Overview of Help-Pages

Frequently asked scientific questions

1. General questions

1. Which elements may be involved in regulation of gene transcription?

2. Promoter identification

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. I know that my sequence functions as a promoter, but PromoterInspector does not identify a promoter region in this sequence!
5. PromoterInspector predicted a promoter region in my sequence at position 650 to 985. Does this mean that the transcription start site is located at position 985?
6. Does PromoterInspector locate known promoter elements like CCAAT and TATA boxes?

3. Genomic mapping and extraction of promoters / genes

1. I know that my input sequence is from a human gene! Why is there no mapping in ElDorado?
2. I get overlapping (+) and (-) strand primary transcripts for my input in ElDorado. How do I know which is the right one?
3. I get a perfect mapping of my sequence onto a human chromosome, but why does "Literature based results" only offer information for other genes?
4. How can I be sure to get the correct promoter sequences from Gene2Promoter?
5. What is the exact meaning of gold, silver, and bronze transcripts?
6. Shall I trust an extracted upstream region as a promoter (from a bronze transcript)?
7. Gene2Promoter extracts more than one promoter sequence for my input. How can I find out the right one?
8. Why did Gene2Promoter extract a promoter of less than 600 bp?
9. Why are my ESTs not mapped? Why is no promoter found for my ESTs? They must be within some mRNA!

4. Identification of transcription factor binding sites

1. How do I search for transcription factor binding sites?
2. I have a promoter sequence, but GEMS Launcher did not find the TATA box!
3. There is a known transcription factor binding site in my promoter, however, it is not found by GEMS Launcher!
4. GEMS Launcher also found transcription factor binding sites on the (-)-strand of my promoter sequence. What is the difference between (+)- and (-)-strand matches?
5. GEMS Launcher 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 GEMS Launcher?
7. Why are there different matrices for the same factor? Which one should I use?
8. What is the difference between core and matrix similarity?
9. 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?
10. How can I identify the functional transcription factor binding sites in a promoter? Are all transcription factor binding sites found by GEMS Launcher functional?

5. 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. I have a set of co-regulated genes found by expression array data. I have the database accession numbers of all these genes. Can I use these database entries directly for a comparative promoter analysis?
6. Is it possible to generate a generic promoter model with GEMS Launcher?

6. Design of mutation experiments

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