Composition for the detection of signaling pathway gene expression

Abstract

The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as array elements in a microarray. The present invention also relates to a method for selecting polynucleotide probes of the composition.

What is claimed is:  
     
         1 . A composition comprising a plurality of polynucleotide probes, wherein said plurality of polynucleotide probes comprise: 
 I) first polynucleotide probes, wherein each of said first polynucleotide probes comprises at least a portion of a gene coding for a receptor-like polypeptide;    II) second polynucleotide probes, wherein each of said second polynucleotide probes comprises at least a portion of a gene coding for a transducing polypeptide; and    III) third polynucleotide probes, wherein each of said third polynucleotide probes comprises at least a portion of a gene coding for an effector-like polypeptide.    
     
     
         2 . The composition of  claim 1 , wherein said polynucleotide probes comprise complementary DNAs.  
     
     
         3 . The composition of  claim 1 , wherein said polynucleotide probes comprise clone DNAs.  
     
     
         4 . The composition of  claim 1 , wherein said polynucleotide probes are immobilized on a substrate.  
     
     
         5 . The composition of  claim 4 , wherein said polynucleotide probes are hybridizable array elements in a microarray.  
     
     
         6 . The composition of  claim 1 , wherein each of said first, second and third polynucleotide probes comprises at least a portion of a sequence selected from the group consisting of SEQ ID Nos: 1-1490.  
     
     
         8 . The composition of  claim 1 , wherein said polynucleotide probes comprise at least a portion of substantially all the sequences of SEQ ID Nos: 1-1490.  
     
     
         9 . The composition of  claim 1 , wherein said polynucleotide probes comprise at least a portion of at least 1000 of the sequences of SEQ ID Nos: 1-1490.  
     
     
         10 . A method for selecting a plurality of polynucleotide probes, said method comprising: 
 (I) obtaining a plurality of query sequences;    (II) screening said query sequences against one or more databases comprising annotated sequences to identify sequence hits; and    (III) selecting said sequence hits with the highest homology to said annotated sequences.    
     
     
         11 . The method of  claim 10 , wherein said plurality of query sequences comprise those sequences selected from the group consisting of expression sequence tags (ESTs) and full length gene coding sequences.  
     
     
         12 . The method of  claim 10 , wherein said screening is performed electronically with the Basic Local Alignment Search Tool (BLAST) algorithm.  
     
     
         13 . The method of  claim 12 , wherein the highest homology is identified by criteria selected from the group consisting of (a) a BLAST score equal to or above 100 at a P-value equal to or below 10 −10  against the GenPept database; (b) a percent identity equal to or above 80% and a BLAST score equal to or above 250 against the GenBank Primate database; (c) a percent identity equal to or above 75% and a BLAST score equal to or above 250 against the GenBank Rodent database; and (d) a match with the lowest P-value against GenPept, Genbank Primate or Genbank Rodent databases.  
     
     
         14 . The method of  claim 10 , wherein said plurality of polynucleotide probes comprise: 
 I) first polynucleotide probes, wherein each of said first polynucleotide probes comprises at least a portion of a gene coding for a receptor-like polypeptide;    II) second polynucleotide probes, wherein each of said second polynucleotide probes comprises at least a portion of a gene coding for a transducing polypeptide; and    III) third polynucleotide probes, wherein each of said third polynucleotide probes comprises at least a portion of a gene coding for an effector-like polypeptide.    
     
     
         15 . The method of  claim 14 , wherein each of said first, second and third polynucleotide probes comprises at least a portion of a sequence selected from the group consisting of SEQ ID Nos: 1-1490.  
     
     
         16 . The method of  claim 10 , wherein said polynucleotide probes comprise at least a portion of substantially all the sequences of SEQ ID Nos: 1-1490.  
     
     
         17 . The method of  claim 10 , wherein said polynucleotide probes comprise at least a portion of at least 1000 of the sequences of SEQ ID Nos: 1-1490.  
     
     
         18 . The method of  claim 10 , wherein said plurality of polynucleotide probes are immobilized on a substrate.  
     
     
         19 . The method of  claim 10 , wherein said plurality of polynucleotide probes are hybridizable array elements in a microarray.