Frequently Asked Questions
What is DAVID?
2. What tools does
DAVID provide to analyze my gene lists?
3. What accession
numbers and gene identifiers does DAVID accept?
4. What file formats
can be uploaded/downloaded by DAVID?
5. Who can use DAVID?
6. Where does DAVID's
knowledgebase come from and how current is it?
7. Who do I contact
if I find an annotation error?
8. How are genes
counted in DAVID Chart Report?
9. Why are there
different levels for GO Annotation?
10. What does it mean to have empty
11. How do I cite DAVID?
12. What is the purpose of the
minimum number of hits and maximun p-value thresholds?
13. What is really going on behind
the scenes when I chose lets say level 1 compared to Level 5. What else is being done in Level 5 that is not
in Level 1?
14. Is the Domain Charts most
beneficial for categorizing ESTs? How else
can I take advantage of this module?
15. What journal articles have
cited DAVID or EASE?
16. Not all of my genes
are annotated! Why?
17. What are the system requirements to run DAVID?
18. Do other site mirror
19. How do my applications
take advantage DAVID functions?
20. What the computing technologies are used in DAVID
applications to enhance speed?
21. What is the
quanlity of tissue expression data in DAVID 2006?
22. What are the choices of population backgrounds in DAVID 2006?
23. Does DAVID limit the maximum number of genes in a
24. What is the format requirement to submit a gene list
25. Which DAVID tools is more suitable to answer my
Why DAVID gives empty results after I walk away for a
1. What is DAVID?
DAVID 1.x was originally designed as a web-based
functional annotation tool, particularly for gene-enrichment
analysis,on DAVID knowledgebase which contains annotations and gene
asccessions linked by LocusLink IDs in 2003 version. As the result of
continuely improving, DAVID 2.x provides a largest integrated
annotation knowledgebase based on newly developed "DAVID Gene
graph theory evidence-based method to agglomerate heterogeneous
distributed public databases. It also
provides an enhanced set of bioinformatics tools, not
only limited to functional annotation, to
summarize the relevant biological patterns from user-classified gene
list. Therefore, users can quickly understand
the biological themes under the study. As committed to
continuely addressing the challenges of system biology, DAVID
will keep upgrading and more tools are under developing.
2. What tools does DAVID provide to analyze my
gene list? DAVID 2.x provides a largest integrated
knowledgebase collected from most of common bioinformatic resources
(see content section for details). To leverage the knowledgebase, three
sets of comprehensive tools had been developed including: Functional
Annotation Tool; Gene Accession Conversion Tool; NIAID Pathogen Genome
Browser; etc. In Functional Annotation Tool, it does
gene-enrichment analysis, pathway
mapping, gene/term similarity search, graphic presentation, homologue
translation, etc.; In Gene Accession Conversion Tool, it
converts a list of gene IDs/accessions to others of your choice
with the most comprehensive gene ID mapping repository in DAVID 2.1.
ambiguity or contamination accessions in the list can also be quickly
and determined by users; In Genome Browser, users can quickly search or
navigate their interesting genes which can be further analyzed by
submitting to Functional Annotation Tool. Moreover, a couple of new
tools, such as Pathway-Centric Microarray Analysis Tool, Gene-Term
Functional Map, etc, are under developing.
3. What accession numbers and gene identifiers
does DAVID accept? DAVID accepts wide-range
types of gene accessions/IDs. Users can view all the gene accession
options from the drop down selection manu in gene list input
4. What file formats can be uploaded/downloaded by DAVID? Plain text (*.txt), tab-delimited files
can be uploaded by DAVID. The first column of your file must
contain the gene identifier and the second column may contain an
optional value (eg., fold change, p-value,
correlation, cluster number, experimental group, etc.). Remove column
headings and save the file as a Tab delimited text file. To
convert an excel file to this format choose File>Save As>
then under save as type choose Text (Tab delimited) (*.txt).
To save your annotated gene list from your browser to your hard drive
as an excel file simply choose File>Save As> then type yourfilename.xls
and save to your hard drive. You can then open this file in Microsoft
excel and perform typical excel-type analysis.
5. Who can use DAVID? DAVID
is free to use for all users. Please see license section
6. Where does DAVID's knowledgebase come from
and how current is it? DAVID 2.x
knowledgebase is design around the "DAVID Gene Concept", a graph theory
evidence-based method to agglomerate species-specific gene/protein
identifiers and their annotations from a variety of public genomic
resources (e.g. NCBI,
PIR, SWISS-PROT, GO, OMIM, PubMed, KEGG, BIOCARTA,
AffyMetrix, TIGR, Pfam, BIND, MINT, DIP, etc.).
