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Contents

• Using the TAIR Gene Search Page
• Search by Name
• Search by Keyword
• Search by Features
• Search by Location

Using the Gene Search

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The TAIR Gene Search window provides three ways of searching for a gene: simple search by name only, feature search using more limits, and search by position. These are offered in three distinct sections of the window.

Search by Name

At the top of the TAIR Gene Search window are the Search by Name options.

This simple search is case insensitive and allows wildcard searching (see "Using Wildcards").

Search by Name, Description, GenBank Accession

Use this drop down menu to search either by gene name, description or GenBank Accession.

In TAIR, there are four types of names associated with a Gene. Searching by name will search all gene names and gene aliases. For more information about the name types see below:

• Symbol

  This is the mnemonic naming used for gene names by researchers. Examples include AG (Agamous), and QRT1 (Quartet1). A symbol for a gene is designated when a gene has been published or if the name and symbol have been registered at Oklahoma State, currently maintained by David Meinke's group or in GenBank.(http://mutant.lse.okstate.edu/genepage/genepage.html).

• ORF name

  An open reading frame (ORF) name from the Arabidopsis Genome Initiative (AGI) groups' annotations. Usually, the convention for naming an ORF in Arabidopsis has been using the clone name followed by a number suffix (e.g., F23H14.13). For chromosome arms that have been completely sequenced, a standard ORF name designation is used:

  • AT (Arabidopsis thaliana)
  • 2 (chromosome number)
  • G (for Gene)
  • 01130 (Number)

    Examples: At2g01130, AT4g00010

• Full name

  The full descriptive name of a gene.Examples: Agamous, Aspartate aminotransferase deficient 3

• Gene product name

  Name of a gene product.Examples: ASPARTATE AMINOTRANSFERASE, CYTOPLASMIC ISOZYME 1, CHALCONE SYNTHASE.For the genes that do not have a full name or symbol (largely the predicted genes (ORFs) from AGI sequencing and annotation), the following product names have been used:

  • Hypothetical protein

    Gene models without any database matches.

  • Unknown protein

    Gene models with only EST matches.

You must select one of these types and then type in the name. You can also use Genbank accession numbers in the name search but selecting "Any" name type and using the input box to insert the accession number.

Search by Keyword

This option allows you to search for genes by keywords.Genes are annotated with keywords describing molecular function,subcellular localization and biological process with controlled vocabularies from the Gene Ontology Consortium. Genes are also annotated with controlled vocabulary terms for plant structures and developmental stages for describing phenotypes and where and when the genes are expressed. Plant structure and development terms are from the Plant Ontology Consortium. Each annotation is associated to an evidence code and one or more reference (the source of the evidence for the annotation).

Keyword type

The keyword types represent the categories of keywords used for annotation. You can restrict your search to include only one type of keyword or choose multiple types. To select more than one type of keyword hold down the Apple (MAC) or CTRL (PC) while clicking with the mouse. If you are not sure of which type the keyword belongs to , use the ANY option which searches all types of keywords.

Evidence

Each annotation in TAIR is associated to some form of evidence that supports the annotation. The evidence can be used to filter annotations, for example, to exclude annotations based on computational methods (inferred by electronic annotation). Evidence is also used to quickly assess the quality of a given annotation. The evidence is also linked to the source of the evidence (i.e. the experimental data or analysis method).

Keyword Term

This option allows you to input a given term and choose the type of search. Exact searches are most restrictive, contains searches are least restrictive but slower. If you are not sure of the format of the term, choose the 'contains' option. For example exact search for protein kinase will return results for only those terms that exactly match protein kinase, whereas a search for contains protein kinase will include matches to terms such as serine-threonine protein kinase AND histidine protein kinase.You can also limit the search to keywords that start with or end with a given term.

Restrict by Features

The Restrict by Features options are below the Search by Name options on the TAIR Gene Search window.

These options let you restrict your search by selecting one or more features or a time restriction. Selecting multiple attributes indicates an "AND" relationship. For example, checking "has full length cDNA" and "is on a map" limits the query set to genes that have a ful-length cDNA and are on a map

Gene Model Type

This feature allows you to restrict your search to specific types of gene models Image Modified.The default search returns any gene model type. To select mutiple gene model types after your first selection click on additional ones while holding down either the CTRL key (PCs) or the Apple key (Mac).

Gene Structure Predicted

This restricts your search to only include genes whose structures have not been experimentally determined (e.g. by sequencing a cDNA).

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