AmiGO! documentation

AmiGO! is an HTML-based browser for The Gene Ontology . It should be fully accessible by anyone with a javascript enabled browser. Those without javascript may still find the browser useful, although not all features will be available. For best results, use a screen with a resolution of 800x600 or better.

Note: Depending on how your AmiGO is configured, you may not have all features that are listed in this text.

Getting Started:

The first screen you will see will look like this:

	Search GO: Exact Match
	TermsGene Products	Advanced Query
Top Docs Gene Ontology GO Links GO Summary	Datasource:

GO:0003673 : Gene_Ontology (46199)

GO:0008150 : biological_process (30188)

GO:0005575 : cellular_component (22371)

GO:0003674 : molecular_function (37018)

DAG view
Get this tree as RDF XML.
Get this data as a GO flat file.

Get a bookmarkable url of this tree.

Note that the page is broken into three sections.

The uppermost section contains the logo, navigation links and query form.
The middle section contains the current graph which you are browsing.
The bottom section contains the small print.

The three links under the logo in the lower left of the navigation bar are general navigation links they point at:

Top: This takes you to the original GO tree you see at the browser homepage. It retains your session settings
Docs: This page.
Gene Ontology: The main gene ontology site at http://www.geneontology.org
GO Links: Links to related pages.
GO Summary: Interactive pie charts which sum up the data in the GO.

There are two useful links on the bottom of the screen.

The first is "Get this GO tree as RDF XML." This will return the data in the tree you have selected in the format of the GO DTD .
The next link is "Get a bookmarkable url of this GO tree. AmiGO uses sessions and will time out after ~ 2 hours. If you'd like to save a tree that you've constructed, click on the link and drop a bookmark in your browser. You'll be able to return to the GO tree at any time.

Browsing the Tree:

The graph initially looks like this:

GO:0003673 : Gene_Ontology (46199)

GO:0008150 : biological_process (30188)

GO:0005575 : cellular_component (22371)

GO:0003674 : molecular_function (37018)

First of all, note that each term gets one horizontal line. The first thing on each line can be either a , or a icon. can be used to expand a term. This gets all of that terms children as well as it's parents back to the top of the tree. can be used to deselect a term, removing any of its children and parents, which are not shared by other selected terms, from the graph. Finally, means that the term on that line has no children. However, that term can still be selected to add any multiple parentages it may have.
The next thing on each line can be either a or icon. They represent, respectively, a part_of or is_a relationship.
The next part of each line is the go id and name of that term seperated by a colon. This can be clicked to get a more detailed view of that term.
The next part of each line is a number in parentheses. This tells the total number of gene associations which have been annotated to this term or to a more specific term below this in the GO tree. Note that this number does not include genes which have been electronically annotated (Evidence code IEA). This is due to the large numbers of these annotations as well as the fact that they may be of lower quality.
One thing to note is that selected terms in each graph are bold.
Selected terms may have be followed by the icon. Clicking this icon will bring you to a pie chart which displays the percentage of gene products annotated to each term below the selected one. This works recursively down the tree to any nodes you've selected.

If you were to click the expander icon for the term "biological_process", this is what you'd see:

GO:0003673 : Gene_Ontology (46199)

GO:0008150 : biological_process (30188)

GO:0007610 : behavior (291)

GO:0000004 : biological_process unknown (3665)

GO:0007154 : cell communication (6212)

GO:0008151 : cell growth and/or maintenance (20547)

GO:0016265 : death (525)

GO:0007275 : development (3620)

GO:0008371 : obsolete (1640)

GO:0007582 : physiological processes (854)

GO:0016032 : viral life cycle (27)

GO:0005575 : cellular_component (22371)

GO:0003674 : molecular_function (37018)

biological_process is now expanded. All of its children are indented below it, and they all have an is_a relationship. ie: "cell communication" is a "biological_process". If you now click the deselect icon at the beginning of the "biological_process" line, you will go back to the original view. Both Gene_Ontology and biological_process are now bold, thus selected.

If you were to then click the deselct icon in front of biological_process, that node would be closed and you would again see the original tree.

