Gene Ontology HTBrowser documentation

The Gene Ontology HTBrowser 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. For general documentation on the GO project, see the GO docs.

Getting Started:

The first screen you will see will look like this:

	Search GO: Exact Match
	TermsGene Products
Top Documentation Gene Ontology		Advanced Query

GO:0003673 : Gene_Ontology (44712)

GO:0008150 : biological_process (22609)

GO:0005575 : cellular_component (8263)

GO:0003674 : molecular_function (13840)

Get this GO tree as RDF XML.

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
Documentation: This page.
Gene Ontology: The main gene ontology site at http://www.geneontology.org

Browsing the Tree:

The graph initially looks like this:

GO:0003673 : Gene_Ontology(0)

GO:0008150 : biological_process(0)

GO:0005575 : cellular_component(4)

GO:0003674 : molecular_function(86)

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 final 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.
The final thing to note is that selected terms in each graph are bold.

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

GO:0003673 : Gene_Ontology(0)

GO:0008150 : biological_process(0)

GO:0007582 : physiological processes(7)

GO:0007154 : cell communication(918)

GO:0008151 : cell growth and maintenance(506)

GO:0000004 : biological_process unknown(3147)

GO:0007610 : behavior(138)

GO:0009581 : perception of external stimulus(0)

GO:0007275 : developmental processes(1039)

GO:0016032 : viral life cycle(0)

GO:0016265 : death(1)

GO:0008371 : obsolete(0)

GO:0003674 : molecular_function(86)

GO:0005575 : cellular_component(4)

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.

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:

Get this GO term as RDF XML.

cell communication

Synonyms: None.
Definition: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

Term Lineage

GO:0003673 : Gene_Ontology(44712)

GO:0008150 : biological_process(22609)

GO:0007154 : cell communication(2504)

Database Cross-References

Database:	Reference:
Interpro	IPR001774 Delta serrate ligand
Interpro	IPR001657 Sonic hedgehog protein
Interpro	IPR001767 Hint module
EGAD	effectors/modulators
EGAD	cell signaling/cell communication > GO:cell-cell signalling ; GO:0007267

Associated Genes

Filter by database:

Filter by Evidence for Association:

Gene Symbol:	Datasource:	Evidence:	Full name:
dco	Flybase	IMP	Not Available
Src42A	Flybase	IDA	Not Available

There are many different elements in this page.

First is the Blue Header. This contains a link to an XML version of the data which is summarized in this page.
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.
Next is a list of External Database References, ie links to this representations of this term in other databases, if any.
Finally, 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.

The first four columns are self-explanatory. The external database reference list has one database reference per line. Some of these are linked to the appropriate page in the external database. However, this is not true of all of the references, since some types of references don't have a single page that represents them. An example of this would be a swissprot keyword. The gene associations table contains one gene association per line. The first column has its gene symbol, usually with a link to an html page with more info about that gene from it's parent database. The second column tells which database that gene association is from(ie Flybase). The next column has a list of all of the evidence for that gene association. Many of these will have the type of evidence, ie GO Evidence Code, linked to that reference in an external database. In cases where that is not possible, the evidence is of the format EV_CODE-database_id . To get desciptions of the different evidence codes, click the link on the 'Evidence:' column header.

Note that the associated gene product list has a selector for filtering gene products of interest. You can choose which databases you'd like to pull gene products from, which evidence codes you'd like to see and then submit the query to get an updated list.

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
	TermsGene Products
Top Documentation Gene Ontology		Advanced Query

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.

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:

Search GO: Exact Match

Simple Query

Terms
Fields:

Gene Products

Fields:
Datasource:
Evidence Type:

Top Documentation Gene Ontology

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.

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

GO Term Name:
endoplasmic reticulum receptor	Browse Term
endoplasmic reticulum	Browse Term
endoplasmic reticulum cisterna	Browse Term
endoplasmic reticulum lumen	Browse Term
endoplasmic reticulum membrane	Browse Term
plasmodesmatal endoplasmic reticulum	Browse Term
rough endoplasmic reticulum	Browse Term
smooth endoplasmic reticulum	Browse Term
ER organization and biogenesis	Browse Term

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 "Browse Term" 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.