The DAVID Gene Concept method groups tens of million of
identifiers from over 65,000 species into 1.5 million unique
protein/gene records. The grouping of such
identifiers allows agglomeration of a diverse array of functional and
sequence annotation, greatly enriching the level of biological
information available for a given gene (e.g. gene
sequence Ids, protein functional
domains, gene ontology, pathways, disease associations, gene general
descriptions, protein-protein interactions, literatures, homologues,
etc.). However, DAVID does not check the quality or accuracy of
all original annotation data, if you happen to find annotation errors
please contact the primary source of annotation. For more details of content
coverage and collecting date, including the last update, please refer to content section.
7. Who do I contact if I find an annotation
error? DAVID's purpose it aggregate biological
knowledge into an organized structure that allows the efficient
dissemination of functional annotations across genome-scale
datasets. DAVID does not guarantee the quality or accuracy of
annotation data, if you happen to find annotation errors please contact
the primary source of annotation. If you feel that the errors may
be due to some systematic error in DAVID's methods please contact use
8. How are genes counted in DAVID Chart Report?
In DAVID 2.x, all charting tools count the number of unique DAVID gene
Ids corresponding to user input gene list user. This means that
if two or more of your identifiers represent alternatively
spliced forms of the same gene it will only be counted once and
reflected in the histograms. This counting method is different from
DAVID 1.x in which the user's gene identifiers are counted.
9. Why are there different levels for GO
Annotation? The structured vocabulary created by
the Gene Ontology Consortium is a pseudo-hierarchy, or directed acyclic
graph (DAG). The different levels provided by GoCharts allows
users to annotate lists of genes at different levels within the
DAG. Level 1 represents the most general categories and provides
the most coverage, whereas Level 5 provides more specific information
and less coverage. Users may also annotate their gene lists with
all annotations available at all levels, for some genes there will be
more than 5. Additionally, users can choose to use only the most
specific categories by selected terminal nodes. Of note, the fact
that proteins are frequently involved in numerous biological processes
is reflected in the Gene Ontology structure. Thus, genes may be
annotated with several categories and be counted in each annotation
category by the charting tools.
10. What does it mean to have empty chart
report? Empyt chart report means that there
are no annotations passed the specified threshold. It does not
mean that no annotation exists.
11. How do I cite
DAVID? Glynn Dennis Jr.,
Brad T. Sherman, Douglas A. Hosack, Jun Yang, Michael W. Baseler, H.
Clifford Lane, Richard A. Lempicki. DAVID:
Database for Annotation, Visualization, and Integrated Discovery.
Genome Biology 2003 4(5): P3. Please refer to
section for more details.
is the purpose of the minimum number of hits and maximum p-value
thresholds? One way of
looking at it is that the thresholds just allow you to filter the
result, that is, just show me categories with 3 or more genes. If you show all categories including those
with only one hit than the charts can get very tall and busy.
In another words, a lot non-specific results
can be show up. Current default is 2 and 0.1
is really going on behind the scenes when I chose lets say GO level 1
compared to GO Level 5. What else is being
done in GO Level 5 that is not in GO Level 1? Refer to this link
http://genomebiology.com/2003/4/5/P3 to the manuscript describing DAVID
for a detailed description and figure. Briefly,
level 1 is a general description whereas level 5 is a more specific
description. The GO vocabulary is a type
of hierarchy and thus a term at level 5 is a child of a term at level 1
for a given gene. The specificity at level
5 comes at a cost though, in that list coverage decreases as you move
out the hierarchy.
Level 1 physiological processes
Level 2 response to external stimulus
Level 3 response to biotic stimulus
Level 4 defense response
Level 5 immune response
in the listing above you can see how the term at
level 5 "immune response" can be considered a child of level 4, which
in turn is a child of level 3, so on and so on up to level 1. The cost of using the more informative terms
at level 5 is lower coverage of your gene list. In
practice levels 2 and 3 are have a pretty good balance between
specificity and coverage. Also, use the
all or terminal node (most specific term available for a gene) to learn
more about the genes in your list.
14. Is the Domain
Charts most beneficial for categorizing ESTs? How
else can I take advantage of this module?
Domaincharts would indeed be useful to group ESTs.
