|
|
Gene2Promoter provides access to promoter sequences of all genes annotated in the available genomes. Promoter regions are thoroughly annotated and validated according to highest scientific standards, including Genomatix proprietary technology (e.g. PromoterInspector, oligo-capping, comparative genomics).
Generally, there are two ways of accessing Genomatix promoters via Gene2Promoter:
Gene2Promoter allows to enter gene names, GeneIDs from EntrezGene, Affymetrix IDs, or sequences as explained in the following table.
| Organism | |
|---|---|
| Check organism | By default the genomes of all organisms listed are searched. Check one or several of the available organisms if you want to restrict your search to individual genomes. |
| Keyword Search | |
| Enter keywords, gene names, accession numbers, GeneIds, PromoterIds, or AffyIds | The gene names included in ElDorado are based on EntrezGene.
The input may contain the following gene related keywords:
|
| or Sequence Input | |
| Choose from your previously uploaded sequences | Select a sequence file from the list of your personal sequence files. |
| or enter the formatted DNA sequence | Enter your correctly formatted sequence(s) directly into the form, e.g.
with copy and paste. The following formats are accepted: There should be only IUPAC characters in the sequence, any other characters will be skipped! |
| or upload a file containing sequence(s) (max. 100MB) | If your browser supports this option, a sequence file can be uploaded. If you use this option, the file should contain the sequence(s) in either one of the following formats: |
| or enter accession number(s) |
If you are interested in one or several special sequences from a database section, you can supply a list of correct accession numbers in the form. If you want to select more than one accession number, please separate the accession numbers by commas or spaces. On the Genomatix server accession numbers from the following databases can be entered:
|
| or upload a file containing accession number(s) or Affymetrix ID(s) | If your browser supports this option, an ASCII text file with
accession numbers or Affymetrix IDs separated by commas or spaces can be
uploaded. Please note that the upload of formatted files from text processors like Microsoft Word does not work. These parameters are hidden by default. You can use the
 next to the section header to reveal them! |
| Parameters | |
|---|---|
| Email address | Here you can choose between two methods for receiving
the results:
The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management! These parameters are hidden by default. You can use the
next to the section header to reveal them! |
The result page contains three sections:
User input that is either of erroneous format (e.g. wrong accession number) or that cannot be found in the available database are listed in this section. For all other input genes/sequences information is shown how many sequences could be mapped, how many loci/transcripts could be found and how many promoters were extracted.
Example:
| 2 keywords were read from input | ||
|---|---|---|
| Results based on ElDorado 11-2007 | ||
| 2 | loci were analyzed | |
| 8 | transcripts were found in the mapped sequences | |
| 8 | unique promoters were found | |
For each input (i.e. sequence/Affymetrix ID/GeneID) the following information is displayed:
Please note that in some cases your input will be mapped to more than one chromosomal locus. It may also occur that a promoter cannot be found. This is generally due to the incomplete annotation of the genome sequences.
Links
Several links (where appropriate) provide access to
Promoters
Each promoter can have additional annotation:
Promoters can be selected for extraction and further analysis by clicking the check boxes in the Selection column. By default, only those promoters are selected where the search term was found to match exactly either the gene name, GeneId, accession number or any other transcript related IDs.
Transcripts
A promoter can be assigned to several alternative transcripts within a locus.
There are three possible quality levels assigned to the alternative
transcripts for a locus:
| gold | experimentally verified 5' complete transcript |
| silver | transcript with 5' end confirmed by PromoterInspector prediction |
| bronze | annotated transcript, no confirmation for 5' completeness |
If a promoter for a locus was identified via corresponding regulatory regions in the genomic sequence of one or more different organisms, there is no transcript listed and the promoter is called a CompGen promoter (see CompGen promoters and promoter sets).
If the search terms used as input were accession numbers, transcripts Ids, or Affymetrix probe set Ids, the transcripts that correspond to the search term are highlighted in orange.
Additionally, if the input were Affymetrix probe set Ids, the number of probes within this transcript is given in dark green.
Example:
When one or more transcription factor families (up to 5) are selected in the popup menu and the "Show" button is pressed, the page is reloaded and additional information is shown for each promoter: if ALL of the selected binding sites are present this is shown in red.
After selection of the desired length the selected promoters in the above result table can either be extracted or used to start an analysis with GEMS Launcher:
| © 1998-2013 Genomatix Software GmbH - All rights reserved |