Expression profile analyses of human HCT-116 colon cancer cell line before and after serum induction

Abstract

Multi-exon genes may generate distinct isoforms in different conditions and exhibit versatile properties. Here we investigated the isoform-specific gene expression and the gene expression changes of without and with serum-induced human HCT-116 colon cancer cell lines. For these analyses, 4 transcriptome sequencing datasets were used and 2 replicates for each condition. We observed that ~73% of those expressed genes in four samples generated only one isoform, while ~27% encoded at least two isoforms. Our results show that human gene expression can exhibit great flexibility in alternative splicing. Those expressed genes generated ~1.4 isoforms for each gene across four samples on average. In addition, most of these expressed genes were expressed at moderate or low levels. We found that these four samples have similar patterns of their gene expression distributions. Furthermore, we also conducted the differential expression analysis between without and with serum-induced two conditions of these four samples. We detected that 123 genes were differentially expressed and 110 of them were up-regulated. Among those differentially expressed genes, we found intriguing phenomena that a portion of them could be clustered into different functional groups and some oncogenes and proto-oncogenes are differentially expressed.