Identify Transcription Factor Binding Sites

Although the human genome has been completely sequenced, there is much to still learn about its biology. For example, the study of gene regulation is an important area of research. Researchers seek to identify promoters and transcription factor binding sites for their genes of interest.

As shown in the earlier exercise on retrieving records annotated with a given biological feature, some existing database records are annotated with biological features such as promoters.

In other cases, scientists are still in the process of identifying the promoter region and other regulatory regions such as transcription factor binding sites.

If a user wants to analyze his/her nucleotide sequence data to identify potential transcription factor binding sites, does NCBI have such an analytical tool? What is an easy way to find out? If not at NCBI, where can a user find restriction map software?

If desired, background information about gene regulation, promoters, and transcription factors is available in the Entrez Books database.

Determine if NCBI has an analytical tool that identifies transcription factor binding sites in a query sequence

1. NCBI Resource Guide - see if the term "transcription factor" exists in the name or description of any NCBI resource



• use your browser's Edit/Find in Page function to see if the term transcription factor exists in the name or description of any NCBI resource
• because the Resource Guide is a catalog of NCBI resources, a key term such as "transcription factor" would be present in the name or description of a relevant resource
• if such a key term does not in the Resource Guide (as is the case), it indicates that NCBI probably does not have that type of resource
• you might want to search the NCBI web site (next step) to confirm this


2. NCBI Site Search - see if the term "transcription factor" exists on other pages within the NCBI web site



• to confirm the results of the Resource Guide search, you can also do an NCBI site search for the term transcription factor. You will retrieve a number of hits on the NCBI web site, but the context in which the search term appears will vary and none of the hits are for software or web tools that allow a user to identify potential transcription factor binding sites in a query sequence.
• because NCBI does not offer the necessary type of tool, search some directories of molecular biology databases and software, such as the examples listed below, to find sites that do.

Search some directories of molecular biology databases and software. Try each of the following and compare results. Some directories focus on either databases or software, while others contain a mixture of both, so you'll find hits in some and not in others.

1. Nucleic Acids Research 2007 Database issue -- published annually on January 1, the database issue features 3-5 page summary articles on over 100 databases each year. Because of the large number of databases in existence, each issue only covers a subset. There is also a companion searchable database of summary articles from current and previous database issues



• search the current Database issue and/or the database of summary articles for the term transcription factor
• as is true for some of the other directories noted on this page, the NAR issue features databases rather than software, so a search for transcription factor will find databases. However, it might be worth looking at the summary articles for those databases because some might be associated with corresponding analytical software.


2. Nucleic Acids Research Web Server issue - launched on July 1, 2003 as a companion to the annual NAR Database Issue, focuses on web servers and analytical tools rather than molecular biology databases

   2003 Web Server editorial (full text); complete table of contents
   2004 Web Server editorial (full text); complete table of contents
   2005 Web Server editorial (full text); overview; complete table of contents
   2006 Web Server editorial (full text); overview; complete table of contents
   2007 Web Server editorial (full text); overview; complete table of contents
   Searchable database of web server summaries

• within each Web server issue table of contents, you can do an "edit/find in page" to search for the term transcription factor. Depending on the servers covered in each issue, you might find hits. As of August 3, 2007, you will find a hits in each issue (2003 issue: SiteSeer, MATCH, Gibbs Recursive Sampler, YMF, Target Explorer; 2004 issue: MSCAN, Weeder Web, SITECON, rVISTA 2.0, POBO, Dragon TF Association Miner; 2005 issue: AthaMap (for Arabidopsis thaliana), WordSpy, P-Match, CONREAL; 2006: Zinc Finger Tools, VOMBAT, POXO, Composite Module Analyst; 2007: MYBS (yeast)).
• alternatively, or in addition, search the complete set of web server summaries for the term transcription factor. As of August 3, 2007, the will find 57 hits, including all of the above (except "Zinc Finger Tools"), plus additional servers.



3. ExPASy Life Science Directory - originally developed by Amos Bairoch, Head of the SWISS-PROT group at the Swiss Institute of Bioinformatics, and now maintained by ExPASy



• use your browser's Edit/Find in Page function to see if the term transcription factor exists in the name or description of any resource on the page
• because the ExPASy page primarily lists molecular biology databases rather than software, you find some hits related to the former (e.g., TRANSFAC - Transcription factors db), but you don't find a sequence analysis tool
• near the top of the page, note there is a category for "Biol. soft. & db catalogs", so if you don't find something on the ExPASy page, just look further in the catalogs (some of which are included on this page)


4. Biocatalog by EBI - a catalog of molecular biology databases and software programs maintained by the European Bioinformatics Institute (EBI)



• browse the catalog by category, following the links for categories such as DNA, Genomes, or Servers, then browsing relevant subcategories. Use your browser's Edit/Find in Page function to find resources that contain the term transcription factor in their name or description.
• or search the Biocatalog using the Sequence Retrieval System (SRS) server:
• select the Library Page tab
• expand the Other Databases category
• check the box beside BIOCATAL
• enter transcription factor as the search term
• press the Quick Search button beside the text box
• the search results page will display a list of database entry numbers that match your query. Use the Display Options dialog box in the left sidebar to display the complete entries.

Web Search

Of course, as an alternative to searching specific directories of molecular biology databases and software, you can do a general search of the web using a tool such as Google. One advantage of searching directories such as the NAR Database and Web Server issues, however, is that the resources you will retrieve have been peer reviewed.