2.4.1 GeneClass menu

A gene class (e.g. all named genes, ESTs, oncogenes, etc.) is a set of genes that belongs to the class of genes in the universe of genes in the particular microarray database. MAExplorer may restrict the set of genes by "Gene Class" membership (currently includes All Genes, All named Genes, ESTs similar to genes, Unknown ESTs, All genes and ESTs, Good genes,
Replicate genes (i.e. with more than one copy of the gene in the array), Calibration DNA, genes from user's plates). The additional Gene Class list of names depends on its availability in a specific database.

GeneClass menu used for selecting a particular subset of genes by gene class membership

Figure Gene Class menu. The user may select a subset of genes that belong to one of the classes of genes. This shows the user selecting the set of "All named genes" that are indicated with red (white) circle over the spots in the array intensity (ratio) pseudoarray image.

The GeneClass 'Replicate genes' showing all genes occurring more than 
once in the array

Figure Example of all replicated genes occurring more than once in the array. This was selected by using the GeneClass 'Replicate genes'. You may use the data Filter "Filter by genes with replicates" instead of the GeneClass. This has the advantage that you may use other GeneClasses (e.g. ESTs, or All named genes, etc.). Alternatively, you can find all of the replicates for a particular gene by 1) use the Gene Guesser to find the particular gene you want; 2) press "Set E.G.L." to save it as an Edited Gene List; 3) enable the Filter "Filter by E.G.L." at the same. This will show all occurrences of that gene.

The set of all genes constitutes a number of different gene classes. It is possible to restrict the subsequent analysis to a particular subset of these genes called a gene class. The GeneClass menu operations include operations to select the current set of genes to analyze from the set of all genes by their membership in a gene class.

Some of the above gene classes are deduced from the gene name supplied with the Gene In Plate Order (GIPO) file for the array. We use the following automatic classification rules shown in Table 2.4.1.

Table 2.4.1 Rules for the automatic classification of gene names into the default Gene Class sets. The gene name is analyzed alphabetic-case independently.

Gene class Rule for class membership
All genes all genes on the array
All named genes not starting with "EST"
ESTs similar to genes genes starting with "EST,"
ESTs genes with the name "EST"
Replicate genes genes with multiple copies
Calibration DNA genes using the configuration file name "calibDNAname" (optional - see Appendix Table C.4.1 )
Your plates clones using the configuration file name "yourPlates" (optional - see Appendix Table C.5.1-C))
Empty Wells empty wells where no spot exists on the array indicated by keywords "empty", "empty well" or "EmptyWell" (optional - see Appendix Table C.5.1-C) )
Good Genes spots on the array where the GIPO QualCheck data was used and was valid. If it was not used, then it assumes all spots are good. (optional - see Appendix Table C.4.1 ) GeneClass ontology subsets [Future]

If the Set Gene Class subset were activated, it might include categories such as the following. If the categories exist and the data is made available to MAExplorer, then it is possible to specify gene subsets by Gene Class name. It is the responsibility of the database creator to define a mapping table supporting these named subsets of named genes. Simulating Gene Class ontologies using Gene Set operations

You can effectively implement finding ontology subsets for Gene Class subsets using the following procedure. The trick is to repeatedly define an E.G.L. gene subset using the gene name guesser to find the genes of interest and save it as a named gene subset. Edit out genes you don't want. Then you would repeatedly do the OR of gene sets of interest, saving the result as a new named set. Then doing the OR of another gene set with the set you just created, etc.


  1. Use the Gene Name Guesser (see Figure 2.3.1) to collect genes belong to a particular ontology. Pressing "Set E.G.L" puts the genes from the guesser into the EGL set. You can then delete any genes that don't belong by clicking on the gene in the pseudoarray image with the SHIFT key pressed.
  2. Save the EGL as a name gene set with a meaningful name representing the ontology construct using the (Edit | Save 'Edited Gene List' as named gene set) (see Section 2.3.2 for gene set editing commands).
  3. Repeat steps [1] and [2] to gather additional sets.
  4. Merge appropriate gene sets to get the complete ontology constructs using the (Edit | OR (Union) of 2 gene sets) as required.
  5. Finally, set the (Edit | Assign 'User Filter Gene Set') to select a particular gene class to use, and then
  6. Enable the data Filter by setting (Filter | Filter by 'User Filter Gene Set' membership) (Section 2.4.3).