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Functional
Annotation Tool
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| Introduction |
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The This tool suite, introduced in the first version of DAVID,
mainly provides typical batch annotation and gene-GO term enrichment
analysis to highlight the most relevant GO terms associated with a
given gene list . The new version of the tool keeps the same enrichment
analytic algorithm but with extended annotation content coverage,
increasing from only GO in the original version of DAVID to currently
over 40 annotation categories, including GO terms, protein-protein
interactions, protein functional domains, disease associations,
bio-pathways, sequence general features, homologies, gene functional
summaries, gene tissue expressions, literatures, etc. The improved
annotation coverage alone provides investigators with much more power
to analyze their genes using many different biological aspects in a
single space. Flexible options are provided to display results in
an individual annotation chart report or a combined chart report. In
addition, with its improved computational power, the new tool accepts
customized gene backgrounds, an option rarely found in other Web-based,
high- throughput annotation tools for typical gene-annotation
enrichment analysis. This feature was added in order to more
specifically meet the users? requirements for the best analytical
results.
The DAVID Functional Annotation
Clustering is a
newly-added feature to the DAVID Functional Annotation Tool. This
function uses
a novel algorithm to measure relationships among the annotation terms
based on
the degrees of their co-association genes to group the similar,
redundant, and
heterogeneous annotation contents from the same or different resources
into
annotation groups. This reduces the burden of associating similar
redundant
terms and makes the biological interpretation more focused in a group
level. The tool also provides a look at
the internal
relationships of the clustered terms by comparing it to the typical
linear,
redundant term report, over which similar annotation terms may be
distributed among
hundreds or thousands of other terms. In addition, to take full
advantage of the
well-known KEGG and BioCarta pathways, the new DAVID Pathway Viewer,
another
feature of the DAVID Functional Annotation Tool, can display genes from
a
user?s list on pathway maps to facilitate biological interpretation in
a
network context. |
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Data
Input
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Please
see the Universal
Gene List Manager |
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Gene-Enrichment
and Functional
Annotation Analysis
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1.
A Typical Analysis
Flow
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Load Gene List ->
View Summary Page -> Explore details through Chart Report, Table
Report, Clustering Report, etc. -> Export and Save Results
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2.
EASE Score, a modified Fisher Exact P-Value
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When members
of two
independent groups can fall into one of two
mutually exclusive categories, Fisher Exact test is used to determine
whether the proportions of those falling into each category differs by
group. In DAVID annotation system, Fisher Exact is adopted to measure
the gene-enrichment in annotation terms.
A Hypothetical Example:
In human genome background (30,000 gene total), 40 genes
are involved in p53 signaling pathway. A given gene list has found
that 3 out of 300 belong to p53 signaling pathway. Then we ask
the question if 3/300 is more than random chance comparing to the
human background of 40/30000.
A 2x2 contingency table is built on above numbers:
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User Genes
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Genome
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In Pathway
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3-1
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40
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Not In Pathway
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297
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29960
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Fisher Exact P-Value = 0.008 (using 3 instead of 3-1). Since P-Value <= 0.01, this
user gene list is specifically associated (enriched) in p53 signaling
pathway than random chance
However, EASE Score is more conservative to examine the situation. EASE Score = 0.06 (using 3-1 instead of 3). Since P-Value > 0.01, this
user gene list is specifically associated (enriched) in p53 signaling
pathway no more than random chance
See more discussion
at DAVID Forum.
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4.
Functional Annotation Summary
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4. Functional
Annotation Chart
Report
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Functional Annotation Chart:
Chart
Report is an annotation-term-focused view which lists annotation terms
and their associated genes under study. To avoid over counting
duplicated genes, the Fisher Exact statistics is calculated based on
corresponding DAVID gene IDs by which all redundancies in original IDs
are removed. All result of Chart Report has to pass the thresholds (by
default, Max.Prob.<=0.1 and Min.Count>=2) in Chart Option
section to ensure only statistically significant ones displayed.