A typical procedure would be to go through GoCharts
first and find an interesting and well-represented biological process,
say "signal transduction". Then drill down
into the molecular function of the genes involved in that process to
see kinases, receptors, transcription factors, etc.
Lastly, users can go to DomainCharts and try to identify
highly represented protein domains like kinase domains, zinc fingers,
etc that may be relevant to the interesting groupings revealed by GoCharts. All of this is an exploratory, iterative
process that helps users become intimately familiar with their gene
lists, thus facilitating decisions regarding where to focus.
What journal articles have
cited DAVID or EASE?
all of my genes are annotated!
reason for this is that the functional annotation of genomes is
incomplete and the particular types of annotation that any given gene
may have can differ. For example,
when using DAVID you may find a gene that has GO classifications and no
functional summary text, while another gene has functional summary text
and no GO classifications, while others will have no annotation what so
ever. This is why the database behind
DAVID is keeping updated, giving researchers access to the current
state of functional annotation, which indeed is always changing.
Another reason is that some user input identifiers (particularly some
Affy IDs) are blur to be mapped to any known genes.
are the system requirements to run DAVID?
Please refere to system requirement
any other sites site mirror DAVID applications ?
Differet versions of DAVID are being hosted at two servers
19. How to take
advantage of DAVID functional analysis modules ? DAVID provides a set of APIs for outside
applications to directly interact with DAVID calculation and
visualization engines. Please refer to Deep Linking Session
20. What computing
technologies are used in DAVID 2006 applications to enhance speed? DAVID 2006 uses tomcat 5.2 in red
hat linux as web server. All calculation engines and dynamic
pages were done with Java/JSP. Extensive object-oriented
programming techniques are involved in
DAVID development, such as html template and style sheet, to
ensure the quality and flexibility of the work. Older
versions of DAVIDs relied on Oracle database for necessory
annotation information query. The common speed bottle neck of all DAVID
applications are due to large amount of data query and IO. Since
DAVID 2006, DAVID starts using Java Remote Method Invocation (RMI) as a
replacement of Oracle for annotation information IO. This change
largely increases the performance speed for all calculation engines in
DAVID applications because it turns large amount data IO from
disk-oriented way to memory-oriented fashion.
21. What is the
quanlity of tissue expression data in DAVID 2006?
DAVID integrated the most popular and world-class tissue expression
data from GNF-Affy,
CGAP-SAGE, CGAP-EST and Unigene-EST. Together with DAVID functional
annotation engines, investigators can quickly indentify the most
enriched gene expression patterns cross hundreds of
normal/disease tissues for any given gene lists. It could
facilitate the biomarker identification and gene expression pattern
discovery. However, due to the higher noise nature of high throughput
gene expression data, the results consistent cross multiple
resources should give better confidence.
22. What are the choices of population background in DAVID enrichment analysis? The
enrichment analysis is indeed to compare the annotation composition
in your gene list to that of a population background genes.
In this sense, the selection of a population background will affect result
significantly. Unfortunately, there is no gold background to win
all the situations of various studies. DAVID default population background in
enrichment calculation is the corresponding genome-wide genes with at least
one annotation in the analyzing cetegories. The default
background is a good choice for the studies in genome-wide scope or close to genome-wide scope.
Since DAVID 2006, more background choices have been added in DAVID applications,
which are Affymetrix chip and Illumina chip backgrounds and user input customized background.
The pre-built Affymetrix chip and Illumina chip backgrounds can be selected through "background" tab on top of Gene List Manager panel. Affymetrix chip and Illumina chip
backgrounds will be a better choice for a gene list derived from Affymetrix
microarray or Illumina studies, respectively; Similarly to submitting a gene list, users can
input a customized population background of a gene list by choosing
"background" radio button in step 3 on the input tab. Customized
background will be a better choice for studies far below genome-wide scope, such as 500 paper array.
DAVID limit the maximum number of genes in a list? The
goal of DAVID's design is to be able to efficiently annotate a list
consisting of 3000 genes. Supported by advanced computing technolgies,
all DAVID tools have been tested with 3000-gene goal and have shown to
return results from a few seconds to no more than one minute. If
running time longer than a minute, you should repeat you web call or
check something else to make sure things right. If you have trouble, please contact DAVID Bioinformatic
Team for help.
