Software
GRIFn
[Gene Relationship Identification in Functional data]
GRIFn is a system for evaluation of datasets and methods using a
functional genomics gold standard based on curation by expert biolgists. It
allows users to assess the ability of their datasets or methods to recapitulate
known biology both in a global sense and in the context of specific biological
processes. GRIFn allows enables fair comparisons between various data types and
methods.
bioPIXIE
[Biological Pathway Inference from eXperimental Interaction
Evidence]
bioPIXIE is a novel system for biological data
integration and visualization for S. cerevisiae. It allows the user to
discover interaction networks and pathways in which the user's gene(s) of
interest participate. The system is based on a Bayesian algorithm for
identification of biological networks based on integrated diverse genomic data.
Myers CL, Robson D, Wible A, Hibbs M, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biology 2005, 6(13):R114.
ChARMview
[Chromosomal Abberation Region Miner and Viewer]
ChARMView is a visualization and analysis system for guided
discovery of chromosomal abnormalities from microarray data. Our system
facilitates manual or automated discovery of aneuploidies through dynamic
visualization and integrated statistical analysis. ChARMView can be used with
array CGH and gene expression microarray data, and multiple experiments can be
viewed and analyzed simultaneously.
Myers CL, Chen X, Troyanskaya OG. Visualization-based discovery and analysis
of genomic abberations in microarray data. BMC Bioinformatics, 6:146,
2005.
Myers CL, Dunham M, Kung SY, Troyanskaya OG. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics, 20:3533-3543, 2004.
GOLEM
[Gene Ontology
Local Exploration Map]
GOLEM is a tool for viewing, navigating,
and analyzing the hierarchical structure and annotations to the gene ontology.
The visualization component allows a user to see the local graph structure
around a GO term of interest and navigate to nearby nodes. GOLEM also provides
the ability to look for statistical enrichment of GO terms in lists of genes and
then observe the relationships between those terms. GOLEM is available both as
an applet for use online and as a standalone download.