From the DTP home page (http://dtp.nci.nih.gov)
Click on " Molecular Targets " on the Navigation bar.
Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status and enzyme activity levels. You can choose to search for a target of interest, or you may browse through a list of targets. Follow the links for a target to retrieve the 60 cell line data (either text or graphical), to run COMPARE (find Targets or Compounds whose patterns correlate with a Target of interest) and to link to various databases with information (function, sequences, disease associations) about the target. For more information on the Molecular Target effort see the frequently asked questions (FAQ). I.Molecular target FAQ II.Search molecular target data III.Browse molecular target data IV.Download molecular target data V. Guided Tour VI.Useful Links
Click on Search molecular target data
Search target by:
HUGO approved gene name: Can be found by searching GeneCards site. Alias: If you don't know a gene name try searching by another name or a short text string (Not available for most microarray targets). Pattern ID: Search is based on the NCI's identification number for the pattern. Microarray Data Clone number: Search is based on IMAGE clone number.
HUGO approved gene name: Can be found by searching GeneCards site.
Alias: If you don't know a gene name try searching by another name or a short text string (Not available for most microarray targets).
Pattern ID: Search is based on the NCI's identification number for the pattern.
Clone number: Search is based on IMAGE clone number.
Enter a HUGO approved gene name into the appropriate box. This search includes microarray targets where a named gene is associated with the microarray clone.
OR
Enter a short text string. This search is currently unavailable for most microarray targets.
In this example we will search for the text string "cyclin".
Click on
Some Targets have more than one pattern associated with a single experiment. For example, for some data we have done a logarithmic transformation of the data, generating a new pattern that can be used as a seed for a COMPARE search. The Experiment ID identifies a single experiment. A Pattern ID identifies a single pattern. An Experiment ID can have multiple Pattern IDs associated with it (e.g. a primary pattern and a log-transformed pattern), which are just different ways of analyzing the same underlying data. Click on the Target of interest to proceed.
A list of targets whose names contain the text string ("cyclin" in our example) is returned.
The list displays
Pattern ID number -Target name (Experiment Id number) (Pattern explanation)
GC13524 - Cdk6 (cyclin-dependent kinase 6) (Experiment Id: 4122) (primary)
In the list above, there are 3 patterns (MT114, MT115, MT117) that derive from a single set of measurements (Experiment Id: 75).
In the list above, there are 2 patterns for Cdk6 (cyclin-dependent kinase 6). But since these have different Experiment ID numbers (Experiment Id: 4122) and (Experiment Id: 4174) , we know that these are independent measurements of the same target.
Targets whose Pattern ID begins with GC are microarray measurements of RNA expression.
Targets whose Pattern ID begins with MT include non-microarray measurements, including protein levels, enzyme activity levels, mRNA levels and mutation status.
To proceed, click on the target of interest . In this example, we will choose:
Cdk6 (cyclin-dependent kinase 6) RNA
and
Experiment Id: 4122 Pattern Id: GC13524 Clone number: 231497 3'Acc: H92463
Relative RNA levels for nearly 10,000 human clones were measured in a microarray experiment. Some of these clones have been linked to known genes (based on clustering information from Unigene) - follow the links to Unigene and GeneCards, where information on possible function can be found. Other clones represent as yet unnamed genes - follow the Unigene link for more information. All gene assignments should be considered tentative. Sequence information for a clone can be found through GenBank or Unigene, and can be used to search sequence databases.
Botstein, Dr. David Stanford University School of Medicine
Weinstein, Dr. John National Cancer Institute
Method: Microarray
Protocol: mRNA was isolated from logarithmically growing cells. Labeled cDNA was prepared by reverse transcription of test cell mRNA in the presence of Cy5-dUTP. Reference probes were made by pooling equal amounts of mRNA from HL-60, K562, NCI-H226, COLO205, SNB-19, LOX-IMVI, OVCAR-3, OVCAR-4, CAKI-1, PC-3, MCF7 and Hs578T cell lines. Labelled cDNA was prepared from the pooled mRNA by reverse transcription in the presence of Cy3-dUTP. Test and reference probes were combined, denatured and hybridized overnight to Synteni microarrays containing cDNA from 9703 human clones. Arrays were scanned using a laser-scanning microscope. The ScanAlyze program was used to analyze the microarray images and prepare data files for further analysis.
A database of human genes, their products and their involvement in diseases. It offers concise information about the functions of human genes.
An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
Presents information on official nomenclature, aliases, sequence accession numbers, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and relevant web sites.
A catalog of human genes and genetic disorders.
Search Pubmed for articles on:
CDK6
Retrieve the data and figure out what it means.
Protocol: mRNA was isolated from logarithmically growing cells. Labelled cDNA was prepared by reverse transcription of test cell mRNA in the presence of Cy5-dUTP. Reference probes were made by pooling equal amounts of mRNA from HL-60, K562, NCI-H226, COLO205, SNB-19, LOX-IMVI, OVCAR-3, OVCAR-4, CAKI-1, PC-3, MCF7 and Hs578T cell lines. Labelled cDNA was prepared from the pooled mRNA by reverse transcription in the presence of Cy3-dUTP. Test and reference probes were combined, denatured and hybridized overnight to Synteni microarrays containing cDNA from 9703 human clones. Arrays were scanned using a laser-scanning microscope. The ScanAlyze program was used to analyze the microarray images and prepare data files for further analysis.
Search PubMed for articles on: