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Overview of Help-Pages

GeneID Toolbox


[Introduction] [Info for GeneIDs] [Orthologous GeneIDs]

Introduction

The GeneID toolbox provides some of tools for one GeneID or lists of GeneIDs. The following actions can be performed:

Retrieve information for a list of GeneIDs

Input

Here you can either paste a list of Entrez GeneIDs (e.g 30818) or Ensemble GeneIds (e.g. ENSG00000115041) into the input field or upload a file with GeneIDs.
In both cases the GeneIDs can be separated by commas, blanks, or new lines.
Note that the algorithm takes the selected species into account, so GeneIds from e.g. mouse will not be found if "Homo sapiens" is selected as current genome (top right).

Output

The output is a table consisting of

The output table can be sorted by clicking on the arrows within the column headers.

The results can be downloaded directly as an Microsoft Excel™ file or in tab-separated format.

Additionally, the gene body positions can be saved in BED file format, allowing further analysis with tasks that take genomic positions as input (e.g. GenomeInspector). Gene body here is defined as the largest extension of all transcripts of a gene, i.e. from start of the most 5' transcript to end of the most 3' transcript.

Please note the following:

Example output:

Example screenshot


Retrieve information for a keyword list

Input

You can either paste a list of symbols/keywords into the input field or upload a file with symbols/keywords. Please also choose which type of keywords you are supplying (Gene Symbols/Names, Affymetrix Probe Set IDs or Transcript Accession Numbers).
In both cases the keywords can be separated by commas, blanks, or new lines.
Note that the algorithm takes the selected species into account, since keywords can be ambiguous across species.

Output

The output is a table consisting of

The output table can be sorted by clicking on the arrows within the column headers.

The results can be downloaded directly as an Microsoft Excel™ file or in tab-separated format.

Additionally, the gene body positions can be saved in BED file format, allowing further analysis with tasks that take genomic positions as input (e.g. GenomeInspector). Gene body here is defined as the largest extension of all transcripts of a gene, i.e. from start of the most 5' transcript to end of the most 3' transcript.

Please note the following:

Example output:

Example screenshot


Search for orthologous GeneIDs

This task identifies GeneIDs in genomes of different species that are orthologous to the GeneIDs in the input. To identify orthologous GeneIDs in a target species, the homology groups of ElDorado (background) are used.
Lists of orthologous GeneIDs can be saved and can be used as input for other Genomatix programs like GeneRanker or GePS.

Parameters

Input
Input You can either paste a list of GeneIDs into the input field or upload a file with GeneIDs. In both cases the GeneIDs can be separated by commas, blanks, or new lines. If both fields are filled, the pasted GeneIDs will be used.
Organism Please select the correct organism for the input GeneIDs; input GeneIDs will only be searched in this species.

Target
Target species The program searches the genomes of the species you select here for GeneIDs which are orthologous to the GeneIDs in the input file. Depending on the source organism only a certain selection of target organisms is available (i.e. orthologs can be searched only within vertebrates, plants, or insects respectively).
Output
Result Here, you can edit the default name of the result file.
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!

We recommend to use the email option for more than 500 input GeneIDs.

Output

The output has three sections:

1. Analysis Parameters

2. Statistics of GeneIDs

Note: "more than one GeneID/not unique" in the output indicates, that one step of the calculation (from GeneID to ElDorado Locus, to Locus in the target organism and then to GeneID in the target organism) was ambiguous, and the program does not list the GeneIDs.

Example screenshot

3. Orthologous GeneIDs

For each input GeneID, the output lists the orthologous GeneIDs with the corresponding gene symbol and ElDorado Locus for each selected target species. The link to the ElDorado locus will open a new window with more details on the locus (see More Gene Info page)

Example screenshot