Note: Obsolete terms are greyed out.

The Detailed view.

If you click the name of term, you will be presented with a javascript popup window with a detailed view of that term. The reason this view was implemented as a popup window is to allow you to save your graph view that you've built while getting the full view of terms of interest in that graph. If your browser doesn't support javascript or if you just really hate popup windows, email me (bradmars@yahoo.com) and we'll talk about implementing an alternative strategy.

Here's what the detailed view of cell communication looks like:

GOst Search
DAG view
Get this GO term as RDF XML.
Get this data as a GO flat file.

antioxidant

Accession:GO:0016209
Synonyms: None.
Definition: Any substance, often an organic compound, that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage. definition_

Term Lineage

Graph view.

GO:0003673 : Gene_Ontology (46199)

GO:0003674 : molecular_function (37018)

GO:0016209 : antioxidant (33)

External References

SP_KW (1)

Associated Genes

Page 1

Gene Filters:

GO Term:
Gene Symbol:	Datasource:	Evidence:	Full name:
GO:0016209 : antioxidant
CG7217	FlyBase	ISS	Not Available
Jafrac1	FlyBase	ISS NAS	Not Available
Jafrac2	FlyBase	ISS NAS	Not Available
Prx2540-1	FlyBase	ISS - With ISS NAS	Not Available
Prx2540-2	FlyBase	ISS - With ISS NAS	Not Available
Prx5037	FlyBase	NAS	Not Available
Prx6005	FlyBase	ISS NAS	Not Available
Trxr-2	FlyBase	NAS	Not Available
AOP2_HUMAN	SPTr	NAS	Antioxidant protein 2
VC0731	TIGR_CMR	ISS10952301	antioxidant, AhpC/Tsa family
VC1350	TIGR_CMR	ISS10952301	antioxidant, putative
GO:0045174 : dehydroascorbate reductase
F14P1.9	TIGR_Ath1	ISS	dehydroascorbate reductase, putative
F22H5.1	TIGR_Ath1	ISS	dehydroascorbate reductase, putative
F5E19.50	TIGR_Ath1	ISS	dehydroascorbate reductase, putative
T30G6.13	TIGR_Ath1	ISS	dehydroascorbate reductase, putative
GO:0004362 : glutathione reductase (NADPH)
NOT Trxr-1	FlyBase	IDA	Not Available
Trxr-1	FlyBase	NAS	Not Available
GSHR_HUMAN	SPTr	TAS E	GLR1	SGD	IDA7942	glutathione oxidoreductase, EC 1.6.4.2
MUJ8.3	TIGR_Ath1	ISS	glutathione reductase, putative
VC0186	TIGR_CMR	ISS10952301	glutathione reductase
GO:0004791 : thioredoxin reductase (NADPH)
Trxr-1	FlyBase	IDA ISS ISS ISS ISS	Not Available
Trxr-2	FlyBase	NAS	Not Available
Q9NNW6	SPTr	NAS	Thioredoxin reductase TR2 (Fragment)
Q9NNW7	SPTr	ISS ISSQ9NNW7	Thioredoxin reductase 2, mitochondrial precursor
TRXB_HUMAN	SPTr	TAS E	Thioredoxin reductase, cytoplasmic precursor
O95840	SPTr	E	Not Available
TRB2_MOUSE	SPTr	ISSQ9JLT4	Thioredoxin reductase 2, mitochondrial precursor
TRB2_BOVIN	SPTr	IDA	Thioredoxin reductase 2, mitochondrial precursor
TRB2_RAT	SPTr	IDA	Thioredoxin reductase 2, mitochondrial precursor
Nxn	MGI	IDA	nucleoredoxin
Txnrd1	MGI	IDA	thioredoxin reductase 1
Txnrd3-pending	MGI	IDA	thioredoxin reductase 3
TRR1	SGD	TAS21329	thioredoxin reductase, EC 1.6.4.5
TRR2	SGD	IDA8312	thioredoxin reductase
VC1182	TIGR_CMR	ISS10952301	thioredoxin reductase

Previous Page Next Page First Page All Gene Products

There are many different elements in this page.

