Overview
Io (ISREC ontologizer) is a program for classifying microarray results in
the Gene Ontology. The strong point of the program is that it allows a
fine evaluation of the results based on various quality thresholds, in
particular on annotation quality.
Io is actually delivered with a reevaluated set of annotation files for
the Affymetrix mouse and human chips. The reevaluation was based on a
work (CleanEx) conducted at
SIB by Viviane Praz.
Io main user interface
Technical information
- Java 1.4, tested under Linux and Windows
- (Does not work properly under MacOS-X 10.x, putatively because of small incompatibilities in Apple's Swing library.)
- Annotation information fully independent from code
- Custom annotation easily pluggable via flat files
Links
Contacts
Io is developed mainly at the
Bioinformatics Core Facility (BCF) of the
Swiss Institute for Experimental Cancer Research
(ISREC). The BCF is a member of the
Swiss Institute for Bioinformatics (SIB).
Code design
Pascale Anderle and Thierry Sengstag
Code development
Thierry Sengstag
Annotation issues
Pascale Anderle and Viviane Praz (tagger)
Links
Pascale Anderle's home
Viviane Praz's home
Thierry Sengstag's home
CleanEx home page
Publications
[1] Anderle P, Sengstag T, Mutch DM, Rumbo M, Praz V, Mansourian R, Delorenzi M, Williamson G, Roberts MA,
Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes,
BMC Genomics, 2005 May 10;6(1):69
PubMed