Classify large gene list into
functional related gene groups
Rank the importance of the
discovered gene groups
Summarize the major biology of
the discovered gene groups
Search other functionally
related genes from genome, but not in your list
Visualize genes and their
functional annotations in a group by a single 2-D view
Explore global view of gene
groups in a Fuzzy Heat Map visualization
More
The advantage
of the tool:
A novel
gene-centric
annotation approach
Your genes are highly organized so
that they are more readable and understanable.
Your genes are ranked so that you can
quickly focus on the most likely important ones.
Your genes are displayed with their
annotation in one single view so that you can cross compare them.
Your genes can be extended so that
you have chance to know other functionally related genes, but not in
your list.
Rational
Concepts:
Fuzzy Heat map Visualization
Fuzzy heat map
visualization allows genes and terms to appear multiple times within
the heat map providing a much clearer view of gene-to-term
relationships within a cluster of related genes and a much clearer view
of cluster-to-cluster relationships.
more
Fuzzy
Heuristic
Partition
We developed a novel
heuristic partitioning procedure that allows an object (gene) to
participate in more than one cluster. The use of this method in
grouping related genes much better reflects the nature of biology in
that a given gene may be associated with more than functional group of
genes. Two additional advancement included in this algorithm are: 1)
the automatic determination of the optimal numbers of clusters (K), and
2) the exclusion of members (genes) that have weak relationships to
other members. Users are permitted to
change default parameters to set cluster membership similarity
stringencies. Fuzzy Heuristic Partitioning
of a gene list yields high quality clusters of highly related genes,
with some genes participating in more than one function cluster.
more
Grouping genes
based on functional similarity can systematically enhance biological
interpretation of large lists of genes derived from high throughput
studies. The Functional Classification Tool generates a gene-to-gene
similarity matrix based shared functional annotation using over 75,000
terms from 14 functional annotation sources. Our novel clustering
algorithms classifies highly related genes into functionally related
groups.
Tools are
provide to further
explore each functional gene cluster including listing of the
?consensus terms? shared by the genes in the cluster, display of
enriched terms, and heat map visualization of gene-to-term
relationships.A global view of
cluster-to-cluster relationships is provided using a fuzzy heat map
visualization.Summary information
provided by the Functional Classification Tool is extensively linked to
DAVID Functional Annotation Tools and to external databases allowing
further detailed exploration of gene and term information.
The Functional
Classification Tool provides a rapid means to organize large lists of
genes into functionally related groups to help unravel the biological
content captured by high throughput technologies.more
Please cite the web site or Genome
Biology 2003; 4(5):P3 within any publication that makes use of any methods inspired
by DAVID.
