Identifying The Differentially Expressed Proteins Between Normal And Cancer Cell Lines By Damapep

The expression profiles of 312 proteins obtained by the DAMA staining for 10 breast cell lines were repeated at least twice and were analyzed by the programs ScanAlyze and DAMAPEP. When using a minimum cutoff value of 2.0 for the absolute value of Ratio(ij), 10 of 312 proteins (leukemia inhibitory factor receptor alpha, Tyk2, Rb p130, SRF, c-Kit, Rb p107, RAIDD, Mos proto-oncogene, IκB-β, and IL-2Rβ) were predicted by DAMAPEP to have different expression levels in cancer cells versus normal cells (Fig. 3a). The first seven proteins were predicted to have higher expression levels in cancer cells, and the latter three were predicted to have lower expression levels. Their corresponding dots in the DAMA images for all 10 cell lines demonstrated the consistency between the DAMAPEP prediction and the original DAMA staining data especially for those confirmed proteins (Fig. 3b and supplemental Fig. S1). When the cutoff value for Ratio(ij) was decreased from 2.0 to 1.5 (representing a 50% intensity change between normal and cancer cells) six extra proteins were added to the prediction list. Among them, ErbB3, c-Raf, and Rad52 were predicted to have higher expression in cancer cells, and Fas (TNFRSF6)-associated death domain protein, FLICE inhibitory protein (short/long), and IL-1R were predicted to have lower expression. However, none of these six proteins was confirmed to have the predicted difference by Western blotting analysis (data not shown). Therefore, 2.0 was used as the cutoff value for Ratio(ij) in the DAMAPEP prediction.

FIG. 3.

Proteins predicted from DAMAPEP to have different expression levels between normal and cancer cellsa, the DAMAPEP-predicted proteins are shown with their name, position in the DAMA staining images, and their corresponding ratio values ranked from high at left to low at rightb, summary of the corresponding dots in the DAMA staining images shown in Fig. 1 for the seven proteins predicted by DAMAPEP with increased expression levels in carcinoma-originated cell lines. LIFR, leukemia inhibitory factor receptor alpha.

 

 

0 replies

Leave a Reply

Want to join the discussion?
Feel free to contribute!

Leave a Reply