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US 6,746,844 B2Granted
Determining signal transduction pathways
AssigneeAffymetrix, Inc.
InventorsJonathan D. Oliner, Earl Hubbell
Life of this patent
Estimating the term…
Abstract
Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
Claims33
A method of determining candidate functional mediators of a selected gene, comprising the steps of:
- a. altering expression of a first selected gene in a first of two populations of identical cells;
- b. comparing expression levels of a first set of genes in the two populations of cells, wherein the expression levels are measured on oligonucleotide arrays;
- c. identifying genes in the first set whose expression levels differ between the two populations of cells, wherein the genes identified are candidate functional mediators of the selected gene;
- d. altering expression of a second selected gene in one of a third and fourth populations of cells, wherein the third and fourth populations comprise identical cells, wherein the second selected gene is a candidate functional mediator of the first selected gene;
- e. comparing expression levels of a second set of genes in the third and fourth populations of cells, wherein the expression levels are measured on oligonucleotide arrays;
- f. identifying genes in the second set whose expression levels differ between the third and fourth populations of cells, wherein the genes identified are candidate functional mediators of the second selected gene.
3 more elements
A method of identifying pathways of functional mediators of a selected gene, comprising the steps of:
- a. altering expression of a first selected gene in a first of two populations of identical cells;
- b. comparing expression levels of a first set of genes in the two populations of cells, wherein the expression levels are measured on oligonucleotide arrays;
- c. identifying genes in the first set whose expression levels differ between the two populations of cells, wherein the genes identified form a set of candidate functional mediators of the first selected gene;
- d. altering expression of a second selected gene in one of a third and fourth populations of cells, wherein the third and fourth populations comprise identical cells;
- e. comparing expression levels of a second set of genes in the third and fourth populations of cells, wherein the expression levels are measured on oligonucleotide arrays;
- f. identifying genes in the second set whose expression levels differ between the third and fourth populations of cells, wherein the genes identified form a set of candidate functional mediators of the second selected gene;
- g. comparing the candidate functional mediators identified of the first and second selected genes, wherein genes which are identified as candidate functional mediators of both selected genes suggest that the first and second selected genes are components of a common pathway, wherein failure to identify a candidate functional mediator of both selected genes suggests that the two selected genes are in different pathways, wherein identification of a set of candidate functional mediators of the first selected gene as a subset of the set of candidate functional mediators of the second selected gene suggests that the first selected gene is downstream in a pathway relative to the second selected gene, and wherein a candidate functional mediator which is identified in only one of the two sets of candidate functional mediators is identified as upstream in the pathway of a selected gene from a point of convergence with the pathway of the other selected gene, if the sets of candidate functional mediator genes of the first and second selected genes contain common members.
4 more elements
A method to determine a pathway of gene products, comprising the step of:
- comparing a first set of candidate functional mediator genes identified by the process of:
- (a) comparing expression levels of a set of genes in two populations of identical cells, wherein a first of the two populations of cells has been treated to alter expression of a first selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (b) identifying genes in the set of genes whose expression levels differ between the two populations of cells, wherein the genes identified are candidate functional mediators of the first selected gene;
- with a second set of candidate functional mediator genes identified by the process of:
- (c) comparing expression levels of the set of genes in a third and fourth population of cells, wherein the third population of cells has been treated to alter expression of a second selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (d) identifying genes in the set of genes whose expression levels differ between the third and fourth populations of identical cells, wherein the genes identified are candidate functional mediators of the second selected gene;
- identifying the first and second selected genes as components of a common pathway when one or more genes are found to be candidate functional mediators of both of said first and said second selected genes.
4 more elements
A method to determine a pathway of gene products, comprising the step of:
- comparing a first set of candidate functional mediator genes identified by the process of:
- (a) comparing expression levels of a set of genes in two populations of identical cells, wherein a first of the two populations of cells has been treated to alter expression of a first selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (b) identifying genes in the set of genes whose expression levels differ between the two populations of cells, wherein the genes identified are candidate functional mediators of the first selected gene;
- with a second set of candidate functional mediator genes identified by the process of:
- (c) comparing expression levels of the set of genes in a third and fourth population of cells, wherein the third population of cells has been treated to alter expression of a second selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (d) identifying genes in the set of genes whose expression levels differ between the third and fourth populations of identical cells, wherein the genes identified are candidate functional mediators of the second selected gene;
- identifying the first and second selected genes as being in different pathways when no gene is identified as being a candidate functional mediator of both of said first and said second selected genes.
4 more elements
A method to determine a pathway of gene products, comprising the step of:
- comparing a first set of candidate functional mediator genes identified by the process of:
- (a) comparing expression levels of a set of genes in two populations of identical cells, wherein a first of the two populations of cells has been treated to alter expression of a first selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (b) identifying genes in the set of genes whose expression levels differ between the two populations of cells, wherein the genes identified are candidate functional mediators of the first selected gene;
- with a second set of candidate functional mediator genes identified by the process of:
- (c) comparing expression levels of the set of genes in a third and fourth population of identical cells, wherein the third population of cells has been treated to alter expression of a second selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (d) identifying genes in the set of genes whose expression levels differ between the third and fourth populations of cells, wherein the genes identified are candidate functional mediators of the second selected gene;
- identifying a gene which is identified as a candidate functional mediator of only one of said first and said second selected genes as upstream in the pathway of the first or second selected gene from a point of convergence with the pathway of the second or first selected gene, if the first and second sets of candidate functional mediator genes contain common members.
4 more elements
A method to determine a pathway of gene products, comprising the step of:
- comparing a first set of candidate functional mediator genes identified by the process of:
- (a) comparing expression levels of a set of genes in two populations of identical cells, wherein a first of the two populations of cells has been treated to alter expression of a first selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (b) identifying genes in the set whose expression levels differ between the two populations of cells, wherein the genes identified are candidate functional mediators of the first selected gene;
- with a second set of candidate functional mediator genes identified by the process of:
- (c) comparing expression levels of the set of genes in a third and fourth population of identical cells, wherein the third population of cells has been treated to alter expression of a second selected gene, wherein the expression levels are measured on oligonucleotide arrays;
- (d) identifying genes whose expression levels differ between the third and fourth populations of cells, wherein the genes identified are candidate functional mediators of the second selected gene;
- identifying the first selected gene as downstream in a pathway relative to the second selected gene if the set of candidate functional mediators of the first selected gene is a subset of the set of candidate functional mediators of the second selected gene.
4 more elements
Dependencies are inferred from the claim text.