Methods for evaluating tissue pair combinations for use in nucleic acid array technology
First Claim
1. A method for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said method comprising:
- (a) conducting differential expression experiments using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate, said probes representing a set of genes where the number of genes in the set is a portion of an expected number of genes in a sample, and (b) selecting a nucleic acid sample pair combination in relation to the members of said combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of said genes that do not exhibit differential expression.
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Abstract
Methods are disclosed for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes. Differential gene expression experiments are conducted using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate, the probes representing a set of genes. The number of genes in the set is a portion of an expected number of genes in a sample. A nucleic acid sample pair combination is selected based on the members of the combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of the genes that do not exhibit differential expression.
6 Citations
28 Claims
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1. A method for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said method comprising:
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(a) conducting differential expression experiments using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate, said probes representing a set of genes where the number of genes in the set is a portion of an expected number of genes in a sample, and (b) selecting a nucleic acid sample pair combination in relation to the members of said combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of said genes that do not exhibit differential expression. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23, 24, 25, 26, 28)
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9. A method for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said method comprising:
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(a) contacting each nucleic acid sample pair from a plurality of nucleic acid sample pairs with a plurality of probes for each of a predetermined number of genes to determine whether said genes exhibit differential expression, (b) determining for each gene and each of said nucleic acid sample pairs whether said gene exhibits or does not exhibit differential expression based on one or more parameters, (c) for a gene that exhibits differential expression in step (b) for a nucleic acid sample pair, assigning a “
yes”
value, and for each gene that does not exhibit differential expression in step (b) for a nucleic acid sample pair, assigning a “
no”
value,(d) tabulating data from step (c) for each combination of said nucleic acid sample pairs to be evaluated, and (e) selecting a combination of nucleic acid sample pairs having a score based on a maximized number of “
yes'"'"'s” and
a minimized number of “
no'"'"'s.” - View Dependent Claims (10, 11, 12, 13)
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14. A method for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said method comprising:
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(a) contacting each nucleic acid sample pair from a plurality of nucleic acid sample pairs with a plurality of probes for each of a predetermined number of genes to determine whether said genes exhibit differential expression, (b) determining for each gene and each of said nucleic acid sample pairs whether said gene exhibits or does not exhibit differential expression based on one or more parameters, (c) analyzing the results of said contacting and said determining utilizing an analysis system comprising a computer, said computer comprising;
(i) means for assigning, for each gene and to each of said nucleic acid sample pairs, a value of 1 if said gene exhibits differential expression or assigning a value of 0 if said gene does not exhibit differential expression, (ii) means for tabulating data from step (i) to determine the total number scores for each combination of said nucleic acid sample pairs to be evaluated, wherein the maximum number of 1'"'"'s for each nucleic acid sample pair per gene is the number “
n”
of nucleic acid sample pairs of said combination, and(iii) means for selecting a combination of nucleic acid sample pairs based on a score representing a maximized number of n'"'"'s and a minimized number of 0'"'"'s. - View Dependent Claims (15, 16)
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17. A computer-based method for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said method comprising:
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(a) contacting each nucleic acid sample pair from a plurality of nucleic acid sample pairs with a plurality of probes for each of a predetermined number of genes to determine whether said genes exhibit differential expression, (b) under computer control, determining for each gene and each of said nucleic acid sample pairs whether said gene exhibits or does not exhibit differential expression based on one or more parameters, (c) under computer control, for a gene that exhibits differential expression in step (b) for a nucleic acid sample pair, assigning a “
yes”
value, and for each gene that does not exhibit differential expression in step (b) for a nucleic acid sample pair, assigning a “
no”
value,(d) under computer control, tabulating data from step (c) for each combination of said nucleic acid sample pairs to be evaluated, and (f) under computer control, selecting a combination of nucleic acid sample pairs having a score based on a maximized number of “
yes'"'"'s” and
a minimized number of “
no'"'"'s.” - View Dependent Claims (18, 19)
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27. A kit for selecting a combination of nucleic acid sample pairs for evaluating the ability of an oligonucleotide probe to measure differential expression of genes, said kit comprising in packaged combination:
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(a) an algorithm for use in conducting differential gene expression experiments using (i) nucleic acid sample pairs and (ii) nucleic acid probes immobilized on a substrate where the probes represent a set of genes, the number of genes in the set being a portion of an expected number of genes in a sample, said algorithm being present on a computer readable medium, and (b) instructions for using the algorithm to select a nucleic acid sample pair combination in relation to the members of said combination having a maximized number of genes from the set of genes that exhibit differential expression and a minimized number of said genes that do not exhibit differential expression.
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Specification