Methods for predicting transcription levels

A method for predicting an expression level of a target gene or gene family in a particular cellular state, comprising:

• a) selecting a target gene or gene family;
• b) experimentally determining the number and type of cis-acting elements and mRNA expression levels of other genes within said target gene family in said cellular state relative to genes not in said cellular state to obtain a first data set;
• and
• c) applying a non-linear model algorithm to said data set, thereby generating the estimated expression level of said target gene as a function of the cellular state and the weighed frequencies of said cis-acting elements present in the 5′ untranslated regulatory region of said target gene.

A method for determining contribution of cis-acting elements to levels of mRNA expression of target genes, comprising:

• a) providing a host cell population;
• b) contacting said host cell with oligonucleotides encoding cis-acting element DNA, said cis-acting elements also being present in said target genes;
• c) isolating mRNA from said host cells;
• d) reverse transcribing said mRNA into cDNA;
• e) performing polymerase chain reaction to amplify said cDNA and assessing alterations of expression levels of said target genes in the presence and absence of said oligonucleotide encoding cis-acting element DNA, altered mRNA expression levels indicating the presence of the oligonucleotide cis-acting element in the untranslated regulatory region of said target gene.