BMC Genomics 2007, 8:117 http://www.biomedcentral.com/1471-2164/8/117 Table 1: The top 16 up-and down-regulated genes between normal cervix and cervical cancer. Clone ID Unigene ID Gene Name Gene Description Fold Change 810131 135975 2497698 2541366 177074 2444518 511428 951241 712505 781089 25389 296155 253009 378365 769921 685026 344139 813823 1607286 32609 855557 366100 2495781 878182 300015 809719 186757 49354 1534435 839623 1636447 813266 Hs.2785 Hs.642947 Hs.156346 Hs.234642 Hs.591205 Hs.465506 Hs.301350 Hs.615092 Hs.334562 Hs.350966 Hs.473721 Hs.434886 Hs.556259 Hs.520421 Hs.93002 Hs.481208 Hs.104672 Hs.406475 Hs.8867 Hs.213861 Hs.472831 Hs.189445 Hs.516578 Hs.212838 Hs.597358 Hs.477128 Hs.591469 Hs.620557 Hs.104839 Hs.69855 Hs.83381 Hs.598421 KRT19 DSP TOP2A AQP3 ZIC2 PPAP2C FXYD3 NUSAP1 CDC2 PTTG1 SLC2A1 CDCA5 PRO1073 PIGPC1 UBE2C AMMECR1 DOC1 LUM CYR61 LAMA4 PKIG MATN2 TFPI A2M LEPR URB DDR2 ANK2 TIMP2 NRAS GNG11 FHL1 keratin 19** desmoplakin* topoisomerase (DNA) II alpha* aquaporin 3** Zic family member 2 phosphatidic acid phosphatase type 2C FXYD domain containing ion transport regulator 3 nucleolar and spindle associated protein 1 cell division cycle 2, G1 to S and G2 to M** pituitary tumor-transforming 1* solute carrier family 2* cell division cycle associated 5** PRO1073 protein p53-induced protein PIGPC1 ubiquitin-conjugating enzyme E2C* Alport syndrome, midface hypoplasia downregulated in ovarian cancer 1 lumican cysteine-rich, angiogenic inducer laminin, alpha 4** protein kinase (cAMP-dependent) inhibitor gamma matrilin 2 tissue factor pathway inhibitor** alpha-2-macroglobulin leptin receptor steroid sensitive gene 1 discoidin domain receptor family ankyrin 2, neuronal tissue inhibitor of metalloproteinase 2 neuroblastoma RAS viral (v-ras) oncogene guanine nucleotide binding protein** four and a half LIM domains 1 21.2 14.8 13 11.8 11.8 11.1 10 9.5 9.4 9.3 8.9 7.1 6.6 6 5.9 5.5 -6.7 -6.8 -6.9 -7 -7 -7.2 -7.3 -8 -8.7 -9.2 -9.8 -10.4 -10.7 -12.6 -15.8 -21.6 A subset of the 140 genes differentially regulated between normal cervix and invasive cervical cancer, as shown in Additional file 1. Genes marked with an (*) were also reported in the cervical cancer literature; genes marked with an (**) were homologs that were reported in the previous cervical cancer literature. Global correlations of cell line models to cervical cancer The correlation of cell lines to both cervical cancer and normal cervix were calculated to evaluate how well differ- ent cell lines and culture conditions modeled the gene expression programs in cervical cancer. The global correla- tion of transcriptional profiles provided a quantitative assessment of how well cell lines model tissue; a higher Pearson correlation coefficient denoted a better model of cervical tissue. The correlations for each cell line and growth condition were summarized in Figure 3. All immortal cell lines were cultured in their ATCC recom- mended media [see Additional file 2]. To assess how changes to the environment affected the correlation between cell lines and cervical tissue, HeLa and SiHa cell lines were also cultured in a different type of media. These cell lines were individually cultured first in Eagle's Mini- mum Essential Medium (MEM) and later in Dulbecco's Modified Eagle's Medium (DMEM). In addition to the media change, HeLa and SiHa cell lines were cultured in an organotypic environment as well as an organotypic, fibroblast free control. The organotypic culture constructs a 3-dimensional growth environment, whereas the organ- otypic control simply results in a monolayer culture on a bed of collagen. The correlation of normal to normal tissue or cancer to cancer tissue samples was calculated to provide a best-case scenario for the cell line correlations and to provide an estimate of patient variation. These results also provided a measure of how well cell lines can be expected to model tissue in general. The Pearson correlation coefficient among cervical cancer specimens was 0.81 while the cor- relation among normal cervix specimens was 0.83, setting the upper expected limit of this measure. The correlation of cervical cancer to normal cervix was higher than any cell line at 0.62. Of the cell lines we tested, the primary cell line was found to be a better model than others, of both cervical cancer and normal cervix in terms of overall Page 3 of 13 (page number not for citation purposes)