Moreover, DAVID tools can run much larger number of genes in a
list than 3000-gene goal. Most of the DAVID tools, except
Functional Classification Tool, have no input limit until you can not
get your results returned by DAVID. We suggested that you try
your larger gene list outside DAVID traffic peak time (10 am - 5 pm
EST). Please let us know your experience with larger gene list
analysis on DAVID Forum.
If you try to download genome-wide annotation data from DAVID web for
your bioinformatics projects, please refer to Download Session
or ask help from DAVID Bioinformatic
is the format requirement for my input gene list? You can either
load a gene list from a file or paste a gene list to the text box.
DAVID was designed to accept the data starting from the first row
without hearder (i.e. accession). The gene list has to be in a format
of one gene in one row and only the first column is considered in the
analysis. DAVID is case insensitive for all the accessions/IDs. Since
DAVID list manager is centrilized, the format requirement to submit a
gene list are the same for ALL DAVID tools. In addition, the submitted gene lists could be used as customized background genes in the enrichment analysis based on your choice at step 3. The indication of a successful
submission is that you should see the corresponding gene lists listed by list tab or background tab. Moreover, an expected gene # should also associated with the gene lists.
In addition, DAVID pre-built two
Demo_lists for users who do not have gene list and want to test DAVID
applications. You just simply click on the links of Demo_list 1 or
Demo_list 2 on top of submission box to start the analysis. Following
are the information regarding the two Demo_list2:
About Demo List 1: One
hundred sixty-four genes found to be upregulated in CD4+/CD62L- T cells
relative to CD4+/CD62L+ T cells.
Cutting edge: L-selectin (CD62L)
expression distinguishes small resting memory CD4+ T cells that
preferentially respond to recall antigen.
Hengel RL, Thaker V, Pavlick MV, Metcalf JA, Dennis G Jr, Yang J,
Lempicki RA, Sereti I, Lane HC.
J Immunol 2003 Jan 1;170(1):28-32
Naive CD4+ T cells use L-selectin (CD62L) expression to facilitate
immune surveillance. However, the reasons for its expression on a
subset of memory CD4+ T cells are unknown. We show that memory CD4+ T
cells expressing CD62L were smaller, proliferated well in response to
tetanus toxoid, had longer telomeres, and expressed genes and proteins
consistent with immune surveillance function. Conversely, memory CD4+ T
cells lacking CD62L expression were larger, proliferated poorly in
response to tetanus toxoid, had shorter telomeres, and expressed genes
and proteins consistent with effector function. These findings suggest
that CD62L expression facilitates immune surveillance by programming
CD4+ T cell blood and lymph node recirculation, irrespective of naive
or memory CD4+ T cell phenotype.
About Demo List 2: Four
hundred three genes found to be induced in peripheral blood mononuclear
cells incubated with purified HIV envelope proteins.
HIV envelope induces a cascade of cell
signals in non-proliferating target cells that favor virus replication.
Cicala C, Arthos J, Selig SM, Dennis G Jr, Hosack DA, Van Ryk D,
Spangler ML, Steenbeke TD, Khazanie P, Gupta N, Yang J, Daucher M,
Lempicki RA, Fauci AS.
Natl Acad Sci U S A 2002 Jul 9;99(14):9380-5
Certain HIV-encoded proteins modify host-cell gene expression in a
manner that facilitates viral replication. These activities may
contribute to low-level viral replication in nonproliferating cells.
Through the use of oligonucleotide microarrays and high-throughput
Western blotting we demonstrate that one of these proteins, gp120,
induces the expression of cytokines, chemokines, kinases, and
transcription factors associated with antigen-specific T cell
activation in the absence of cellular proliferation. Examination of
transcriptional changes induced by gp120 in freshly isolated peripheral
blood mononuclear cells and monocyte-derived-macrophages reveals a
broad and complex transcriptional program conducive to productive
infection with HIV. Observations include the induction of nuclear
factor of activated T cells, components of the RNA polymerase II
complex including TFII D, proteins localized to the plasma membrane,
including several syntaxins, and members of the Rho protein family,
including Cdc 42. These observations provide evidence that
envelope-mediated signaling contributes to the productive infection of
HIV in suboptimally activated T cells.
DAVID tools to choose? Following
table may help you make decisions.
Why DAVID gives empty results after I walk away for a
The session timeout of DAVID web was set to 30 min. In
another words, if your web browser has no activities with DAVID
site for 30 min, all your web session information will be flood.
The only way to resume your work is to re-submit your gene list to
DAVID web site.