TELiS Review
TELiS stands for The Transcription Element Listening System. This is
Java server-side application which identifies transcription-factor
binding motifs (TFBMs) that are over-repressented among the promoters.
It consists of two parts: PromoterScan and PromoterStats. PromoterScan
finds number of occurences of specific TFBMs in promoters and stores
results in MySQL database. It can be compared with Match module of
CMA software (both are products of BIOBASE GmbH). Most of useful genes (e. g. Human, Mouse and Rat genome)
are already analysed and can be fetched from database. PromoterStats
uses z-statistics to find matrices which are over-represented (or
under-represented) on the specific differentially expressed promoter
set, obtained from microarray experiment. It resembles yes/no mode of
CMA (from BIOBASE) with linear composite module model.
TELiS services are available from:
http://www.telis.ucla.edu
Advantages:
Disadvantages:
* Match (owned by BIOBASE) data are fully precalculated
* Computational complexity is proportional to number of sequences
multiplied by number of matrices (quite fast comparing to CMA from BIOBASE)
* Numerical values of over-(under-)represetativity of individual
matrices may be useful
* Matrices are analyzed individually, module approach is not used
* TFBMs positions are ignored, it doesn't matter for TELiS whether
found TFBMs are close to each other or not
* Numerical expression values are not used
* Java implementation slows down computational speed. This especially
affects PromoterScan module, which can take weeks to analyse huge
promoter set. C++ implementation is much faster.
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