First is the Blue Header. This contains four links:
- "GOst Search" is a link to the GOst (Gene Ontology Blast Server), query interface
- "DAG View" draws a 'balls and sticks' view of the GOgraph you're viewing.
- "Get this Go Term as RDF XML" retrieves an XML version of the current graph.
- "Get this data as a GO Flat File" returns the current graph in the GO flat file format
The term name is next.
Next are any synonyms of the term, if any.
Next is the term's definition, if any.
Next is the lineage of the term. This shows the term with all of it's parent relationships but no children. Note that this particular term has multiple paths of parentage. If you don't see what I mean, see the later section of viewing multiple parentage. If you'd prefer to not be shown this section, you may collapse it with the minus icon and reopen it with the plus icon. Note that in the header of this section there is a link called, "Graph view". Clicking this link shows you a "balls and sticks" image of the selected graph.'
Next is a list of External Database References, ie links to this representations of this term in other databases, if any. Each reference can have one or two links with icons representing the database they are linking to. In this example the references are from InterPro. Clicking the InterPro icon will bring you to that accession in the InterPro database. Clicking the Amigo icon will show all GO terms which have that InterPro reference. Note that this opens a list of terms in the main navigation window, NOT in the popup window where no navigation is allowed. If you'd prefer to not be shown this section, you may collapse it with the minus icon and reopen it with the plus icon. Note that the cross references to each database can also be expanded and contracted with the plus and minus icons.
Next there is a list of Gene Associations to this term. Note that there is a widget in the header of this section which allows you to filter which gene associations you'd like to see based on the database they come from and the evidence type which was used to associate them. By using the shift key, you can highlight multiple databases or multiple evidence codes. For more info on the contributing databases and evidence codes see the main Gene Ontology page. Note that the list of gene associations has the genes directly associated to the term of interest as well as genes which are directly associated to sub-terms. If you'd prefer to not be shown this section, you may collapse it with the minus icon and reopen it with the plus icon. The columns in the Gene Associations table are:
- Gene Symbol: The symbol of the gene;) This links to a detailed view of that gene product, including all terms to which it is associated as well as its sequence, if available. Certain Gene Products have sequences which the groups have contributed. If your AmiGO is set up to run GOst jobs, any gene products with sequences in the database will be followed by the icon. Clicking this will perform a blast search with the selected sequence against the rest of the GO database.
- Datasource: The group which contributedthe annotation. This generally will tell you which organism the association is from. In cases where the contributing group has a representation of the data, that representation is linked to.
- Evidence: This is the evidence by which the geneproduct was associated to the term. Normally this will be the three letter evidence code, linked to a citation from the contributing group if the link is available. In the case of the ISS (Inferred by Sequence Similarity) evidence, if the sequence it was similar to is available it be linked with the link name "- with". Like this: "ISS -with".
- Full Name: The full gene name when it is available.
Finally there is a page selector. By default this view only shows 1000 terms. By using next page and previous page you can move through them, or you may choose to get all terms at once.

Querying:

On the right side of the Navigation bar at the top of the page on the first screen, there is a form to query the Gene Ontology graph. It looks like this:

	Search GO: Exact Match	Blast Search	Datasource:
	TermsGene Products	Advanced Query
Top Docs Gene Ontology GO Links GO Summary

To perform a query, simply enter your query into the box, then hit enter or click on the submit box. If you leave the default seection to searcg GO terms, the query will search the terms name, synonyms and GO accession. The term id can be formatted as a GO id or simply as a number, ie GO:0003700 or 3700. By default, wild cards are inserted at the beginning and end of your query, so endoplasm becomes *endoplasm*. You can turn this off by clicking the 'Exact Match' box. You can add your own wild cards, ie endoplasm*. If you'd like to search GO associated gene products, click the gene products box and enter the gene symbol which you'd like to search by, ie "Cat". By default, the full names of the genes are not searched since most of them are not available.

To perform a GOst (Gene Ontology blaST) search, click the 'Blast Search' link.

