DTP Branches and Offices
Molecular Target Tour
How do I find Molecular Target data for my favorite gene/protein?
This guided tour will walk you through the steps to search for a target of interest. After each step you will see a display of what would appear on your monitor if you followed the step. In this tour the links are not clickable — simply scroll down the screen to continue the tour.
Step 1
From the DTP home page (http://dtp.cancer.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).
- Molecular target FAQ
- Search molecular target data
- Browse molecular target data
- Download molecular target data
- Guided Tour
- Useful Links
Step 2
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.
Step 3
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
Results of search
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.
- GC13524 — Cdk6 (cyclin-dependent kinase 6) (Experiment Id: 4122) (primary)
- GC13576 — Cdk6 (cyclin-dependent kinase 6) (Experiment Id: 4174) (primary)
- GC11864 — Cyclin D1 (Experiment Id: 2462) (primary)
- GC16539 — Cyclin D2 (Experiment Id: 7137) (primary)
- GC16401 — Cyclin E (Experiment Id: 6999) (primary)
- GC12449 — Cyclin dependent kinase inhibitor p19 (Experiment Id: 3047) (primary)
- MT114 — Waf1 (cyclin-dependent kinase inhibitor 1A) mRNA induction after ionizing radiation (Experiment Id: 75) (primary)
- MT115 — Waf1 (cyclin-dependent kinase inhibitor 1A) mRNA induction after ionizing radiation (Experiment Id: 75) (binary, 0 if <100)
- MT117 — Waf1 (cyclin-dependent kinase inhibitor 1A) mRNA induction after ionizing radiation (Experiment Id: 75) (log)
- GC14127 — cyclin-dependent kinase inhibitor 1A (p21, Cip1) (Experiment Id: 4725) (primary)
- MT227 — p16 (cyclin-dependent kinase inhibitor 2A) (Experiment Id: 115) (primary)
- GC10413 — p16 (cyclin-dependent kinase inhibitor 2A) (Experiment Id: 10717) (primary)
Step 4
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).
- MT114 is a primary pattern — the data are presented as supplied by the investigator.
- MT115 is a binary pattern — values less than 100 were assigned a value of 0, all others were assigned a value of 1.
- MT117 is a log pattern — the log10 of the primary values was calculated.
- These different patterns may be used as a seed to run COMPARE, which may identify different sets of compounds or targets.
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:
GC13524 — Cdk6 (cyclin-dependent kinase 6) (Experiment Id: 4122) (primary)
Cdk6 (cyclin-dependent kinase 6) RNA (primary)
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Primary reference(s): Cdk6 (cyclin-dependent and Cdk6 (cyclin-dependent Experiment Id: 4122 Pattern Id: GC13524 Clone number: 231497 3'Acc: H92463 |
Rationale: 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. |
Investigator(s): Botstein, Dr. David Stanford University School of Medicin Weinstein, Dr. John National Cancer Institute |
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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. |
Target Data: |
Compare: |
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GeneCards A database of human genes, their products and their involvement in diseases. It offers concise information about the functions of human genes.
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UNIGENE An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
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LocusLink Presents information on official nomenclature, aliases, sequence accession numbers, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and relevant web sites. |
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OMIM A catalog of human genes and genetic disorders. |
PubMed Search Pubmed for articles on: CDK6 |
Other Names:
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Step 5
Retrieve the data and figure out what it means.
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Primary reference(s): Cdk6 (cyclin-dependent and Cdk6 (cyclin-dependent Experiment Id: 4122 Pattern Id: GC13524 Clone number: 231497 3'Acc: H92463 |
This portion of the table provides links to the journal article(s), if any, in which the target measurement was described. This target is part of the NCI60 microarray data, for which there are 2 journal articles.
The Clone number is presented for microarray data and identifies the IMAGE clone from which the cDNA spotted onto the microarray was derived.
The 3'Acc is presented for microarray data and is the GenBank accession number for sequence data derived from the 3' end of the clone
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Rationale: 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. |
This portion of the table provides a brief explanation of what was measured.
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Investigator(s): Botstein, Dr. David Stanford University School of Medicin Weinstein, Dr. John National Cancer Institute |
This field identifies the investigator(s) who measured this molecular target and their affiliation.
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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 brief description of the methodology is provided. For more detailed information, see the primary references.
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Target Data: |
Clicking on will return the data in text form, identifying values for each of the cell lines from the NCI panel of 60 human tumor cell lines.
Clicking on will return a bar graph of the data.
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Compare: |
COMPARE is currently unavailable, but check back soon.
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GeneCards A database of human genes, their products and their involvement in diseases. It offers concise information about the functions of human genes.
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For Molecular Targets which can be associated with a named gene, there is a link to GeneCards. This resource, developed and maintained by the Weizmann Institute, provides information on gene function and provides links to many other useful sources of information on the gene of interest.
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UNIGENE An experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters.
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For virtually all Molecular Targets there is a link to Unigene. This resource, developed and maintained by the NCBI at NIH, can provide clues as to possible function of a DNA sequence. Even microarray clones that are not linked to a named gene may have information in Unigene (e.g. sequence homology to a known gene). Unigene also provides links to other NCBI resources.
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LocusLink Presents information on official nomenclature, aliases, sequence accession numbers, phenotypes, EC numbers, MIM numbers, UniGene clusters, map information, and relevant web sites. |
Targets associated with a named gene have a link to LocusLink. This resource, developed and maintained by the NCBI at NIH, provides concise summaries and links to information available from numerous sources.
We do not link to LocusLink for microarray targets, but it can be accessed by following the Unigene link.
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OMIM A catalog of human genes and genetic disorders. |
Targets associated with a named gene have a link to OMIM. This resource, developed and maintained by the NCBI at NIH, provides information on association of a particular gene with human disease.
We do not link to OMIM for microarray targets, but it can be accessed by following the Unigene link.
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PubMed Search Pubmed for articles on: CDK6 |
Click on the gene name (CDK6 in this example) to run a PubMed search.
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Other Names:
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Many genes and proteins are known by multiple names. For some of the Molecular Targets we provide a list of some of the names, other than the official gene name, by which this Molecular Target is known. This can be useful in searching PubMed for articles, if the search using the gene name was unsuccessful.