Qualitative and Quantitative Expression Status of the Human Chromosome 20 Genes in Cancer Tissues and the Representative Cell Lines

Under the guidance of the Chromosome-centric Human Proteome
Project (C-HPP),, we conducted a systematic survey
of the expression status of genes located at human chromosome 20 (Chr.20)
in three cancer tissues, gastric, colon, and liver carcinoma, and
their representative cell lines. We have globally profiled proteomes
in these samples with combined technology of LC–MS/MS and acquired
the corresponding mRNA information upon RNA-seq and RNAchip. In total,
323 unique proteins were identified, covering 60% of the coding genes
(323/547) in Chr.20. With regards to qualitative information of proteomics,
we overall evaluated the correlation of the identified Chr.20 proteins
with target genes of transcription factors or of microRNA, conserved
genes and cancer-related genes. As for quantitative information, the
expression abundances of Chr.20 genes were found to be almost consistent
in both tissues and cell lines of mRNA in all individual chromosome
regions, whereas those of Chr.20 proteins in cells are different from
tissues, especially in the region of 20q13.33. Furthermore, the abundances
of Chr.20 proteins were hierarchically evaluated according to tissue-
or cancer-related distribution. The analysis revealed several cancer-related
proteins in Chr.20 are tissue- or cell-type dependent. With integration
of all the acquired data, for the first time we established a solid
database of the Chr.20 proteome.