If you'd like more search options, you should click on the 'Advanced Queries' link. It will bring you to a search box which looks like this:

Finally, there is a menu of datasources and a second submit button. If you would like to chnage the databases you're searching, select them in the menu and click 'go'. You may select multiple databases by holding the shift key and clicking the names.

Simple Query

Terms
Fields:

Gene Products

Fields:
Datasource:
Evidence Type:

Top Documentation Gene Ontology GO Links

This box lets you choose which fields you'd like to search for either query. If you're doing a gene product query, you can select which datasources and evidence codes the gene products must have to be selected. Note that by holding down the shift or control key, you can select multiple evidence codes or databases.

If you do a Go term query, you will be selected with a list of "hits". A search for the term 'endoplasmic reticulum' brings up this list:

GO Term Name:		Definition:
endoplasmic reticulum	Tree View
endoplasmic reticulum cisterna	Tree View	The flattened sac-like space enclosed between paired membrane of the endoplasmic reticulum.
endoplasmic reticulum lumen	Tree View
endoplasmic reticulum membrane	Tree View
endoplasmic reticulum membrane, integral protein	Tree View	An integral membrane protein found in membranes of the endoplasmic reticulum.
endoplasmic reticulum receptor	Tree View
ER organization and biogenesis	Tree View
plasmodesmatal endoplasmic reticulum	Tree View	A complex fatty substance considerably impervious to water; present in plants as an impregnation of epidermal walls and as a separate layer, the cuticle, on the outer surface of the epidermis.
rough endoplasmic reticulum	Tree View
smooth endoplasmic reticulum	Tree View

Each row of the table contains one GO term. Clicking the name of that term will bring you to the detailed view. Clicking the link to "Tree view" will replace your list of hits with the term selected in the browsing view where you can expand nodes to explore that terms parents, siblings and children. The last column has the definition of term, if there is one.

Note the checkboxes on the left side of the term names. You may select as many terms as you'd like. Next to the input box is an option to either draw these terms as a new tree or append the terms to your existing tree.

If you search for gene products, you get a slightly more complex list of results. Here are the results of a query for "Cat".

Gene Product:	Datasource:	Associated To Terms:		Association Evidence:

CARL_HUMAN	SPTr	carbohydrate metabolism	Tree View	P Traceable Author Statement
Chst2	MGI	N-acetylglucosamine metabolism sulfotransferase	Tree View Tree View	Traceable Author Statement Inferred from Direct Assay
Chst8	MGI	cellular_component unknown N-acetylgalactosamine-4-O-sulfotransferase peptide hormone processing proteoglycan biosynthesis	Tree View Tree View Tree View Tree View	ND Inferred from Direct Assay Traceable Author Statement Inferred from Direct Assay
Clecsf6	MGI	lectin membrane fraction	Tree View Tree View	Traceable Author Statement Traceable Author Statement
Q9Y6F2	SPTr	development inflammatory response sulfotransferase	Tree View Tree View Tree View	P Traceable Author Statement P Traceable Author Statement E Traceable Author Statement

This list has 5 columns.

The first column has the gene product symbol and link to that product in the approriate database. If there is a icon following the gene product symbol, it means that that gene product has a sequence in the database. Clicking the icon will perfrom a GOst search with that sequence as the query.
The second column lists the external database that gene product is from.
The third column lists all GO terms to which the product has been associated. The terms are linked to their detailed views.
The fourth column has links to view each of the selected GO terms from the third column in the browser view.
The last column has the types of evidence linking the gene product to that term.

Note that in front of each gene product there is a checkbox. Following the list is a pull-down menu where you can choose to either get a detailed view of the selected gene products or pull their fasta sequences from the database.

Viewing Multiple Parentage:

More complex graphs can illustrate multiple parentage. Here's an example of one such graph, the browser view of the term "cell wall (sensu Bacteria)".

GO:0003673 : Gene_Ontology (28348)

GO:0008150 : biological_process (21805)

GO:0005575 : cellular_component (13866)

GO:0030312 : external protective structure (55)

GO:0005618 : cell wall (41)

GO:0009274 : cell wall (sensu Bacteria) (0)

GO:0005576 : extracellular (1060)

GO:0009274 : cell wall (sensu Bacteria) (0)

GO:0003674 : molecular_function (20801)

As you can see, The term GO:0009274, cell wall (sensu bacteria), shows up both under cell wall and extracellular.

