Website tested with Firefox v.3.5 Website tested with Internet Explorer v.8 IT3F: An Interspecies Transcription Factor Function Finder for Plants
    Website URL: http://jicbio.nbi.ac.uk/IT3F; old URL: http://jicbio.bbsrc.ac.uk/IT3F
Purpose of this website: For plant biologists who want to understand the function of a transcription factor (TF), or at least learn about the relative relationship between a gene encoding a TF and other members of the same gene family. This web page allows you to submit "new" query sequence(s), and in an instance - the aim is within 30 seconds - returns a web page displaying an "existing" neighbor-joining TF family tree with the query sequence(s) added.

     For each gene, additional information is shown that is important to consider together when investigating the function of a particular gene, for example, corresponding gene expression profiles and genes found in regions of a contemporary genome that have been duplicated in a relatively recent ancestor so may exhibit some functional redundancy.

     With the data views provided, it is possible to observe closely related genes across different species clustering as "subgroups" (or "clades"). These subgroups can be explored further with "inner" trees and "global" protein alignments for them. It is also possible to understand how a large gene family can be broken down into these subgroups by looking at the Global Alignment Display.

How to use this web page: Paste query sequence(s) into the Interrogative Tree Web Form and select a matching TF family or subfamily. Query sequence(s) must be amino acid sequence in FASTA format and should be as complete as possible over the DNA binding domain. Tips...

The Interrogative Tree Web Form:

Select a protein family or sub-family:
(Note - lines ending in a colon e.g. "MYB Superfamily:" are descriptive, not options.)


Then to browse the family, simply press the submit button, or in 
addition, input one or more query sequences below in FASTA format:
Example (for the R2R3MYB family - will appear red in the tree):
>AtR2R3MYBwhat?
MGRSPCCEKAHTNKGAWTKEEDERLVAYIKAHGEGCWRSLPKAAGLLRCGKSCRLRWINY
LRPDLKRGNFTEEEDELIIKLHSLLGNFFFKWSLIAGRLPGRTDNEIKNYWNTHIRRKLI
(Note - The first 15 characters (or until the first space) on the FASTA header line will 
be used in the tree display. Non-alphanumerical characters will be replaced by '-' 
characters.)



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Website developer / feedback
or problems to: Paul Bailey at:      Last update 11th June 2012    Acknowledgements   web counter unique hits since 1.6.07  web counter

The IT3F website uses the following data:
sets of predicted protein sequences from the genomes of Arabidopsis (file: TAIR9_pep_20090619, June 2009)), Lotus (file: protein_sequence.gz, build 1.0, May 2009), Medicago (file: Mt3.5_GenesProteinSeq_20100825.fa inside Mt3.5v3_annotation_files.tar.gz, August 2010), rice (file: all.pep, rice MSU Osa1 release 6.1, June 2009), Brachypodium (file: Bd21_v1_Protein[1].fa, version 1.0, April 2009) and moss (file: proteins.Phypa1_1.FilteredModels.fasta, in Phytozome version 5.0, August 2009). Using a Perl pipeline outside this website, significant hit sequences to each protein family are found using HMMSEARCH with an HMM profile corresponding to the conserved domain, obtained from PFAM, or in some instances, optimised in house.
    The number of proteins found for each TF family are compared against: TAIR Gene families, Plant Transcription Factor Databases (PlantTFDB) that includes Database of Arabidopsis transcription Factors (DATF) and Database of Rice Transcription Factors (DRTF), Plant Transcription Factor Database (PlntTFDB). Other related website resources: Arabidopsis Gene Regulatory Information Server (AGRIS), RIKEN Arabidopsis Transcription Factor Database (RARTF), Plant Associated Protein Database (PlanTAPDB), Database of Arabidopsis Transcription Factors with Alignments and Primers (DATFAP), GreenPhyl.
    Data for recently duplicated Arabidopsis genes are taken from Blanc, Hokamp and Wolfe (2003). Gene expression data are taken from the AtGenExpress experiment, the embro development data set of Spencer et al (2007), and an experimental series in rice by Jain et al (2007). The raw Affymetrix .cel files are normalised using RMAExpress. To display the gene expression experiments, the normalised raw signal intensity values are assigned RGB (Red-Green-Blue) colours using a six colour opacity index table (colour ramp) obtained from http://paulbourke.net/texture_colour/colourspace (01.dat).
The IT3F website uses the following software:
CLUSTALW [version 1.83], PRANK [version 090707], modified PHYLIP [version 3.65] programs (PROTDIST, NEIGHBOR, RETREE, DRAWGRAM) and the HMMER program suite (HMMBUILD, HMMALIGN, HMMSEARCH and HMMSCAN). Dynamically generated web pages are created using the Perl CGI module and Perl-generated HTML code. The Perl GD wrapper module to the GD Graphics Library is used for generating the tree display. BioPerl modules are used in the pipeline described briefly above (AlignIO, Fasta, ResultI, SearchIO, Seq, SeqIO, TreeI and TreeIO).

Related Website publications:

Paul C. Bailey, Jo Dicks, Trevor L. Wang, Cathie Martin (2008) IT3F: A Web-based Tool for Functional Analysis of Transcription Factors in Plants. Phytochemistry 69(13): 2417
DOI: 10.1016/j.phytochem.2008.08.003      [the correct paper to cite when referring to this website]

Dale Shelton, Maria Stranne, Lisbeth Mikklesen, Nima Pakseresht, Tracey Welham, Hideki Hiraka, Satoshi Tabata, Shusei Sato, Suzanne Paquette, Trevor L. Wang, Cathie Martin, Paul Bailey (2012) Transcription factors of Lotus japonicus: regulation of isoflavonoid biosynthesis requires co-ordinated changes in transcription factor activity. Plant Physiology 159(2): 531-547 DOI:10.1104/pp.112.194753