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DBD--taxonomically broad transcription factor predictions: new content and functionality.

Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA - Nucleic Acids Res. (2007)

Bottom Line: All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family.We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes.Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. dbd@mrc-lmb.cam.ac.uk

ABSTRACT
DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

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Examples of new search capabilities and content. (a) Search for TFs from a particular organism containing a specified DBD. The example used here is TFs from Homo sapiens containing the homoeobox domain. (b) The search in (a) results in TF predictions from Homo sapiens containing the homoeobox DNA-binding domain. (c) Selection of HOXA9 from (b) results in a web page with detailed information on this particular TF. (d) Clicking on the Pfam domain combination link in (c) retrieves the subset of TF predictions, which have the same two-domain arrangement as the HOXA9 transcription factor.
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Figure 1: Examples of new search capabilities and content. (a) Search for TFs from a particular organism containing a specified DBD. The example used here is TFs from Homo sapiens containing the homoeobox domain. (b) The search in (a) results in TF predictions from Homo sapiens containing the homoeobox DNA-binding domain. (c) Selection of HOXA9 from (b) results in a web page with detailed information on this particular TF. (d) Clicking on the Pfam domain combination link in (c) retrieves the subset of TF predictions, which have the same two-domain arrangement as the HOXA9 transcription factor.

Mentions: Researchers can use the DBD database in several ways. For instance, all TF predictions are available to download. However, most users are only interested in a small number of TFs, so we have expanded the website search options to allow retrieval of individual TFs and subsets of TFs. New search capabilities include: searching for gene names, for example lacI or P53; listing all TFs that contain either a specified DBD or non-DBD family, for instance all TFs containing the bZIP (leucine zipper) family; retrieving all TFs containing a specified DBD family, which occur in a particular organism, e.g. all homoeodomain-containing TFs in human (Figure 1a and b).Figure 1.


DBD--taxonomically broad transcription factor predictions: new content and functionality.

Wilson D, Charoensawan V, Kummerfeld SK, Teichmann SA - Nucleic Acids Res. (2007)

Examples of new search capabilities and content. (a) Search for TFs from a particular organism containing a specified DBD. The example used here is TFs from Homo sapiens containing the homoeobox domain. (b) The search in (a) results in TF predictions from Homo sapiens containing the homoeobox DNA-binding domain. (c) Selection of HOXA9 from (b) results in a web page with detailed information on this particular TF. (d) Clicking on the Pfam domain combination link in (c) retrieves the subset of TF predictions, which have the same two-domain arrangement as the HOXA9 transcription factor.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238844&req=5

Figure 1: Examples of new search capabilities and content. (a) Search for TFs from a particular organism containing a specified DBD. The example used here is TFs from Homo sapiens containing the homoeobox domain. (b) The search in (a) results in TF predictions from Homo sapiens containing the homoeobox DNA-binding domain. (c) Selection of HOXA9 from (b) results in a web page with detailed information on this particular TF. (d) Clicking on the Pfam domain combination link in (c) retrieves the subset of TF predictions, which have the same two-domain arrangement as the HOXA9 transcription factor.
Mentions: Researchers can use the DBD database in several ways. For instance, all TF predictions are available to download. However, most users are only interested in a small number of TFs, so we have expanded the website search options to allow retrieval of individual TFs and subsets of TFs. New search capabilities include: searching for gene names, for example lacI or P53; listing all TFs that contain either a specified DBD or non-DBD family, for instance all TFs containing the bZIP (leucine zipper) family; retrieving all TFs containing a specified DBD family, which occur in a particular organism, e.g. all homoeodomain-containing TFs in human (Figure 1a and b).Figure 1.

Bottom Line: All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family.We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes.Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

View Article: PubMed Central - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. dbd@mrc-lmb.cam.ac.uk

ABSTRACT
DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

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