Title:Genes Selectively Expressed in Rat Organs
Volume: 25
Issue: 4
Author(s): Dan Li, Xulian Wan, Yu Yun, Yongkun Li and Weigang Duan*
Affiliation:
- School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, China
Keywords:
High-throughput sequencing, selective expression, organic markers, rat, genetic variations, DNA.
Abstract:
Background: Understanding organic functions at a molecular level is important for scientists
to unveil the disease mechanism and to develop diagnostic or therapeutic methods.
Aims: The present study tried to find genes selectively expressed in 11 rat organs, including the adrenal
gland, brain, colon, duodenum, heart, ileum, kidney, liver, lung, spleen, and stomach.
Materials and Methods: Three normal male Sprague-Dawley (SD) rats were anesthetized, their organs
mentioned above were harvested, and RNA in the fresh organs was extracted. Purified RNA
was reversely transcribed and sequenced using the Solexa high-throughput sequencing technique.
The abundance of a gene was measured by the expected value of fragments per kilobase of transcript
sequence per million base pairs sequenced (FPKM). Genes in organs with the highest expression
level were sought out and compared with their median value in organs. If a gene in the highest
expressed organ was significantly different (p < 0.05) from that in the medianly expressed organ,
accompanied by q value < 0.05, and accounted for more than 70% of the total abundance, the gene
was assumed as the selective gene in the organ.
Results & Discussion: The Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology
(GO) pathways were enriched by the highest expressed genes. Based on the criterion, 1,406 selective
genes were screened out, 1,283 of which were described in the gene bank and 123 of which
were waiting to be described. KEGG and GO pathways in the organs were partly confirmed by the
known understandings and a good portion of the pathways needed further investigation.
Conclusion: The novel selective genes and organic functional pathways are useful for scientists to
unveil the mechanisms of the organs at the molecular level, and the selective genes’ products are
candidate disease markers for organs.