EASE Score Threshold (Maximum Probability):
The
threshold
of EASE
Score, a modified Fisher
Exact P-Value,
for gene-enrichment analysis. It ranges from 0 to 1. Fisher Exact
P-Value = 0 represents perfect enrichment. Usually P-Value is equal or
smaller than 0.05 to be considered strongly enriched in the annotation
categories. Default is 0.1. More details.
Count Threshold (Minimum Count):
The
threshold
of minimum gene counts belonging to an annotation term. It has to be
equal or greater than 0. Default is 2. In short, you do not trust the
term only having one gene involved.
RT (Related Term Search):
Related Term Search can identify other similar terms. More details.
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5. Functional
Annotation Clustering
Report
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Functional Annotation
Clustering: new!
Due to the
redundant
nature of annotations, Functional Annotation Chart presents similar/relevant annotations
repeatedly. It dilutes the focus of the biology in the report. To
reduce the redundancy, the newly developed Functional Annotation
Clustering
report groups/displays similar annotations together which makes the
biology
clearer and more focused to be read vs. traditional chart
report. The grouping algorithm is based on the hypothesis that similar
annotations should have similar gene members. The Functional
Annotation Clustering integrates the same techniques of Kappa
statistics to measure the degree of the common genes between two
annotations, and fuzzy
heuristic clustering (used in Gene
Functional
Classification Tool ) to classify the groups of similar
annotations according kappa values. In this sense, the more common
genes annotations share, the
higher chance they will be grouped together.
The p-values associated with each annotation terms
inside each clusters are exactly the same meaning/values as p-values
(Fisher Exact/EASE Score) shown in the regular chart report for the
same terms.
The Group Enrichment Score new! , the geometric mean (in
-log scale) of member's p-values in a corresponding annotation cluster, is used to rank their
biological significance. Thus, the top ranked annotation groups most
likely have consistent lower p-values for their annotation members.
Options:
Similar idea as the options in
Gene Functional Classification.
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6. Other reports/views
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Functional
Annotation Table:
Table Report is
a
gene-centric view which lists the genes and their associated
annotation terms (selected only). There is no statistics applied in
this report.
Gene Report:
A highly
integrated
view of a single gene and its general annotations/accessions from
multiple resources. It can quickly give a global idea about the gene.
The hyperlinks throughout the report will lead to users to original
resources for further details.
DAVID Pathway Mapping:
To allocate
user input
genes on static pathway maps generated by BioCarta and KEGG. This
mapping strategy of "View Dynamic Data on Static Map Picture" is
uniquely developed in DAVID package. |
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Some
Terminology in DAVID System
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Annotation
Category:
A
group of
annotation sources collecting similar biological questions, such
as: "Pathways" is an annotation category consisting of BioCarta, KEGG,
etc.
Annotation Source:
An
independent
database in a category , such as: BioCarta Pathways.
Term:
A
detailed item
in an annotation source, such as: p53 signaling pathway in BioCarta.
hierarchical Structure: Category ->
Annotation Source -> Term
Pathways
-> BioCarta -> p53 signaling pathway
DAVID Gene ID:
It is
an
internal ID generated on "DAVID Gene Concept" in DAVID system.
One DAVID gene ID represents one unique gene cluster belonging to one
single gene entry.
Gene-Enrichment: A set of user's
input genes is highly associated with certain terms, which is
statistically measured by Fisher Exact in DAVID system.
EASE Score:
It is
an
alternative name of Fisher Exact Statistics in DAVID system, referring
to one-tail
Fisher Exact Probability Value used for gene-enrichment
analysis.
DAVID Id %:
After
converting user input gene IDs to corresponding DAVID gene ID, it
refers
to the percentage of DAVID genes in the list associated with particular
annotation term. Since DAVID gene ID is unique per gene, it is more
accurate to use DAVID ID% to present the gene-annotation association by
removing any redundancy in user gene list, i.e. two user's IDs
represent same gene.
DAVID Knowledgebase:
It represents
DAVID oracle databases which collect large volume of annotation
information from wide range of bioinformatic public resources. It
is probably the most largest and comprehensive integrated
database in the field. |
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Last Edit: Feb. 2007
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