Academician Workstation, Changsha Medical University, Changsha 410219, China.
College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China.
Biomed Res Int. 2020 May 2;2020:6782046. doi: 10.1155/2020/6782046. eCollection 2020.
Gene coexpression analysis is widely used to infer gene modules associated with diseases and other clinical traits. However, a systematic view and comparison of gene coexpression networks and modules across a cohort of tissues are more or less ignored. In this study, we first construct gene coexpression networks and modules of 52 GTEx tissues and cell lines. The network modules are enriched in many tissue-common functions like organelle membrane and tissue-specific functions. We then study the correlation of tissues from the network point of view. As a result, the network modules of most tissues are significantly correlated, indicating a general similar network pattern across tissues. However, the level of similarity among the tissues is different. The tissues closing in a physical location seem to be more similar in their coexpression networks. For example, the two adjacent tissues fallopian tube and bladder have the highest Fisher's exact test value 8.54-291 among all tissue pairs. It is known that immune-associated modules are frequently identified in coexperssion modules. In this study, we found immune modules in many tissues like liver, kidney cortex, lung, uterus, adipose subcutaneous, and adipose visceral omentum. However, not all tissues have immune-associated modules, for example, brain cerebellum. Finally, by the clique analysis, we identify the largest clique of modules, in which the genes in each module are significantly overlapped with those in other modules. As a result, we are able to find a clique of size 40 (out of 52 tissues), indicating a strong correlation of modules across tissues. It is not surprising that the 40 modules are most commonly enriched in immune-related functions.
基因共表达分析被广泛用于推断与疾病和其他临床特征相关的基因模块。然而，对一个队列的组织中的基因共表达网络和模块进行系统的观察和比较或多或少被忽略了。在这项研究中，我们首先构建了 52 个 GTEx 组织和细胞系的基因共表达网络和模块。网络模块富集了许多组织共有的功能，如细胞器膜和组织特异性功能。然后，我们从网络的角度研究了组织之间的相关性。结果表明，大多数组织的网络模块显著相关，表明组织之间存在一般相似的网络模式。然而，组织之间的相似程度是不同的。物理位置接近的组织在共表达网络中似乎更为相似。例如，两个相邻的组织输卵管和膀胱在所有组织对之间的 Fisher 精确检验值最高，为 8.54-291。已知免疫相关模块经常在共表达模块中被识别。在这项研究中，我们在许多组织中发现了免疫模块，如肝脏、肾皮质、肺、子宫、皮下脂肪和内脏网膜脂肪。然而，并非所有组织都有免疫相关模块，例如脑小脑。最后，通过团分析，我们确定了最大的模块团，其中每个模块中的基因与其他模块中的基因显著重叠。结果，我们能够找到一个大小为 40 的模块团（52 个组织中的 40 个），表明组织之间的模块存在强烈的相关性。毫不奇怪，这 40 个模块最常富集在与免疫相关的功能中。
