Description of the principles of the prediction process
The analysis of general and translational properties of the mRNAs of eukaryotic genes revealed several parameters allowing to discriminate between the high-and low-expression mRNAs (the set of the high-expression genes was consisted of the tissue-specific (Rbcs, Ca/b .. ), constitutive (actins, tubulins, histones, ribosomal proteins, etc.), and inducible (hsp, alcoholdehydrogenases, aldolases, etc.) genes; the set of low-expression genes was consisted of transcriptional factors, protein kinases, homeobox-containing genes, etc.). The main idea was that the leader sequences of low-expression mRNAs were often hard for the scanning by the 40S ribosomal subunits (according to scanning model, Kozak, 1989).
The results of the analysis demonstrated that some 5'UTR parameters differed significantly between the two samples (formalized description is available in file LEADER_WHY):
The computer system determines the set of the above mentioned parameters of the nucleotide sequence of the 5'UTR tested and make the prognosis of its transltional properties and the level of expression of the corresponding gene. The prognosis is made as a sum of all parameters used (computer system allows the user to correct the list of parameters and their relative significance). The use of the system to discriminate the mRNAs of high- and low-expression genes (the control set) showed that 84% of high- and 76% of low-expressed genes were predicted correctly. The prediction was significant at alpha<0.001.
The system may be also useful to design the gene-engineering experiments to predict the changes in translation properties of modified mRNA sequences.
Here you can find examples of translatability prediction for HIGH and LOW expression genes.