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Moreover, progranulin was selected as an upregulated secreted protein by screening for the most frequently upregulated genes in breast cancer [ 5].
Out of 2187 genes, 1075 were found upregulated in OSPC when compared with HOSE (Table 2 depicts the 15 most frequently upregulated genes whereas Supplementary Table 1a and b lists all upregulated and downregulated genes, respectively).
Stromal and immune response-related genes were the most frequently upregulated, particularly in lesions that responded to treatment by stabilizing or regressing.
Figure 2A shows the genes most frequently upregulated at recurrence according to the location of the primary tumor.
The most frequently upregulated genes are involved in the kinetochore (ASPM, KIF11) or in neural development (CD133, Wnt and Notch pathways).
The Ras/Raf/MEK/Erk pathway is one of the most frequently upregulated pathways in cancer.
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The most highly and frequently upregulated gene in both arrays, however, was the mRNA IGFBP-3.
NKG2D ligands are poorly expressed by normal cells, but are frequently upregulated in tumor cells and in certain infected cells.
Interestingly, PARD6B is enriched in gain of function categories and, in concordance with published data, frequently upregulated in breast cancer (Figure 6a; Cunliffe et al.34).34
DNA methyltransferases, expressed at relatively low levels in somatic cells, are frequently upregulated in cancer cells.
NQO1 is frequently upregulated in ovarian carcinoma.
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