Welcome to the AGRIS tutorial on the ATTFDB
The following tutorial was developed to help guide a new user through conducting a search through the ATTFDB and provides information on using the website as a whole.
The header contains links to “HOME” the homepage, the “ATCISDB” a cis-regulatory database consisting of the 5' regulatory sequences of all 25,080 annotated genes with a description of the corresponding cis-regulatory elements. The “ATTFDB” a database of information on almost 1,550 transcription factors (TF) arranged into 39 families. “NSF2010” will provide information about the NSF information of Arabidopsis 2010 project, “DOWNLOADS” will provide information about the data download information for AtcisDB and AtTFDB, “PEOPLE” will provide information about the individuals that have currently contributed to the website, “LINKS” contains links to additional Arabidopsis resources, “NEWS” will provide information about recent updates and events. In addition, there are links to various departments at The Ohio State University that have contributed to the project.
Search the ATTFDB
On the ATTFDB homepage, a search can be conducted in two ways – through a specific search or through browsing by family.
Specific Search: using one of the following
· Locus ID: a unique locus name that corresponds to a transcribed region in the Arabidopsis genome. The names were designated as part of the genome sequence annotation and are associated with genes, genetic markers, polymorphic states, or map features. The format of the LocusID is, AtXgYYYYY. The “At” refers to Arabidopsis thaliana, the “X” number corresponds to the chromosome number, the “g” refers to gene and the 5 following “Y”s correspond to the five-digit code, numbered from top to bottom of the chromosome.
· Part of Description: using part of the description or gene name
And then click “Search”
Browse Families: select on of the 39 families listed to see all transcription factors currently identified.
Search Results Page-
Search Results are listed as a table.
Name of the family – “MADS, MYB”
Description – Description of the family
Reference – Reference information for the specific family
ClustAlW Alignment – ClustAlW alignment for protein sequences in the family
Hidden Markov Model – Hidden Markov Model for the entire family
Nucleotide Sequences – Nucleotide sequences for the genes in the family
Protein Sequences – Protein sequences for the genes in the family
Locus Id – Locus Id of the gene
Gene Name – Name of the gene
Links – Links to T (TIGR), M (MIPS), S (SALK), T (TAIR) websites for the specific gene
Direct Targets – Confirmed / Unconfirmed – Displays the identified direct targets for the gene
Regulatory Network – Displays the interaction between the direct targets.
Links: you can view additional information from various Arabidopsis resources TIGR,
MIPS, SALK, and TAIR.
For example, if a search was conducted using MYB15, the following pages would be displayed utilizing the various link.
(M) for MIPS (Munich Institute for Protein Sequences): the MATDB within the
MIPS website contains all Arabidopsis sequences and annotations produced by the
Arabidopsis Genome Initiative plus mitochondrial and chloroplast genomes.
Sequences were consolidated from European sequencing projects, Cold Spring
Harbor Lab, and Washington University. Information obtained from MIPS website includes name, title, function, PROSITE motifs, and Arabidopsis ESTs (as seen in figure below).
(T) for TIGR (The Institute for Genomic Research): An alternative DB of
Arabidopsis sequences and annotations from all AGI labs. The user can view various information about the gene searched on, including Gene Product and Locus name, attributes, gene structure and function (as seen in following figure).
(S) for SALK: Utilizing the SIGnAL Arabidopsis Gene Mapping Tool, it provides a map of the genome area in which the locus is found. On the map, cDNA (full-length cloned copies of mRNA) and T-DNA (sites of insertion of Agrobacterium T-DNA in the Arabidopsis genome) information is displayed in relation to the LocusID entered (as seen in figure below).
(T) for TAIR (The Arabidopsis Information Resource): A genomic data resource collected from a wide variety of sources, with information about genes, markers, polymorphisms, maps, sequences, clones, DNA and seed stocks, gene families and proteins. A link to the TAIR database contains information on TAIR accession number, gene model, description, nucleotide sequence, protein data, and map locations.