Here is the graph of endoplasmic reticulum receptor in the browsing view:

GO:0003673 : Gene_Ontology (44712)

GO:0003674 : molecular_function (13840)

GO:0004871 : signal transducer (1057)

GO:0004872 : receptor (631)

GO:0004888 : transmembrane receptor (518)

GO:0005045 : endoplasmic reticulum receptor (8)

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:
alpha-Cat	Flybase	actin binding cytoskeletal protein binding protein catenin cytoskeletal anchor protein cytoskeletal anchoring	Term Browser Term Browser Term Browser Term Browser Term Browser	Inferred from Sequence Similarity Inferred from Sequence Similarity Inferred from Sequence Similarity Inferred from Sequence Similarity Inferred from Sequence Similarity
CAT5	SGD	mitochondrial inner membrane ubiquinone metabolism	Term Browser Term Browser	Traceable Author Statement Traceable Author Statement
Acate2-pending	MGI	mitochondrion acyl-CoA thioesterase	Term Browser Term Browser	Inferred from Direct Assay Inferred from Direct Assay
Catna1	MGI	zonula adherens	Term Browser	Inferred from Direct Assay
alpha-catenin-related	Flybase	actin binding zonula adherens	Term Browser Term Browser	Inferred from Sequence Similarity Inferred from Sequence Similarity Inferred from Sequence Similarity
Cat	Flybase	catalase	Term Browser	Inferred from Sequence Similarity Inferred from Direct Assay
CAT2	SGD	amino acid metabolism lipid metabolism peroxisome mitochondrion carnitine O-acetyltransferase peroxisomal matrix	Term Browser Term Browser Term Browser Term Browser Term Browser Term Browser	Traceable Author Statement Non-traceable Author Statement Inferred from Mutant Phenotype Inferred from Sequence Similarity Inferred from Sequence Similarity Non-traceable Author Statement Inferred from Sequence Similarity
cato	Flybase	nucleus transcription factor	Term Browser Term Browser	Inferred from Sequence Similarity Inferred from Sequence Similarity
cathD	Flybase	cathepsin D	Term Browser	Inferred from Sequence Similarity
Acate3-pending	MGI	mitochondrion acyl-CoA thioesterase	Term Browser Term Browser	Inferred from Direct Assay Inferred from Sequence Similarity

This list has 5 columns.

The first column has the gene product symbol and link to that product in the approriate database.
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.

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 (0)

GO:0005575 : cellular_component (4)

GO:0005618 : cell wall (1498)

GO:0009274 : cell wall (sensu Bacteria) (28)

GO:0009280 : cell wall inner membrane (0)

GO:0009275 : cell wall (sensu gram-positive Bacteria) (0)

GO:0009276 : cell wall (sensu gram-negative Bacteria) (0)

GO:0009278 : murein sacculus (0)

GO:0009279 : cell wall outer membrane (81)

GO:0005576 : extracellular (5309)

GO:0009274 : cell wall (sensu Bacteria) (28)

GO:0009280 : cell wall inner membrane (0)

GO:0009275 : cell wall (sensu gram-positive Bacteria) (0)

GO:0009276 : cell wall (sensu gram-negative Bacteria) (0)

GO:0009278 : murein sacculus (0)

GO:0009279 : cell wall outer membrane (81)

As you can see, The term GO:0009274, cell wall (sensu bacteria), shows up both under cell wall and extracellular. The term itself has been opened to show its children.

Datasources

The list of go references in the datasource field are described as follows:

All: All datasources in the Go database

Flybase:Drosophila data
http://flybase.bio.indiana.edu/

SGD:Saccharomyces cerevisiae data
http://genome-www.stanford.edu/Saccharomyces/

MGI:Mouse Genome Informatics data
http://www.informatics.jax.org/mgihome/

Pombase:S. pombe data
http://www.hgmp.mrc.ac.uk/Registered/Option/pombase.html

Compugen:Compugen data
http://www.compugen.co.il/

TAIR:Arabidopsis data
http://www.arabidopsis.org/

Wormbase:C. elegans data
http://www.wormbase.org/

Apicomplexa:Apicomplexan orgamisms
Toxoplasma gondii; Plasmodium falciparum; Cryptosporidium parvum

cr11000sc:Cryptosporidium parvum orfs (11000) compared against Saccharomyces cerevisiae GO sequence

cr19000:Cryptosporidium parvum orfs (19000) compared against all Go sequence

cr19000sc:Cryptosporidium parvum orfs (19000) compared against Saccharomyces cerevisiae GO sequence

bovine: Bovine taurus EST sequence compared against all GO sequence

Evidence Types

Datatsources plsorf; cr11000; cr11000sc; cr19000; cr19000sc; bovine; tx were all assembled into this GO database via IEA (inferred from electronic annotation).
It is best to choose All when using these datasources.

Contents:

Overview:

Getting Started:

Browsing the Tree:

The Detailed view.

cell communication

Querying:

Viewing Multiple Parentage:

Datasources

Evidence Types