Identification and validation of commonly overexpressed genes in solid tumors by comparison of microarray data

Neoplasia. Nov-Dec 2004;6(6):744-50. doi: 10.1593/neo.04277.


Cancers originating from epithelial cells are the most common malignancies. No common expression profile of solid tumors compared to normal tissues has been described so far. Therefore we were interested if genes differentially expressed in the majority of carcinomas could be identified using bioinformatic methods. Complete data sets were downloaded for carcinomas of the prostate, breast, lung, ovary, colon, pancreas, stomach, bladder, liver, and kidney, and were subjected to an expression analysis using SAM. In each experiment, a gene was scored as differentially expressed if the q value was below 25%. Probe identifiers were unified by comparing the respective probe sequences to the Unigene build 155 using BlastN. To obtain differentially expressed genes within the set of analyzed carcinomas, the number of experiments in which differential expression was observed was counted. Differential expression was assigned to genes if they were differentially expressed in at least eight experiments of tumors from different origin. The identified candidate genes ADRM1, EBNA1BP2, FDPS, FOXM1, H2AFX, HDAC3, IRAK1, and YY1 were subjected to further validation. Using this comparative approach, 100 genes were identified as upregulated and 21 genes as downregulated in the carcinomas.

Publication types

  • Comparative Study

MeSH terms

  • Female
  • Gene Expression Profiling
  • Gene Expression*
  • Humans
  • Male
  • Neoplasms / genetics*
  • Oligonucleotide Array Sequence Analysis
  • Reproducibility of Results