## 3 Results
### MS Analysis  
MS analysis of DNA affinity chromatography-purified proteins identified a number of previously reported and several novel IGF-IR promoter binding proteins. The proteins identified were categorized using the Gi (gene index) identification tool, coverage (percentage of amino acids covered by the  
Figure 3: IGF-IR and ER\(\alpha\) expression in MCF7 and C4.12.5 breast cancer cell lines. MCF7 and C4.12.5 cells were lysed as described under _Materials and Methods_. Cellular extracts (80 \(\upmu\)g) were electrophoresed through 10% SDS-PAGE, transferred to nitrocellulose membranes, and blotted with anti-total IGF-IR-\(\beta\), anti-pIGF-IR, and anti-ER\(\alpha\). Blots were then blotted with a tubulin antibody as a loading control. identified peptide), and source (Table 1). The specific proteins bound to the IGF-IR promoter were classified based on cellular localization and biological function (Table 2). Most of the proteins were localized in the nucleus, but some of them were found also in the cytoplasm as well as in the plasma membrane. Furthermore, Table 2 illustrates the variety of biological processes associated with the identified IGF-IR promoter-binding transcription factors in ER-positive and ER-depleted breast cancer cells. Out of 91 proteins identified by MS, 6 correspond to cytoskeleton-associated proteins, 6 are involved in transcription, regulation of nucleobase, nucleoside and nucleic acid metabolism, 2 in nuclear stability, chromatin structure, cycle control, and gene expression, 20 in DNA repair, breaking, replication, and cell death, 24 in RNA splicing and processing, and translation, and 33 in other functions, including proliferation, apoptosis, and proteosomal degradation. \begin{table}
\begin{tabular}{l l c c c} \hline \multicolumn{2}{c}{**Protein Name**} & **Coverage** & **Coverage** & **Source** \\ \hline  & & **MCF7** & **C4.12.5** & & \\
4760598 & Adenylate kinase isozyme 2 & 4 & - & Mus musculus \\
61743954 & AHNAK nucleoprotein isoform 1 & 1 & 3 & Homo sapiens \\
1061128 & Anpg & 25 & 21 & Homo sapiens \\
5453541 & Anterior gradient 2 homolog & 26 & – & Homo sapiens \\
6753086 & Apurinic/apyrinidinic endonuclease 1 & 8 & – & Mus musculus \\
10947139 & Arginase, type I & – & 3 & Homo sapiens \\
6680748 & ATP synthase, H\({}^{+}\) transporting, mitochondrial F1 & 3 & 7 & Mus musculus \\  & complex, alpha subunit, isoform 1 & & & \\
10863945 & ATP-dependent DNA helicase II & 20 & 28 & Homo sapiens \\
4503841 & ATP-dependent DNA helicase II, 70 kDa subunit & 22 & 28 & Homo sapiens \\  & ATP-dependent DNA helicase Q1 (DNA-dependent & – & 4 & Homo sapiens \\
1040689 & ATPase Q1) & – & & \\
42740907 & Clusterin isoform 2 & – & 8 & Homo sapiens \\
22208854 & Cytidine monophospho-N-acetylneuraminic acid & 3 & 3 & Mus musculus \\ synthetase & & & & \\
4557515 & Damage-specific DNA binding protein 2 (48 kD) & 6 & 18 & Homo sapiens \\  & Damage-specific DNA binding protein 2 splicing variant & 7 & 13 & Homo sapiens \\
45476309 & D4 & & & \\
4758138 & DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 & 15 & 13 & Homo sapiens \\
506756 & Desmyoykin & – & 6 & \\
1706481 & DNA ligase III & 23 & 37 & Homo sapiens \\
11225260 & DNA topoisomerase I & 10 & 11 & Homo sapiens \\
347019 & DnaK-type molecular chaperone hsp72-ps1 & 8 & 10 & Rattus norvegicus \\
1722884 & DNA-repair protein complementing XP-C cells & – & 6 & Drosophila \\  & & & & melanogaster \\
38201714 & ELAV-like 1 & 10 & – & Homo sapiens \\
4503471 & Eukaryotic translation elongation factor 1 \(\alpha\) 1 & 6 & 2 & Homo sapiens \\
4503477 & Eukaryotic translation elongation factor 1 \(\beta\) 2 & 7 & – & Homo sapiens \\
25453472 & Eukaryotic translation elongation factor 1 \(\delta\) isoform 2 & 22 & – & Homo sapiens \\ \hline \end{tabular}
\end{table} 
Table 1: IGF-IR promoter-binding proteins identified by MS in MCF7 and C4.12.5 cells.