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Help : Genelist Help


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Description

Genelists are text files which specify a set of "genes".  They can be used to customize data retrieval, normalization and other tasks. "Genes" can be identified by name, suid, and other identifiers.

Only registered users of the database may use genelists, since the files are stored locally in your loader account, in the "genelists" directory.  They are accessible via sFTP, and may be downloaded, created or edited on your desktop machine, and uploaded as desired.

Genelists may be used for data retrieval.  Groups of "genes" may be combined into a genelist and selected as a group in Advanced Results Search for retrieving a subset of the full data.  Genelists may also be used to normalize data, Calculate Q-score and collapse data using Synthetic genes.

There are several applications that use genelists specific for the application. These specialized genelists are available for all SMD users. Specialized genelists are available during data retrieval as part of the gene selection process, for the Synthetic Gene tool and for Q-score calculation.

Creating a genelist on your desktop computer

Genelists are tab-delimited text files, which may be easily created in a spreadsheet program like Excel.  See below for the format.  It may also be convenient to download an already-created genelist, and edit it to add or remove genes or annotation.  Examples for genelists can be downloaded from here: using cloneids or goids.

When finished, save the list as a tab-delimited text file, and upload it to your loader "genelists" directory using sFTP.

Genelist format

Genelists are tab-delimited text files.  The order of the columns is arbitrary and only the column headers specified in the table below are understood

Allowed Column Headers
Requirements
Description
NAME, SUID, LUID, SPOT, GOID or GOTERM
One and only one must be included.
Identifies the type of gene identifier.
  • NAME: can mean either CLONEID or ORFNAME
    (E.g.: IMAGE:1542757; YLR326W; HPY1808)
  • SUID: SMD unique identifier - unique for a sequence
  • LUID: SMD unique identifier for an instance of a sequence
  • SPOT: The spot/feature within a print design
  • GOID: Gene Ontology id to which a gene was annotated (e.g.: GO:0006616)
  • GOTERM: Exact name of the Gene Ontology term to which a gene was annotated (e.g.: 'nuclear envelope')
ANNOTATION
Optional column
Annotation for the 'gene' that you would like to include in your analysis in place of SMD-derived annotation.
WEIGHT
Required for synthetic gene application.
Weight for the gene in calculating the synthtic gene value. It should be a value between 0 and 1.
CHILDREN
Optional, used when the identifier used is GOID or GOTERM.
0, or missing value indicates that only genes that are directly annotated to the GOID/GOTERM are to be retrieved. Any other value will retrieve genes that are annotated either directly to the GOID/GOTERM or to its children.

Using Genelists

Data Retrieval: Data from the database will be retrieved for only the "genes" that are listed in your genelist file. You can select the genelist on the "Gene Selection and Annotation" page of data retrieval. First, you need to indicate you would like to use a genelist from your loader account by selecting the radio button, then select a genelist from the pulldown menu. (See Figure 1.). If you have annotation in the genelist file that you would like to keep during the rest of your analysis, you can do this on the same page. Select "Genelist Annotation" under the biological annotation section (see Figure 2.).

Retrieve Data by Genelist
Figure 1: Data Retrieval by Genelists.


Biological Annotation by Genelist
Figure 2: Keep biological annotation from Genelists.
Q-Score: Q-Score calculations for arrays will be performed using only the "genes" that are listed in a selected genelist. For further help, please look at the help document for Q-Score.

Normalization by Genelist: Using this application you can calculate a normalization value for an array using only the "genes" listed in a selected genelist. For further help, please look at the related help document.

Synthetic Genes: For further help, please look at the related help document.


Please send comments or questions to: array@genome.stanford.edu