Back to results
US 2003/0152969 A1Published application
Non-metric tool for predicting gene relationships from expression data
AssigneeCalifornia Institute of Technology
InventorsStephen R. Quake, R. Michael van Dam, James P. Brody, Rebecca Shafee
Life of this patent
Estimating the term…
Abstract
Techniques for processing gene expression data and predicting gene relationships are provided. More specifically, a method for processing gene expression ratios may include discretizing a first expression ratio for a first gene and a second expression ratio for a second gene for each of a plurality of experiments into one of three indications, calculating the probability that the combination of the discretized expression ratios for each of the plurality of experiments arises by random chance, and determining whether the first gene and the second gene are related.
Claims27
A method for predicting gene relationships comprising:
- providing a control sample and a plurality of experimental samples;
- performing one experiment on each of the plurality of experimental samples;
- measuring a first gene control signal corresponding to a first gene from the control sample;
- measuring a first gene experimental signal corresponding to the first gene from each of the plurality of experimental samples;
- calculating a first expression ratio corresponding to the first gene for each of the plurality of experimental samples;
- discretizing the first expression ratio for each of the plurality of experimental samples into one of three indications, where the three indications representing the first gene up-regulated, not changed, or down-regulated;
- measuring a second gene control signal corresponding to a second gene from the control sample;
- measuring a second gene experimental signal corresponding to the second gene from each of the plurality of experimental samples;
- calculating a second expression ratio corresponding to the second gene for each of the plurality of experimental samples;
- discretizing the second expression ratio for each of the plurality of experimental samples into one of the three indications, where the three indications representing the second gene up-regulated, not changed, or down-regulated;
- calculating the probability that the combination of the discretized first expression ratio for each of the plurality of experimental samples and the discretized second expression ratio for each of the plurality of experimental samples arises by random chance;
- and
- determining whether the first gene and the second gene are related.
10 more elements
A method for processing gene expression ratios comprising:
- gathering gene expression data, the gene expression data comprising a first expression ratio for a first gene for each of a plurality of experiments and a second expression ratio for a second gene for each of the plurality of experiments;
- discretizing the first expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the first gene up-regulated, not changed, or down-regulated;
- discretizing the second expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the second gene up-regulated, not changed, or down-regulated;
- calculating the probability that the combination of the discretized first expression ratio for each of the plurality of experiments and the discretized second expression ratio for each of the plurality of experiments arises by random chance;
- and
- determining whether the first gene and the second gene are related.
3 more elements
A method for processing gene expression ratios comprising:
- gathering gene expression data, the gene expression data comprising a first gene control signal and a first gene experimental signal for a first gene for each of a plurality of experiments, and a second gene control signal and a second gene experimental signal for a second gene for each of the plurality of experiments;
- discretizing the first expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the first gene up-regulated, not changed, or down-regulated;
- discretizing the second expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the second gene up-regulated, not changed, or down-regulated;
- calculating the probability that the combination of the discretized first expression ratio for each of the plurality of experiments and the discretized second expression ratio for each of the plurality of experiments arises by random chance;
- and
- determining whether the first gene and the second gene are related.
3 more elements
A method for processing gene expression ratios comprising:
- gathering a first plurality of gene expression data for a first plurality of experiments with a first control sample;
- calculating a first probability in response to the first plurality of gene expression data that a pair genes are related;
- gathering a second plurality of gene expression data for a second plurality of experiments with a second control sample;
- calculating a second probability in response to the second plurality of gene expression data that said pair genes are related;
- calculating a combined probability in response to the first probability and the second probability;
- and
- determining whether said pair of genes are related.
4 more elements
A computer-readable medium including instructions for processing gene expression ratios comprising:
- one or more instructions for gathering gene expression data, the gene expression data comprising a first expression ratio for a first gene for each of a plurality of experiments and a second expression ratio for a second gene for each of the plurality of experiments;
- one or more instructions for discretizing the first expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the first gene up-regulated, not changed, or down-regulated;
- one or more instructions for discretizing the second expression ratio for each of the plurality of experiments into one of three indications, the three indications representing the second gene up-regulated, not changed, or down-regulated;
- one or more instructions for calculating the probability that the combination of the discretized first expression ratio for each of the plurality of experiments and the discretized second expression ratio for each of the plurality of experiments arises by random chance;
- and
- one or more instructions for determining whether the first gene and the second gene are related.
3 more elements
Dependencies are inferred from the claim text.