SAGE Tag sequence | Gene symbol (name)^{a} | Accession no.^{b} | Fold Inc SAGE D54^{c} | Fold Inc PCR D54^{d} | Fold Inc PCR U87c^{e} | Fold Inc PCR U87x^{e} | Fold Inc PCR U118^{e} | Fold Inc PCR U251^{e} |
---|---|---|---|---|---|---|---|---|
TAAAAACAAA | COL8A1 (Collagen, type VIII, α 1) | BC013581 | 22x | 154x | 4.3x | (−16x) | 4.6x | 2.4x |
ACAGATTTGA | COL8A1 (Alternative Transcript of COL8A1) | AL359062 | 22x | 30x | 11.5x | (−3x) | 6.6x | 2.2x |
GCCAAATGTT | IL13RA2 (Interleukin 13 receptor, α 2) | NM_000640 | 16x | 4.0x | 3.8x | (−183x) | 2.5x | 1x |
CATTTTGCTT | FAP (fibroblast activation protein α) | NM_004460 | 8x | 7.3x | 9.8x | 5.6x | 2.9x | 1x |
TGCAGTCACT | MMP1 (matrix metalloproteinase 1) | NM_002421 | 8x | 12x | 5.2x | (−9.4x) | (−3.1x) | 2.2x |
AATCTGTCTC | MME (Membrane metalloendopeptidase) | NM_007289 | 6x | 4x | 7.5x | 46.3x | 1.5x | 1x |
TGCAATATGC | FBN1 (fibrillin 1) | NM_000138 | 6x | 4.3x | 6x | (−2x) | 2.4x | 1x |
MMP13^{f} (matrix metalloproteinase 13) | NM_002427 | - | 29x | 2.5x | ND^{g} | ND^{g} | 1x | |
EGFRvIII^{h} | - | 42x | 60x | 18x | 36x | 13x |
^{a} HUGO/GDB nomenclature committee approved symbols for individual genes when available. Genes with no approved symbols are marked with an asterisk (*). Each gene sequence had a poly(A)signal and/or poly(A)tail and was matched to the SAGE tag.
^{b} The GenBank accession number was used to identify the gene and contains the differentially expressed tag.
^{c} The fold increase in gene expression predicted by SAGE was calculated by normalizing the total number of tags in the two SAGE libraries and taking the ratio of the tags in D54-EGFRvIII to D54-lacZ.
^{d} The fold increase in gene expression by real-time PCR was calculated by comparing the rate of amplification of a gene-specific product in D54-EGFRvIII and D54-lacZ-derived cDNA relative to a set of standards.
^{e} The fold increase in gene expression by real-time PCR in different glioblastoma cell lines (U87c, U118, and U251) and xenografts (U87x) expressing EGFRvIII compared to either the parental cell line or the same cell line expressing β-galacatosidase. Values in brackets with a negative sign indicate a fold decrease in gene expression.
^{f} MMP13 was identified as induced by EGFRvIII using DNA filter arrays.
^{g} There was no detectable PCR product.
^{h} The fold induction of EGFRvIII was calculated in the different glioblastoma systems using real-time PCR.