Determining signal transduction pathways

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.

1 - 33 . (Cancelled)  
     
     
         34 . 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 a first and a second population of cells, wherein the first population of cells is identical to the second population of cells but for an alteration in a first selected gene;  
 (b) identifying genes in the set whose expression levels differ between the first and the second 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 is identical to the fourth population of cells but for an alteration in a second selected gene;  
 (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 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.    
     
     
         35 . 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 a first and a second population of cells, wherein the first population of cells is identical to the second population of cells but for an alteration in a first selected gene;  
 (b) identifying genes in the set whose expression levels differ between the first and the second 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 is identical to the fourth population of cells but for an alteration in a second selected gene;  
 (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 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.    
     
     
         36 . 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 a first and a second population of cells, wherein the first population of cells is identical to the second population of cells but for an alteration in a first selected gene;  
 (b) identifying genes in the set whose expression levels differ between the first and the second 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 is identical to the fourth population of cells but for an alteration in a second selected gene;  
 (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 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.    
     
     
         37 . 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 a first and a second population of cells, wherein the first population of cells is identical to the second population of cells but for an alteration in a first selected gene;  
 (b) identifying genes in the set whose expression levels differ between the first and the second 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 is identical to the fourth population of cells but for an alteration in a second selected gene;  
 (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.    
     
     
         38 . The method of claim  1  wherein the alteration in the first selected gene is a deletion.  
     
     
         39 . The method of claim  2  wherein the alteration in the first selected gene is a deletion.  
     
     
         40 . The method of claim  3  wherein the alteration in the first selected gene is a deletion.  
     
     
         41 . The method of claim  4  wherein the alteration in the first selected gene is a deletion.  
     
     
         42 . The method of claim  1  wherein the alteration in the second selected gene is a deletion.  
     
     
         43 . The method of claim  2  wherein the alteration in the second selected gene is a deletion.  
     
     
         44 . The method of claim  3  wherein the alteration in the second selected gene is a deletion.  
     
     
         45 . The method of claim  4  wherein the alteration in the second selected gene is a deletion.  
     
     
         46 . The method of claim  1  wherein the alteration in the first selected gene is a mutation.  
     
     
         47 . The method of claim  2  wherein the alteration in the first selected gene is a mutation.  
     
     
         48 . The method of claim  3  wherein the alteration in the first selected gene is a mutation.  
     
     
         49 . The method of claim  4  wherein the alteration in the first selected gene is a mutation.  
     
     
         50 . The method of claim  1  wherein the alteration in the second selected gene is a mutation.  
     
     
         51 . The method of claim  2  wherein the alteration in the second selected gene is a mutation.  
     
     
         52 . The method of claim  3  wherein the alteration in the second selected gene is a mutation.  
     
     
         53 . The method of claim  4  wherein the alteration in the second selected gene is a mutation.  
     
     
         54 . The method of claim  1  wherein the first selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         55 . The method of claim  21  wherein the second selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         56 . The method of claim  2  wherein the first selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         57 . The method of claim  23  wherein the second selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         58 . The method of claim  3  wherein the first selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         59 . The method of claim  25  wherein the second selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         60 . The method of claim  4  wherein the first selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         61 . The method of claim  27  wherein the second selected gene is selected from the group consisting of BRCA1, p53, ATM, MDM2, p16, CDK4, cyclin D1, RB, p21, WT1, amphiregulin, and GADD45.  
     
     
         62 . The method of claim  1  wherein the expression levels are mRNA levels.  
     
     
         63 . The method of claim  2  wherein the expression levels are mRNA levels.  
     
     
         64 . The method of claim  3  wherein the expression levels are mRNA levels.  
     
     
         65 . The method of claim  4  wherein the expression levels are mRNA levels.  
     
     
         66 . The method of claim  1  wherein the expression levels are protein levels.  
     
     
         67 . The method of claim  2  wherein the expression levels are protein levels.  
     
     
         68 . The method of claim  3  wherein the expression levels are protein levels.  
     
     
         69 . The method of claim  4  wherein the expression levels are protein levels.  
     
     
         70 . The method of claim  1  wherein the alteration in the first selected gene is a deletion of the first selected gene.  
     
     
         71 . The method of claim  2  wherein the alteration in the first selected gene is a deletion of the first selected gene.  
     
     
         72 . The method of claim  3  wherein the alteration in the first selected gene is a deletion of the first selected gene.  
     
     
         73 . The method of claim  4  wherein the alteration in the first selected gene is a deletion of the first selected gene.  
     
     
         74 . The method of claim  1  wherein the alteration in the second selected gene is a deletion of the first selected gene.  
     
     
         75 . The method of claim  2  wherein the alteration in the second selected gene is a deletion of the first selected gene.  
     
     
         76 . The method of claim  3  wherein the alteration in the second selected gene is a deletion of the first selected gene.  
     
     
         77 . The method of claim  4  wherein the alteration in the second selected gene is a deletion of the first selected gene.  
     
     
         78 . The method of claim  1  wherein the alteration in the first selected gene is a null mutation.  
     
     
         79 . The method of claim  2  wherein the alteration in the first selected gene is a null mutation.  
     
     
         80 . The method of claim  3  wherein the alteration in the first selected gene is a null mutation.  
     
     
         81 . The method of claim  4  wherein the alteration in the first selected gene is a null mutation.  
     
     
         82 . The method of claim  1  wherein the alteration in the second selected gene is a null mutation.  
     
     
         83 . The method of claim  2  wherein the alteration in the second selected gene is a null mutation.  
     
     
         84 . The method of claim  3  wherein the alteration in the second selected gene is a null mutation.  
     
     
         85 . The method of claim  4  wherein the alteration in the second selected gene is a null mutation.