Using GOst

GOst is the Gene Ontology blaST server. As we've already seen, a GOst job may be automatically launched by clicking on any

icon in AmiGO. Additionally, by clicking on the GOst search links in the blue header sections, you can get to the GOst query interface:

New GOst Search
Last Job Submitted
Welcome to GOst, the Gene Ontology Blast server.
Enter a SWISS-PROT sequence ID:
Paste in a FASTA sequence:

Or upload a fasta file:
Threshhold:

Copyright The Gene Ontology Consortium. All rights reserved.

As you can see, there are several ways to supply a sequence to blast against the GO database. You may enter the SWISS-PROT ID of any sequence which is in the GO database to launch a blastp job using that sequence as a query sequence. You may also paste in your own fasta or plain text sequence into the large text box. If this is a peptide sequence blastp will be launched, otherwise blastx. You may also give the address of a local fasta file to upload a query sequence.

All efforts have been made to keep this query form as simple as possible. Therefore, the only common blast parameter that can be changed is the threshhold for hits. The default is 0.001.

After a successful blast job, you will see a page which looks like this:

New GOst Search
Last Job Submitted

GOst Results:

Your query sequence:

>Q9V3P0
MPQLQKPAPAFAGTAVVNGVFKDIKLSDYKGKYLVLFFYPLDFTFVCPTE
IIAFSESAAEFRKINCEVIGCSTDSQFTHLAWINTPRKQGGLGSMDIPLL
ADKSMKVARDYGVLDEETGIPFRGLFIIDDKQNLRQITVNDLPVGRSVEE
TLRLVQAFQYTDKYGEVCPANWKPGQKTMVADPTKSKEYFETTS

High Scoring Gene Products:

Gene Product:	Datasource:	Associated To Terms:		Association Evidence:

Jafrac1	FlyBase	antioxidant cytosol NOT glutathione peroxidase peroxidase thioredoxin peroxidase	Tree View Tree View Tree View Tree View Tree View	Inferred from Sequence Similarity Non-traceable Author Statement Non-traceable Author Statement Inferred from Direct Assay Non-traceable Author Statement Inferred from Direct Assay Inferred from Sequence Similarity Non-traceable Author Statement
PDX2_HUMAN	SPTr	cytoplasm electron transporter response to oxidative stress thioredoxin peroxidase	Tree View Tree View Tree View Tree View	NR P Traceable Author Statement NR P Traceable Author Statement
PDX1_HUMAN	SPTr	cell proliferation skeletal development	Tree View Tree View	P Traceable Author Statement P Traceable Author Statement
PDX4_HUMAN	SPTr	I-kappaB phosphorylation thioredoxin peroxidase	Tree View Tree View	E Traceable Author Statement E Traceable Author Statement
PDX3_HUMAN	SPTr	alkyl hydroperoxide reductase	Tree View	P Traceable Author Statement
Jafrac2	FlyBase	antioxidant extracellular peroxidase thioredoxin peroxidase	Tree View Tree View Tree View Tree View	Inferred from Sequence Similarity Non-traceable Author Statement Non-traceable Author Statement Non-traceable Author Statement Inferred from Sequence Similarity Non-traceable Author Statement
TSA1	SGD	cytoplasm regulation of redox homeostasis response to oxidative stress thioredoxin peroxidase	Tree View Tree View Tree View Tree View	Inferred from Direct Assay Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Mutant Phenotype Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Direct Assay Inferred from Mutant Phenotype Traceable Author Statement
Prx5037	FlyBase	Tree View Tree View	Non-traceable Author Statement Non-traceable Author Statement Inferred from Sequence Similarity
TSA2	SGD	nucleus regulation of redox homeostasis thioredoxin peroxidase	Tree View Tree View Tree View	Inferred from Direct Assay Inferred from Sequence Similarity Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Sequence Similarity
Prx6005	FlyBase	antioxidant non-selenium glutathione peroxidase peroxidase	Tree View Tree View Tree View	Inferred from Sequence Similarity Non-traceable Author Statement Inferred from Sequence Similarity Non-traceable Author Statement
YBL064C	SGD	mitochondrion regulation of redox homeostasis thioredoxin peroxidase	Tree View Tree View Tree View	Inferred from Direct Assay Inferred from Sequence Similarity Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Direct Assay Inferred from Mutant Phenotype Inferred from Sequence Similarity
Prx2540-2	FlyBase	antioxidant non-selenium glutathione peroxidase peroxidase	Tree View Tree View Tree View	Inferred from Sequence Similarity Inferred from Sequence Similarity Non-traceable Author Statement Inferred from Sequence Similarity Inferred from Sequence Similarity Non-traceable Author Statement
AOP2_HUMAN	SPTr	antioxidant cytosol non-selenium glutathione peroxidase peroxidase peroxidase reaction phospholipase A2 phospholipid catabolism	Tree View Tree View Tree View Tree View Tree View Tree View Tree View	Non-traceable Author Statement Non-traceable Author Statement Inferred from Direct Assay Non-traceable Author Statement Inferred from Direct Assay Non-traceable Author Statement Inferred from Direct Assay Inferred from Direct Assay

