MatInspector is Genomatix' internationally renowned tool for transcription factor binding site analysis. It utilizes MatBase, our comprehensive transcription factor knowledge base, to locate transcription factor binding sites in sequences of any length.

What's new in MatInspector?

• Promoter finding*
• Additional lines of evidence for found transcription factor binding sites
  • literature support
  • contextual analysis for Promoter Modules
• Interactive handling of result tables, e.g. sorting and filtering by various criteria

What can you do with the new MatInspector?

• Search for transcription factor binding sites in
  • promoters, automatically determined from gene names*
  • your own sequences
  • promoters for your own sequences, determined by mapping to the genome*
  • sequences from genomic databases
• View a graphical, interactive representation of the results
• Extra lines of evidence for each match:
  • Known interaction/regulation
    • expert curated knowledge from literature (Genomatix proprietary data)
    • e.g. at least one of the TFs associated with the matrix family regulates the selected gene
  • Known cocitation
    • incorporates Genomatix literature analysis methods (LitInspector) into MatInspector
    • selected gene and at least one of the TFs associated with the matrix family are cocited
  • Part of known promoter module
    • input sequences are checked against Genomatix' proprietary Promoter Module library
    • all individual matches that are also part of a model match are marked
• Associated tissues are listed for each match
• Extraction of matches and sequences for further analysis

The first version of MatInspector is described in Quandt et al., 1995 (NAR). A paper describing additional features of MatInspector has been published in 2005 (Cartharius et al., 2005, Bioinformatics).

Improved input features*

In addition to analyzing your own sequences or complete databases you can now search the promoter of any gene of interest for all the organisms available in ElDorado. Simply start typing the name and choose a suggestion from the resulting drop-down list. If there is more than one promoter due to alternative transcripts for a gene you will be able to select one or more of them for analysis.

(e.g. human glucagon on chromosome 2)

Additional lines of evidence

Quickly get supporting evidence for each transcription factor binding site. Three categories are available:

• GCG is regulated by V$GATA (TF: GATA4)
  Known interaction (based on expert curated data)
  
  
• GGCG is cocited with V$PAX6 (TF: PAX4, PAX6)
  Known cocitation (incorporates Genomatix' automated literature analysis (LitInspector))
  
  
• part of model match of NFAT_SORY_01
  Promoter Modules (get information on relevant TF promoter modules instantly)

Result tables allow for filtering and sorting!

Interactive graphics

The interactive Java applet graphic gives you a quick overview of the position and strand of all binding sites identified. You can instantly modify the output to suit your needs by using one or more of the provided filter options. Output can be saved in various graphics formats for use in reports, publications, etc.

* these features are only available in combination with an ElDorado license.

Read more in the MatInspector online help.