Wang Jian-Fei, Huang Yan, Lu Sheng-Feng, Hong Hao, Xu Shun-Juan, Xie Jin-Song, Wu Zhou-Ye, Tang Yi, Xu Hou-Xi, Fu Shu-Ping, Xi Zhao-Qing, Zhu Bing-Mei
The First Clinical College, Nanjing University of Chinese Medicine Nanjing 210023, P. R. China.
The Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine Nanjing 210023, P. R. China.
Am J Cardiovasc Dis. 2020 Jun 15;10(2):84-100. eCollection 2020.
Mining data in depth of genome-wide sequencing data generated from pathological target tissues under disease conditions is necessary for seeking novel functional genes, and developing more biological study directions for the field. Based on our previous published RNA-seq data generated from acute myocardial ischemia and ischemia-reperfusion in rat heart, we re-analysed these two data sets using bioinformatics tools. All these raw fastq files were extracted from Illumina BCL using the Illumina CASAVA program. Four groups were obtained: UD (genes up-regulated in MI but down-regulated in I/R injury), DU (genes down-regulated in MI but up-regulated in I/R injury), UU (genes both up-regulated in MI and I/R injury), and DD (genes both down-regulated in MI and I/R injury) groups. The results showed that 304 common genes in the UD group, 236 common genes in the DU group, 318 common genes in the UU group, and 159 common genes in the DD group detected by comparing data sets of the MI and the I/R injury. We then listed the top 30 DEGs for each group, and carried out GO and KEGG analyses for enrichment and pathway studies for those top expressed genes. Further analysis of INTERPRO Protein Domains and Features enriched by DEGs showed that 20% of the Domains enriched were related to c-type lectin, and 17% of these domains are related to neurotransmitter-gated ion-channel. 15% of PFAM Protein Domains were about Neurotransmitter-gated ion-channel. There were only 8 SMART Protein Domains DEGs enriched and 37.5% of which were concerned about leucine-rich. Collagen involvement in Reactome Pathways accounted for 22.7%. We found that only a few DEGs in these two disease conditions have been reported in the literatures, suggesting that there are many new genes would be considered in the future studies. These analyses would provide some information for seeking more novel targets of these two clinic diseases, acute myocardial ischemia and myocardial ischemia/reperfusion.
深入挖掘疾病状态下病理靶组织产生的全基因组测序数据，对于寻找新的功能基因以及为该领域开拓更多生物学研究方向是必要的。基于我们之前发表的大鼠心脏急性心肌缺血和缺血再灌注产生的RNA-seq数据，我们使用生物信息学工具对这两组数据集进行了重新分析。所有这些原始fastq文件均使用Illumina CASAVA程序从Illumina BCL中提取。获得了四组：UD（在心肌梗死中上调但在缺血再灌注损伤中下调的基因）、DU（在心肌梗死中下调但在缺血再灌注损伤中上调的基因）、UU（在心肌梗死和缺血再灌注损伤中均上调的基因）和DD（在心肌梗死和缺血再灌注损伤中均下调的基因）组。结果显示，通过比较心肌梗死和缺血再灌注损伤的数据集，在UD组中检测到304个共同基因，DU组中236个共同基因，UU组中318个共同基因，DD组中159个共同基因。然后我们列出了每组的前30个差异表达基因（DEGs），并对这些高表达基因进行了基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析以进行富集和通路研究。对由DEGs富集的INTERPRO蛋白质结构域和特征的进一步分析表明，富集的结构域中有20%与c型凝集素相关，其中17%的结构域与神经递质门控离子通道相关。15%的PFAM蛋白质结构域与神经递质门控离子通道有关。仅富集了8个SMART蛋白质结构域DEGs，其中37.5%与富含亮氨酸有关。胶原蛋白参与反应组通路的比例为22.7%。我们发现，在这两种疾病状态下只有少数DEGs在文献中被报道，这表明在未来的研究中有许多新基因值得考虑。这些分析将为寻找急性心肌缺血和心肌缺血/再灌注这两种临床疾病的更多新靶点提供一些信息。
