Methods for predicting transcription levels
First Claim
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1. A method for predicting an expression level of a target gene or gene family 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 to obtain a first data set; and
c) applying a PROBE algorithm to said data set, thereby generating the estimated expression level of said target gene as a function of the weighed frequencies of said cis-acting elements present in the 5′
untranslated regulatory region of said target gene.
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Abstract
Methods are provided for empirically determining transcription levels of target genes based on the number of cis-acting elements provided in untranslated regulatory regions.
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Citations
16 Claims
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1. A method for predicting an expression level of a target gene or gene family comprising:
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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 to obtain a first data set; and
c) applying a PROBE algorithm to said data set, thereby generating the estimated expression level of said target gene as a function of the weighed frequencies of said cis-acting elements present in the 5′
untranslated regulatory region of said target gene. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method for predicting an expression level of a target gene or gene family in a particular cellular state, comprising:
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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. - View Dependent Claims (8, 9, 10, 11, 12, 13)
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14. A method for determining contribution of cis-acting elements to levels of mRNA expression of target genes, comprising:
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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. - View Dependent Claims (15, 16)
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Specification