The computational analysis of human testis transcriptome reveals closer ties to pluripotency.
The computational analysis of human testis transcriptome reveals closer ties to pluripotency.
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DOI：
10.4103/0974-1208.106339
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发表时间：
2012-09
影响因子：
--
通讯作者：
Prasad BV
中科院分区：
文献类型：
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作者：
Anand M;Prasad BV
本研究的目的是鉴定人睾丸中的差异表达基因（DEG），并评估人睾丸、人胚胎干细胞（hESC）、小鼠睾丸和小鼠ESCs （mESC）之间的关系。这是一种计算设计的前瞻性分析。方法和材料：从NCBI-GEO获取人睾丸、hESCs、小鼠睾丸和mESCs的微阵列数据，分析鉴定deg。然后将结果与小鼠睾丸进行比较，并扩展到ESCs。使用各种Bioconductor包在R中分析数据。为了识别deg，使用2倍截止和低于0.01的错误发现率（FDR）标准。与其他正常组织相比，人类睾丸中共有2868个转录本（deg）显著上调，2011个转录本显著下调。在上调的转录本中，232个转录本被归类为未分类，即在分析时具有未知的注释。基于基因本体（Gene Ontology， GO）的睾丸特异性deg功能注释表明，大多数deg（约80%）参与各种代谢过程。途径分析显示泛素介导的蛋白水解途径的过度代表性。在人类睾丸、小鼠睾丸、hESCs和mESCs中发现了67个转录本的核心组。睾丸似乎是代谢非常活跃相对于其他正常组织的功能注释表明。人类和小鼠睾丸的比较显示了两种物种中涉及的保守功能和途径。大量基因在睾丸和ESCs之间被发现是保守的，这表明生殖器官与去分化和重编程等复杂现象有着非常密切的表达水平关系。
The purpose of this study was to identify the differentially expressed genes (DEG) in human testis and also evaluate the relationship between human testis, human Embryonic Stem Cells (hESC), mouse testis and mouse ESCs (mESC). It is a prospective analysis designed computationally. Methods and Material: The microarray data for human testis, hESCs, mouse testis and mESCs were obtained from NCBI-GEO and analyzed for identification of DEGs. The results were then compared with mouse testis and extended to ESCs. Data was analyzed in R using various Bioconductor packages. To identify DEGs, 2-fold cut-off and a False Discovery Rate (FDR) below 0.01 criterions was used. A total 2868 transcripts (DEGs) were found to be significantly up-regulated and 2011 transcripts significantly down-regulated in human testis compared to other normal tissues. Of the up-regulated transcripts, 232 transcripts were grouped as unclassified i.e. had unknown annotations at the time of analysis. Gene Ontology (GO) based functional annotation of testis specific DEGs indicate that most of the DEGs (~80%) are involved in various metabolic processes. Pathway analysis shows over-representation of Ubiquitin-mediated proteolysis pathway. A core group of 67 transcripts were found to be common among human testis, mouse testis, hESCs and mESCs. Testis seems to be metabolically very active relative to other normal tissues as indicated by functional annotation. The comparison of human and mouse testis shows conserved functions and pathways involved in both species. Large numbers of genes were found conserved between testis and ESCs suggesting very close expression level relationship between reproductive organs and complex phenomenon such as dedifferentiation and reprogramming.