Li Dan, Wan Xulian, Yun Yu, Li Yongkun, Duan Weigang
The Department of Pharmacology, School of Basic Medicine, Kunming Medical University, Kunming, 650500, China.
School of Basic Medicine, Yunnan University of Traditional Chinese Medicine, Kunming, 650500, China.
Curr Genomics. 2024;25(4):261-297. doi: 10.2174/0113892029273121240401060228. Epub 2024 Apr 8.
Understanding organic functions at a molecular level is important for scientists to unveil the disease mechanism and to develop diagnostic or therapeutic methods.
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.
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 ( < 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.
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.
在分子水平上理解有机功能对于科学家揭示疾病机制以及开发诊断或治疗方法至关重要。
本研究试图寻找在11种大鼠器官中选择性表达的基因，这些器官包括肾上腺、脑、结肠、十二指肠、心脏、回肠、肾脏、肝脏、肺、脾脏和胃。
对三只正常雄性Sprague-Dawley（SD）大鼠进行麻醉，采集上述器官，并提取新鲜器官中的RNA。使用Solexa高通量测序技术对纯化后的RNA进行逆转录和测序。通过每百万碱基测序中每千碱基转录本序列的片段预期值（FPKM）来衡量基因的丰度。找出各器官中表达水平最高的基因，并与它们在各器官中的中位数进行比较。如果最高表达器官中的某个基因与中位数表达器官中的该基因存在显著差异（<0.05），且q值<0.05，并且占总丰度的70%以上，则该基因被认定为该器官中的选择性基因。
京都基因与基因组百科全书（KEGG）和基因本体论（GO）通路被最高表达的基因富集。基于该标准，筛选出1406个选择性基因，其中1283个已在基因库中描述，123个有待描述。各器官中的KEGG和GO通路部分得到了已知认识的证实，且很大一部分通路需要进一步研究。
新的选择性基因和有机功能通路有助于科学家在分子水平上揭示器官的机制，并且选择性基因的产物是器官疾病的候选标志物。
