The extracellular matrix (ECM) provides an essential structural framework for cell attachment, proliferation, and differentiation, and undergoes progressive changes during senescence. To investigate changes in protein expression in the extracellular matrix between young and senescent fibroblasts, we compared proteomic data (LTQ-FT) with cDNA microarray results. The peptide counts from the proteomics analysis were used to evaluate the level of ECM protein expression by young cells and senescent cells, and ECM protein expression data were compared with the microarray data. After completing the comparative analysis, we grouped the genes into four categories. Class I included genes with increased expression levels in both analyses, while class IV contained genes with reduced expression in both analyses. Class II and Class III contained genes with an inconsistent expression pattern. Finally, we validated the comparative analysis results by examining the expression level of the specific gene from each category using Western blot analysis and semiquantitative RT-PCR. Our results demonstrate that comparative analysis can be used to identify differentially expressed genes.
Bibliographical noteFunding Information:
This work was supported by a Korea Basic Science Grant (KBSI-T31614) and the Mid-career Researcher Program through an NRF Grant funded by Ministry of Education, Science and Technology (No. RO1-2008-000-20253-0). We special thank K-Mep team for technical assistance.
All Science Journal Classification (ASJC) codes
- Molecular Biology
- Cell Biology