Table of Contents
Reporter, a term coined by the MAGE object model refers to spotted DNA sequence on a microarray. Reporters are therefore usually described by a sequence and a series of database identifiers qualifying that sequence. Reporters are generally understood as the thing biologists are interested in when carrying out DNA microarray experiments.
In BASE, reporters also refer to Affymetrix Probeset ID but reporters can be used to describe genes, transcripts, exons or any other sequence entity of biological relevance.
Reporter Type allows classification of reporters based on their usage and qualification defined during the array design specification.
You can manage the reporter types by going to→ → .
The name of the reporter type. It is advised to define the name so that it is compatible with the MIAME requirements and recommendations issues by microarray data repositories. Alternately, the local reporter type could be submitted to those repositories for term inclusion.
A description of the reporter type.
Go to→ to view and manage the reporters.
Reporters are used to represent genes, transcripts, exons and therefore come in their thousands. To solve this problem, BASE relies on Reporter import plug-ins. Those need to be specifically configured to deal with a particular input file format. This input file can be typically be an Axon GAL file or an Affymetrix CSV file which both provide information about reporters and their annotations. See Chapter 19, Import of data for more information about importing and Section 22.4, “Plug-in configurations” for more information about configuring file formats.
|Exchanging plug-in configurations|
As for any other plug-in, configuration parameters
can be saved as an XML file and exchanged with
another BASE instance, thereby reducing
configuration burden (provided the two instances have
|Dealing with Affymetrix probesets|
In BASE, Affymetrix probesets should be treated as reporters. The probeset ID could be stored in both the Name and the External ID fields of the reporter table. Storing the probeset ID should be enough as most analysis tools allow retrieval of updated information based on the probeset ID from web resources.
For some Affymetrix chips the associated CSV file does not list all reporters on the actual chip. This will lead to problems in later use of the affected chip types. Simply use the associated CDF file to import the missing probesets into BASE, make sure not to upgrade existing reporters when starting the plug-in. The CDF file contains no annotation information and consequently annotation information is removed if the CDF used to upgrade annotations.
Reporters can also be created or edited manually one-by-one. This follows the same pattern as for all other items and is described in general terms in Section 6.3, “Working with items”.
This tab shows core information that would be common to all BASE instances.
The name of the reporter. This is often the same as the External ID.
The external ID of the reporter as it is defined in some database. The ID must be unique within BASE. The external ID is what plug-ins uses to match reporter information found in raw data files, array design files, etc.
Optionally select a reporter type.
The gene this reporter represents.
Reporters belong to a special class whose properties
can be defined and extended by system
administrators. This is done by modifying the
extended-properties.xml file during
database configuration or upgrade. All fields on
this tab are automatically generated based on this
configuration and can be different from one server
to the next.
See Section 21.3, “Installation instructions”
and Appendix D, extended-properties.xml reference
for more information.
It is possible to configure the extended properties so that links to the primary external databases can be made. For example, the Cluster ID is linked to the UniGene database at NCBI.
|Deleted reporters cannot be restored|
Reporters are treated differently from other items (e.g biosources or protocols) since they does not use the trashcan mechanism (see Section 6.5, “Trashcan”). The deletion happens immediately and is an unrecoverable event. BASE will always show a warning message which you must confirm before the reporters are deleted.
Reporters which has been referenced to from reporter lists, raw data, array designs, plates or any other item cannot be deleted.
A common problem is to delete reporters that has been accidentally
created. The regular web interface is usually no good since it
only allows you to select at most 99 reporters at a time. To solve
this problem the reporter import plug-in can be used in delete mode.
You can use the same file as you used when importing. Just select
delete option for the mode
parameter in the configuration wizard and continue as usual.
If the plug-in is used in delete mode from a reporter list it will
only remove the reporters from the reporter list. The reporters are not
deleted from the database.
It may be a bit confusing to delete things from an import plug-in. But since plug-ins can only belong to one category and we wanted to re-use existing file format definitions this was our only option.
BASE allows for defining sets of reporters for a particular use, for instance to define a list of reporters to be used on an array. There are two ways to do so:
Use thebutton on the → page.
Use thebutton on the → page.
The name of the reporter list.
An optional external ID. This value is useful, for example, for a tool that automatically updates the reporter list from some external source. It is not used by BASE.
Select one of the options for specifying which reporters should be included in the list.
|This option is only available when creating a reporter list from the→ page, not when editing an existing list or creating it from the → page.|
To add or remove reporters to the list use the Reporters tab on the single-item view page of a reporter list. This tab lists all reporters in the list and there are functions for removing, adding and importing reporters to the list.
A description of the reporter list.