AtGeneSearch Help

Overview:

AtGeneSearch's search page is divided into four fields, each capable of running a different type of search. All searches are case-insensitive, so searching "sucrose", "SUCROSE", and "sUcRoSe" would all give the same result. Each search is run independently, and a single table is returned with the results of each search in the following order: Locus/Affy IDs, AFGC IDs, Phrase, and Pathway. A description of each field is below.

Phrase:

Searches the Tair Annotations and GO terms for all of the given words. You can search for a word or part of a word by simply typing it into this field. To match phrases or whole words, put the terms you want to search within quotation marks ("). You can exclude a term by putting a hyphen (-) before it. To keep the server from getting bogged down, unquoted terms must have at least five characters, while quoted terms must have at least three letters. See the examples below for more information.

Example Searches
Search TextWhat it does
trehalose phosphate Matches any gene whose Tair annotation or GO terms contain the strings trehalose and phosphate. These could be whole words (i.e. the words "trehalose" or "phosphate"), or substrings (so this search would match the term "monophosphate" or "trehalose-6-phosphate").
"trehalose phosphate" Matches only those genes whose Tair annotation or GO terms contain exactly the phrase "trehalose phosphate". Terms in quotes must appear exactly as typed, so this search would not match "trehalose-6-phosphate", "trehalose, phosphate", "phosphate trehalose", etc. Words in quotes are still case-insensitive.
phosphate -trehalose Matches all genes whose Tair annotation or GO terms contain the string phosphate, but not the string "trehalose". A gene will be rejected automatically if trehalose appears in any of these fields, even if phosphate does not appear in the same field.
"inorganic pyrophosphatase" -"pyrophosphate phospho-hydrolase" Matches genes whose Tair annotation or GO terms contain the phrase "inorganic pyrophosphatase", but do not contain the phrase "pyrophosphate phospho-hydrolase". Note that the hyphen only excludes a term if it appears after a space.

Pathway:

Searches pathways using the supplied terms, and fetches information on the genes in the matched pathways. The syntax for this field is identical to the phrase field, so see the above examples for more information.

Gene IDs: (Locus, Affy8k, Affy20/25k)

Searches the database for information on the given genes. Any values that are not valid Locus IDs, Affy8k IDs, or Affy20/25k IDs will be ignored. This means that you can paste large blocks of text into this field and it will pick out and search any gene IDs in the text. Genes will appear in the result table in the order they appear in this field. Terms can be separated by spaces, new lines, parentheses, commas, semicolons, and single and double quotes. All other characters will be treated as search terms.

Example Searches
Search TextWhat it does
244901_at 12345_at AT1G03160 Fetches information on the gene with Affy20/25k ID 244901_at, the gene with Affy8k ID 12345_at, and the gene with Locus ID AT1G03160, in that order.
"244901_at", -12345_at (AT1G03160) Fetches information on 244901_at and AT1G03160, but not 12345_at. Since the hyphen is treated as a normal character in this field, the term "-12345_at" will be pulled out. Since this is not a valid gene ID, it is ignored.

AFGC IDs

Searches the database for information on genes with the given AFGC IDs. Since there are valid AFGC IDs with spaces in them, IDs in this field MUST be separated by a comma (,) or a semicolon (;).

Example Searches
Search TextWhat it does
186A22T7, 221E14T7 Fetches information on the gene with AFGC IDs 186A22T7 and 221E14T7, in that order.
186A22T7 221E14T7 Returns an empty table, because there is no gene with AFGC ID "186A22T7 221E14T7"