Overview of Help-Pages

Frequently asked scientific questions

[Technical FAQ]

1. General questions

  1. Which elements may be involved in regulation of gene transcription?
  2. What is the difference between all ElDorado versions?

2. Promoter identification and extraction

  1. How can I identify the promoter sequence of a gene?
  2. What is the length of a promoter?
  3. I have the complete coding sequence (CDS) of a gene. Can I use this information to identify the promoter?
  4. What is the exact meaning of gold, silver, and bronze transcripts?
  5. Shall I trust an extracted upstream region as a promoter (from a bronze transcript)?

3. Identification of transcription factor binding sites

  1. How do I search for transcription factor binding sites?
  2. I have a promoter sequence, but MatInspector did not find the TATA box!
  3. There is a known transcription factor binding site in my promoter, however, it is not found by MatInspector!
  4. MatInspector also found transcription factor binding sites on the (-)-strand of my promoter sequence. What is the difference between (+)- and (-)-strand matches?
  5. MatInspector found a transcription factor binding site with a matrix similarity of 0.81. Is this a good match?
  6. How are matrix families defined in MatInspector?
  7. Why are there different matrices for the same factor? Which one should I use?
  8. I run an analysis using the matrix family describing the binding sites of the TF I am interested in. The result does not contain any entry for this TF, only other matrices of this family are shown in the result. Does this mean that no potential binding sites for my TF are found?
  9. What is the difference between core and matrix similarity?
  10. I have several different binding sites (e.g. footprints, oligos) for a transcription factor. How can I define a pattern description for all these sites?
  11. I am trying to determine the potential in silico binding sites for my gene of interest and MatInspector found several hundred binding site matches. Are there any resources to help better determine functional binding sites, or at least to try to narrow down this list to more specific matches?
  12. I have a consensus binding sequence for a transcription factor. I want to see if this consensus binding site is in the promoter of a handful of genes shown to be up/down-regulated in one of our experiments. What is the best way to go about this with your software?

4. Identification of promoter models

  1. What is comparative sequence analysis?
  2. What can I do with a promoter model?
  3. I only have a single promoter sequence. How to perform a functional sequence analysis?
  4. I have a promoter/ a CDS/ expression array data. How to identify other target genes?

5. Design of mutation experiments

  1. How can I specifically delete/insert/modify a transcription factor binding site in my promoter sequence?

6. Characterization of gene sets

  1. I want to export the GePS ranking results for my gene set. How can I do this?