- How do I navigate the promoter map?
Click and drag the gray selector box over the area of interest. Hold SHIFT-key, click and drag to resize selector box. Double-click to download the highlighted sequence.
- Why is the map page blank when I select a target gene?
If the transcription start site (TSS) for a given target gene has not yet been mapped, then the map page will not display the graphs.
- What are CpG Islands?
Genome sequences of >200 base pairs that have high G+C content and CpG frequency near and in approximately 40% of promoters of mammalian genes. The GC percentage is usually greater than 50% and the observed/expected CpG ratio is usually greater than 0.6.
- How do I read the CpG plot?
The program defines a CpG island as a region where the calculated % composition is over 50% and the calculated Obs/Exp (i.e., Observed/Expected) ratio is over 0.6 and the conditions hold for a miniumum of 200 bases. The CpG plots were created using emboss cpgplot. The CpG plot's x-axis is 0-10,000bp and the y-axis is the exp/obs raio. Mouse-over the image for additional plots (percentage and putative islands).
- What are Matrix Associated Regions (MARs)?
Matrix Association Regions, or MARs constitute a significant functional block within DNA sequences and facilitate the processes of differential gene expression and DNA replication. In order to discover the presence of MARs within DNA sequences we have used the MAR-Finder tool. MAR-Finder uses statistical inference to deduce the presence of matrix association regions, or MARs, in DNA sequences.
Matrix attachment region (MAR) are sequences in DNA where the nuclear matrix attaches. MARs mediate structural organization of the chromatin within the nucleus. These elements constitute anchor points of the DNA for the chromatin scaffold and serve to organize the chromatin into structural domains. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by MAR elements plays an important role in the regulation of gene expression.
- How do I read the MAR Map?
The MAR map is generated using a web-based tool developed by FutureSoft Corporation, MAR-Wiz. MAR-Wiz attempts to locate MARs within a given sequence using a computational approach, which is based upon the presence of specific DNA patterns that are known to occur in the neighborhood of MARs. All MAR maps have been generated using the default settings; the MAR Map displays 10,000 base pairs and the associated MAR Potential for that region.
- Can I see a list of B and/or T cell stages?
A list of B cell stages can be found here. T cell stages can be found here. The list contains surface markers, rearrangements and target genes associated with each stage.
- How do I send comments/feedback?
You can use our online form to send comments/feedback.
- How do I reference this database?
Please include the following reference in publications citing LymphTF-DB:
Childress, P. J., Fletcher, R. L., and Perumal, N. B. (2007) LymphTF-DB: A Database of Transcription Factors involved in Lymphocyte Development. Genes and Immunity, 8, 360 - 365.
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