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TRANSCRIPT
User Manual Zhou Du ([email protected])
Version 1.0
1. What is agriGO?
The agriGO is designed to automate the job for experimental biologists to identify enriched Gene
Ontology (GO) terms in a list of microarray probe sets or gene identifiers (with or without
expression information) and it is also a GO‐related database. The agriGO specially focus on
agricultural species.
2. Why use agriGO?
The agriGO provides heavy support to agricultural species. Not only limited to SEA analysis, GSEA
which is achieved using PAGE method is also available. Furthermore we have BLAST4ID tool for
ID transfer or annotation. And search as well as download function is accessible. The agriGO can
give out rich outputs like graphical result, bar chart result and hierical tree which composing a
comprehensive understanding of biological meaning of user's input data.
3. What data argiGO contains?
We currently support on 35 species including 280 datatypes. Please check the data statistics page
for detail information. We will continue adding more species and datatypes.
4. How agriGO prepare its data?
Raw GO annotation data is generated using BLAST, Pfam, InterproScan by agriGO or obtained
from B2G‐FAR center or from Gene Ontology. Arabidopsis genome data is from TAIR. Rice TIGR
genome data is from Rice Genome Annotation Project. Rice KOME data is from KOME database.
Rice Gramene data is from Gramene center. Populus genome data is collected from JGI. Soybean
and Sorghum genome data is compiled from phytozome. Grape genome data is compiled from
Genoscope. Medicago genome data is from Medicago truncatula sequencing resources. Maize
genome data is from MaizeSequence.org. Castor bean genome data is from Castor Bean Genome
Database. Brachypodium distachyon genome data is from Ensembl. Bovien genome data is from
Bovine Genome Database. Silkworm genome data is from SilkDB. M. grisea genome data is from
Magnaporthe grisea Database. affymetrixmetrix CSV files and array sequences are from NetAffx.
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6. FAQ
What is agriGO?
The agriGO is designed to automate the job for experimental biologists to identify
enriched Gene Ontology (GO) terms in a list of microarray probe sets or gene
identifiers (with or without expression information) and it is also a GO‐related
database. The agriGO specially focus on agricultural species.
What is GO?
"The Gene Ontology (GO) project provides a controlled vocabulary to describe gene
and gene product attributes in any organism. The GO project is a collaborative effort to
address the need for consistent descriptions of gene products in different databases.
The GO collaborators are developing three structured, controlled vocabularies
(ontologies) that describe gene products in terms of their associated biological
processes, cellular components and molecular functions in a species‐independent
manner. There are three separate aspects to this effort: first, we write and maintain
the ontologies themselves; second, we make cross‐links between the ontologies and
the genes and gene products in the collaborating databases, and third, we develop
tools that facilitate the creation, maintainence and use of ontologies." Definition from
http://www.geneontology.org/
What is updated in agriGO compare with EasyGO?
The agriGO is a successor of EasyGO, and it go further. 1. We create new website
interface. The database structure and scripts of agriGO are redesigned. Both page
loading speed and analysis speed of agriGO now are improved because of the change.
2. The agriGO service is especially focus on agricultural species. It supports species is
extended to 35 including as much as 280 datatypes. 3. We added new analysis tools for
new agriGO, such as PAGE analysis and BLAST4ID tool. 4. The result output and
information are richer compare with EasyGO. 5. The agriGO could also work as a GO
database with search and download service.
What are the unique features of agriGO compare with other GO webserver/database?
The agriGO provides heavy support to agricultural species. Not only limited to SEA
analysis, GSEA which is achieved using PAGE method is also available. Furthermore we
have BLAST4ID tool for ID transfer or annotation. And search as well as download
function is accessible. The agriGO can give out rich outputs like graphical result, bar
chart result and hierical tree which composing a comprehensive understanding of
biological meaning of user's input data.
What is SEA analysis?
SEA analysis means Singular enrichment analysis which is tranditional but widely used.
SEA analysis is designed to identify enriched Gene Ontology (GO) terms in a list of
microarray probe sets or gene identifiers. Finding enriched GO terms corresponds to
finding enriched biological facts, and term enrichment level is judged by comparing
query list to a background population from which the query list is derived.
Which statistics method should I choose in SEA tool?
When the input list is compared with the previously computed background, or is a
subset of reference list, choose hypergeometric or fisher, for latter only when your
query number is quite small. When the input list has few or no intersections with the
reference list, the Chi‐square tests are more appropriate.
What is PAGE analysis?
PAGE is Parametric Analysis of Gene Set Enrichment [Kim et. 2005 BMC Bioinfomatics].
PAGE method is using Central Limit Theorem in statistics, this method is simple and
efficient. Different to SEA, it takes expression level into account, and can deal with a
long list of genes/probesets. PAGE use a two‐tailed test to count Z score, and the
caculation of p‐value will be:
if Z score >= 0: p‐value is 2 * (1 ‐ x)
if Z score < 0: p‐value is 2 * x
What is BLAST4ID?
The BLAST4ID tool is not an analysis tool, but an associated one used mainly for two
purposes: 1. Transfer your IDs which are not available to agriGO to available ones, 2.
use blast search to annotate your sequences with GO.
Which tool should I choose?
It will depend on what data you have. If you only have a list of identifiers or only
interested about them, SEA will be your choice. And if you like take expression data
into count and would like compare several dateset then you may try PAGE. The
BLAST4ID is only an associated tool, use it if you really need it.
Why graphical/chart image does not display on my PC?
The bar chart result need flash player to browse correctly. And you may need different
tool to display different format graphical result, for example: Adobe reader, SVG
brower. Contact me if you install related tool but still can not see the results.
How many datatypes are supported by agriGO?
We currently support on 35 species including 280 datatypes. Please check the data
statistics page for detail information. We will continue adding more species and
datatypes.
How agriGO obtains its data source?
Raw GO annotation data is generated using BLAST, Pfam, InterproScan by agriGO or
obtained from B2G‐FAR center or from Gene Ontology. Arabidopsis genome data is
from TAIR. Rice TIGR genome data is from Rice Genome Annotation Project. Rice KOME
data is from KOME database. Rice Gramene data is from Gramene center. Populus
genome data is collected from JGI. Soybean and Sorghum genome data is compiled
from phytozome. Grape genome data is compiled from Genoscope. Medicago genome
data is from Medicago truncatula sequencing resources. Maize genome data is from
MaizeSequence.org. Castor bean genome data is from Castor Bean Genome Database.
Brachypodium distachyon genome data is from Ensembl. Bovien genome data is from
Bovine Genome Database. Silkworm genome data is from SilkDB. M. grisea genome
data is from Magnaporthe grisea Database. affymetrixmetrix CSV files and array
sequences are from NetAffx.
How often does agriGO update?
Normally we will update our database every 3 months, but if we will update agriGO if
some important data source is newly available. Improvement and updating to agriGO
tools are irregulated.
Can I check result from old version by new agriGO ?
Sorry, but no. Because we reconstructed the database and redesigned the website
organization, analysis result from EasyGO is not supported in agriGO.
How to make agriGO add new customized datatype?
User can contact the agriGO administrator by email ([email protected]) to
discuss more details.