Our widgets for functional genomics use Orange, a data mining
and machine learning suite. Orange can be accessed through scripting in
Python,
or by visual programming in Orange Canvas.
In functional genomics, we have also designed a web-based tool for mutant data analysis called GenePath (also featured
in Science's NetWatch).
"Go Term Finder" widget is used
here to demonstrate functional unrelatedness of the CDC46 and PIG1,
confirming the proposed model of adjacent genes' coexpression given by Cho and
coworkers. They proposed that adjacent genes were coexpressed in their
experiment because of the effect of upstream regulatory sequence sharing or
local positional effects on gene transcription, rather than because of
functional relatedness. While CDC46 is involved in the processes of DNA
replication initiation, DNA unwinding, establishment of chromatin silencing and
pre-replicative complex formation and maintenance, PIG1 is involved in
the process of regulation of glycogen biosynthesis � the genes are thus
functionally unrelated, according to GO annotation, however, as shown in the "Expression
Profiles" widget, they are coexpressed.