GeneOntology.pdf

From Array Suite Wiki

Jump to: navigation, search

Contents

Gene Ontology

Overview

The Gene Ontology (GO) module will perform built-in gene ontology classification on one or more significant lists. Once the user generates a list of significant variables, Array Studio can go through all possible GO terms (across different class levels) to see how many variables in the list are covered by the GO terms. The users can infer different biological attributes (such as functions, corresponding biological process) of the variables in the list. A classification Table will be generated under the Ontology tab of the Solution Explorer. It uses the Gene Ontology database. More information can be found at http://www.geneontology.org.

To run this module, click MicroArray | Annotation | Gene Ontology.

Warning.png WARNING: Array Studio does not provide the mapping between the probesets/genes to GO ID. The user needs to make sure each variable (either probesets/gene) has the GO ID in the annotation table.

Gene Ontology menu.png

[back to top]

Input Data Requirements

This module works on -Omic data types with ontology information in the annotation file.

[back to top]


General Options

GeneOntol0.png

[back to top]

Input/Output

  • Project & Data: The window includes a drop-down box to select the Project and Data object to be filtered.
  • List for classification: Define which list of variables should be examined in the specified -Omic data set.
  • GO term columns: The user need to specify the columns containing GO terms in the annotation table, so that for each variable in the classification list, Array Studio can find the corresponding relationship between different classes in the GO.
  • Output name: The user can choose to name the output data object.
[back to top]


Options

  • Classification level (0-6): This box allows the user to specify the GO ontology classification level. Gene Ontologies are based on a tree. The Classification level will set how far up the tree the user is interested in seeing, with the higher levels corresponding to more detailed ontologies.
  • Biological Process: This is one of the three main domains in Gene ontology. Checking this box will allow Array Studio go through user specified class(es) under Biological Process to classify each variable. Note that to classify the variable under this domain, the user must provide the corresponding GO ID for the variable under this domain.
  • Molecular function:This is one of the three main domains in Gene ontology. Checking this box will allow Array Studio go through user specified class(es) under Molecular function to classify each variable. Note that to classify the variable under this domain, the user must provide the corresponding GO ID for the variable under this domain.
  • Cellular component: This is one of the three main domains in Gene ontology. Checking this box will allow Array Studio go through user specified class(es) under Cellular component to classify each variable. Note that to classify the variable under this domain, the user must provide the corresponding GO ID for the variable under this domain.
  • Update frequency (days): This box allows the user to specify how often Gene Ontology information is downloaded (as it is a database that is updated frequently). The default is 30, i.e., if the user ran this analysis 30 days ago, Array Studio would check the database again on GO website.
  • Calculate p-values: By default, the Gene Ontology Classification will only count the number of variables in the selected lists that belong to each ontology. However, if the Calculate p-values (assumes variable independence) checkbox is selected, this command will also generate p-values for each count/classification (Based on Fisher-exact tests).
    • Choose universal list: The user can define a list to compare with current classification list. By default, it is all, so Array Studio will simply classify all variables to compare the results with user's variable list.
    • Multiplicity: The user can define the adjust method for p value.
[back to top]


Output Results

An example result is shown below. Each Category lists a GO Term (with a link to the Gene Ontology website), as well as the number of hits for that category in a particular list (The column name is the list name). A corresponding p-values to see whether the Go Term is highly correlated to the list will also be generated (if the box is checked).

GeneOntol1.png

[back to top]


OmicScript

Gene Ontology Classification

[back to top]


Related Articles

[back to top]

EnvelopeLarge2.png