Blast Text:

BLASTP 2.0MP-WashU [09-Nov-2000] [linux-i686 19:13:41 11-Nov-2000]

Copyright (C) 1996-2000 Washington University, Saint Louis, Missouri USA.
All Rights Reserved.

Reference:  Gish, W. (1996-2000) http://blast.wustl.edu

Query=  tmpseq tmpseq
        (194 letters)

Database:  /data/blast/db/aa_godb.fst
           21,918 sequences; 11,602,770 total letters.
Searching....10....20....30....40....50....60....70....80....90....100% done

                                                                     Smallest
                                                                       Sum
                                                              High  Probability
Sequences producing High-scoring Segment Pairs:              Score  P(N)      N

FB|FBgn0040309
SPTR:Q9V3P0 symbol:Jafrac1  HSSP:P30041 In...  1021
2.8e-104  1
SPTR|P32119
SPTR:P32119 symbol:PDX2_HUMAN "Peroxiredoxin ...   723
1.1e-72   1
SPTR|Q06830
SPTR:Q06830 symbol:PDX1_HUMAN "Peroxiredoxin ...   721
1.7e-72   1
SPTR|Q13162
SPTR:Q13162 symbol:PDX4_HUMAN "Peroxiredoxin ...   715
7.5e-72   1
SPTR|P30048
SPTR:P30048 symbol:PDX3_HUMAN "Thioredoxin-de...   671
3.4e-67   1
FB|FBgn0040308
SPTR:Q9V3Q4 symbol:Jafrac2  InterPro:IPR00...   657
1.0e-65   1
SGD|S0004490 SPTR:P34760 symbol:TSA1 "thioredoxin-peroxid...   597  2.4e-59   1
FB|FBgn0038519
SPTR:Q9VEJ0 symbol:Prx5037  EMBL:AE003718 ...   596
3.1e-59   1
SGD|S0002861 SPTR:Q04120 symbol:TSA2 "thioredoxin-peroxid...   572  1.1e-56   1
FB|FBgn0031479
SPTR:Q9VQI7 symbol:Prx6005  HSSP:P30041 In...   252
8.7e-23   1
SGD|S0000160 SPTR:P34227 symbol:YBL064C  SGD:S0000160 EMB...   249  1.8e-22   1
FB|FBgn0033518
SPTR:Q9V5K9 symbol:Prx2540-2  HSSP:P30041 ...   239
2.1e-21   1
SPTR|P30041
SPTR:P30041 symbol:AOP2_HUMAN "Antioxidant pr...   208
4.0e-18   1



 

>FB|

Contents:

Other Documentation:

Overview:

Getting Started:

Browsing the Tree:

The Detailed view.

antioxidant

Querying:

Viewing Multiple Parentage:

Using GOst

GOst Results:

Your query sequence:

High Scoring Gene Products:

Blast Text: