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Gene2Promoter: Retrieval and analysis of promoters


[Introduction] [Parameters] [Output]
[Available Genomes]

Introduction

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:

  1. to extract and/or to interactively analyze up to 1000 promoters (details below)
  2. extract large sets of promoters and/or filter promoters for transcription factor binding sites (see Gene2Promoter large scale for details)
    Note: promoter sequences are always extracted in 5' → 3' direction.

For a given list of input genes, Gene2Promoter provides the chromosomal location and a short description of the corresponding gene together with the promoters and alternative transcripts. Several tasks for comparative analysis of the selected promoters can be started directly from the Gene2Promoter output.

Gene2Promoter Features (interactive)


Parameters

Gene2Promoter allows to enter gene names, GeneIDs from EntrezGene, Affymetrix IDs, or sequences as explained in the following table.

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:
  • Gene symbols (e.g. HMGA1).
  • Full gene names (e.g. high mobility group AT-hook 1) or more general expressions describing a complex group of genes (e.g. transcription factor or G protein coupled receptor). Wildcards (e.g. COX*) are also possible.
  • GeneIDs from EntrezGene (e.g. 3159).
  • Accession numbers of transcripts that have been mapped to the ElDorado genomes. These include accession numbers from RefSeq (e.g. NM_002131) and Ensembl (e.g. ENST00000327014) as well as full-length transcripts from GenBank (e.g. AK096863).
  • Genomatix Promoter Ids starting with "GXP_" like GXP_311812
  • SNP identifiers from dbSNP (e.g. rs11557697).
  • MicroRNA IDs from miRBase (e.g. mmu-mir-668 or MI0004134).
  • Affymetrix probe set Ids (e.g. 210457_x_at).
    • Only Affymetrix probe set Ids from the default chips of the organisms are searched. You can view and change the default chips on the "Personal" page of your account.
    • The assignment of Affymetrix probe set identifiers to transcripts is based on genomic mapping of each single probe. A transcript will be displayed if at least one single oligo-nucleotide probe of the probe set (usually 11 probes) matches. For mixed probe sets (cross-hybridisation) all relevant transcripts are displayed.

Per default, all ElDorado database tables containing gene related keywords are searched in a defined order. To restrict your search to a certain keyword (e.g. Gene IDs or gene symbols), choose it from the list to the right of the text field.

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:

  • GenBank (sections Bacteria, Invertebrates, Other Mammalian, Other Vertebrates, Plants, Primates, Rodents, Viruses, ESTs) (e.g. 'M65229')
  • Eukaryotic Promoter Database (EPD) (e.g. 'EP30014')
  • NCBI Reference Sequences (mRNA sequences) (e.g. 'NM_000402')
  • Genomatix Promoter Database (e.g. 'GXP_107276')
  • dbSNP (e.g. 'rs1234')
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. Clicking on will reveal them.
Genome(s) to Search
Select organism(s) By default the genome of the currently selected genome (top right on the page) is searched. Check one or several of the other available organisms if you want to extend your search to other genomes.
Parameters
Email address Here you can choose between two methods for receiving the results:
  • Show result directly in browser window
    In this option the URL of the result is directly shown in your browser window.

    Warning: Please use this option only for analyses which can be performed in a short time.
    If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to".

  • Send the URL of the result via email
    In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished.

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. Clicking on will reveal them.

Output

The result page contains three sections: