Methods and compositions for diagnosing and treating rheumatoid arthritis

A computer system, comprising:

• a database comprising values representing expression levels of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3);
• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S100 A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6, in a cell characteristic of R.A.;
• and,
• a processor having instructions to,
• receive at least one query value representing at least one level of expression of at least one gene represented in the database, and,
• compare the at least one query value and the at least one database value.

A composition comprising a plurality of detection agents of genes which are characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3);

• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S100 A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6, which detection agents are capable of detecting the expression of the genes or the polypeptides encoded by the genes, and wherein less than about 50% of the detection agents are genes which are not characteristic of R.A.

The composition of claim 12, comprising isolated nucleic acids which hybridize specifically to at least five genes selected from the group consisting of SOCS3 (CISH3);

• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S1OO A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6.

A solid surface to which are linked a plurality of detection agents of genes which are characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3);

• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S100 A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6, which detection agents are capable of detecting the expression of the genes or the polypeptides encoded by the genes, and wherein less than about 50% of the detection agents on the solid surface are not detecting genes characteristic of R.A.

A composition comprising antagonists of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3);

• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S100 A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6.

A method for determining the difference between levels of expression of a plurality of genes characteristic of R.A. in a cell and reference levels of expression of the genes, comprising

• providing RNA from a cell;
• determining levels of RNA of a plurality of genes characteristic of R.A. including a plurality of genes selected from the group consisting of SOCS3 (CISH3);
• RAGE (AGER);
• LST-1 (LY117);
• SAA 1-3;
• HMG-1;
• S100 A8, A9, and A12;
• SLPI;
• GILZ;
• PTPN-18;
• GADD-45A and B;
• Legumain (PRSC1);
• FST1;
• Lcn2;
• GPI;
• SpiL;
• and TSG-6 to obtain the levels of expression of the plurality of genes in the cell;
• and
• comparing the levels of expression of the plurality of genes in the cell to a set of reference levels of expression of the genes,
• to thereby determine the difference between levels of expression of the plurality of genes characteristic of R.A. in the cell and reference levels of expression of the genes.

A method for identifying a compound for treating R.A., comprising

• providing levels of expression of a plurality of genes characteristic of R.A. in a cell characteristic of R.A. incubated with a test compound;
• providing levels of expression of a normal counterpart cell;
• and
• comparing the two levels of expression, wherein similar levels of expression in the two cells indicates that the compound is likely to be effective for treating R.A.