian male with colorectal cancer. 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. 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. Colors represent the nine nci60 cell line classes as in figure 1. 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.
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. The nci60 human tumor cell lines screen has served the global cancer research. Oct 18, 20 data from the nci 60 cell line panel revealed only modest correlation between mbz and abz, indicating differences in mechanism of action. Nci60 human tumor cell line screen service altogen labs. Ncih716 cells were one of several colorectal cancer cell lines originally described in 1987 park et al. These data are publicly available from the dtp human tumor cell line screen andor the dtp aids antiviral screen.
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. Correlation of expression profiles between micrornas and. 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. To cite the tool, the primary literature references are shankavaram, bmc genomic, 2009 and reinhold, cancer res, 2012.
The nci60 human cancer cell line panel contains 60 lines from nine different tissue types. Permissivity of the nci60 cancer cell lines to oncolytic. Global proteome analysis of the nci60 cell line panel. An automated comparison against a database of more than 88,000 pure compounds and more than 34,000.
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. Repositioning of the anthelmintic drug mebendazole for the. Analyzing the nci60 cancer cell lines using data obtained. Molecular profiles and drug response for the nci60 cell lines. Cellminer cross database cdb is the first web application to allow translational researchers to conduct analyses across all major cancer cell line. Transcript and protein expression profiles of the nci60. 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.
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. I want to purchase the sf539 and snb75 glioma cell lines from the nci 60 collection but they are not available from atc. Quantitative proteome landscape of the nci60 cancer cell lines. I tried to browse for datasets but can only find microarray data for these cell lines. 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 nci60 database includes drug sensitivity data from more than 50. Please note the links for more information on the snb19, u251, nci adrres, and mdamb435 cell lines. National cancer institute to screen 100,000 compounds plus natural products since 1990 710. This is a list of the 60 human cancer cell lines used in the screen and maintained at ncifrederick. Implementation of the nci60 human tumor cell line panel to. 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. What i forget to say is data on the drugcell line result and the copy number on the nci 60.
I am working on nci60 database for data mining purpose. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. 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. Integrating global gene expression and radiation survival. The nci60 cell line panel screen includes 60 human tumor cell lines derived. The nci60, a panel of 60 diverse human cancer cell lines used by the developmental therapeutics. The nci60 cell line set is likely the most molecularly profiled set of human tumor cell lines in the world. Microrna expression profiles for the nci60 cancer cell panel. 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. I am wondering if such a listdatabase is available for cancer in general or cell lines in nci60. A description of the nci60 assay and calculations can be found here. 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.
These cell lines have undergone extensive study, including response to treatment with over 100,000 chemical compounds. Neither the cell line nor products derived from it may be sold or used for commercial purposes. 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. 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. Abz ranked very low when mbz was used as the query signature. Jun 26, 2018 full release of endpoints calculated from concentration curves. Predictive models for each drug are individually created by combining two data sources. 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. Systems analysis of the nci60 cancer cell lines by. Database and query tool for the nci60 cancer cell lines. Hi i am trying to see if there is any publically available rnaseq data for nci 60 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. 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. Here we describe a proteomic data resource for the nci60 cell lines generated by pressure cycling technology and swath mass spectrometry. Systems analysis of the nci60 cancer cell lines by alignment. The nci60 cell lines were assembled by the national cancer institute as an in vitro anticancer drug screen, which went into operation in 1990. Ncih660 expresses elevated levels of ldopa carboxylase and bombesinlike immunoreactivity. In this work we computed the correlation of expression profiles between mirnas and target mrnas using the nci60 expression data. 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. I want to purchase the sf539 and snb75 glioma cell lines from the nci60 collection but they are not available from atc.
The nci60, a panel of 60 diverse human cancer cell lines used by the developmental therapeutics program of the u. Breast cancer cell lines are spread out over 3 clusters. Cell lines in the in vitro screen nci60 human tumor cell lines. 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. Comprehensive transcriptomic analysis of cell lines as. The nci almanac database therefore constitutes a valuable resource. The project was published online in cancer research 20. The panel comprises 60 human cancer cell lines representing nine tissue of origin types.
The length of the arrow is proportional to the divergence between the data sets. Data from the nci 60 cell line panel revealed only modest correlation between mbz and abz, indicating differences in mechanism of action. Analysis for gene expression data of the nci 60 cancer. Genomes released of nci60 cancer cell lines bioit world. Hi i am trying to see if there is any publically available rnaseq data for nci60 cell lines. 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. Nov 26, 2019 2d versions of nci open database compounds as of october 1999, with biological test data added. Cellminer is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the nci60 and other cancer cell types. 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. Further information regarding the ncbi60 panel can be found on the national cancer institute website. 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. Cellminer is a web application that provides molecular profile data and query tools for the nci 60 and additional cell types.
The nci transcriptional pharmacodynamics workbench. Cellminer is a web application that provides molecular profile data and query tools for the nci60 and additional cell types. The people involved in the stanford nci60 cancer microarray project. A description of the nci 60 assay and calculations can be found here. National cancer institute to screen over 100,000 chemical compounds and natural products since 1990. The nci60 panel is the national cancer institutes s collection of 60 human cancerous cell lines. The nci60 human tumor cell lines screen has served the global cancer research community for 20 years. 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.
Microrna expression profiles for the nci60 cancer cell. The nci60 cancer cell line panel is a group of 60 human cancer cell lines used by the national. Nci60 human cancer cell line screen nci60 human tumor. The nci60 panel of human tumor cell lines has been used in cancer research for almost. The base medium for this cell line is atcc formulated rpmi1640 medium. Quantitative proteome landscape of the nci60 cancer cell. 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. Please note the links for more information on the snb19, u251, nciadrres, and mdamb435 cell lines. Analysis for gene expression data of the nci 60 cancer cell. Is there such data available and if yes when can i can download the raw data for these if possible.
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. Mutation profiles of over 1,000 cell lines used in cancer research. Small noncoding rna transcriptome of the nci60 cell line. For that analysis, we present here two new nci60 transcript profile data sets a based on affymetrix hgu95 and hgu3a chips. However,what confuses me is that where can i download the nci 60 data. The national cancer institute developmental therapeutics program. A relational database and query tool for the nci60 cancer cell lines. 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. It provides matched molecular and drug activity profiling data. The nci60 cell lines used by ncis human tumor cell lines screen as described on the website of the developmental therapeutics program. Found the population mean and sigma for the expression of each of the genes across all the 60 cancer cell lines 3.
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