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| 基于基因调控网络对鸡胚皮肤发育的枢纽基因和关键通路分析 |
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胡斯乐1,3,勿都巴拉2,3,陈宇杰1,3,丽春2,3,霍红雁1,3,白海花1,吴江鸿2,3*
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| (1.内蒙古民族大学 生命科学与食品学院, 内蒙古 通辽 028000;2.内蒙古民族大学 动物科学技术学院, 内蒙古 通辽 028000;3.内蒙古民族大学 生物信息学重点实验室, 内蒙古 通辽 028000) |
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| 摘要: |
| 为挖掘脊椎动物胚胎发育过程中皮肤调控模式的改变，以鸡胚作为模型，利用来源于NCBI数据库的SRA数据子库中胚胎发育第6~21天的皮肤组织RNA-Seq数据进行聚类分析，在基因共表达网络、信号通路、蛋白互作网路3个层面基于网络拓扑属性逐步挖掘核心基因集，并分析核心基因集在不同发育阶段的互作网络变化。结果表明:1)鸡胚皮肤发育过程在基因谱水平上可分成5个阶段，分别为6~9 d、10~12 d、13~14 d、15~17 d和18~21 d；2)功能富集分析表明发育早期的皮肤分化程度低、可塑性强，中期是皮肤毛囊发育关键期，最后4 d为皮肤细胞外基质建立期，分子发育过程存在严格的顺序模式；3)在基因调控网络层面深度挖掘并筛选鸡胚皮肤发育的分子调控过程。综上，本研究根据网路拓扑属性结合蛋白互作数据库提出参与不同发育模块的关键枢纽基因，为转录组测序数据的分析及脊椎动物皮肤发育过程的分子机制研究提供一些新的视角和分析方法。 |
| 关键词: 鸡胚 皮肤发育 基因调控网络 蛋白互作网络 顺序发育模式 |
| DOI：10.11841/j.issn.1007-4333.2021.07.10 |
| 投稿时间：2020-11-29 |
| 基金项目:内蒙古自治区自然科学基金项目(2019LH03012, 2018MS03034)；内蒙古民族大学博士科研启动基金(BS526,BS527)；内蒙古民族大学科学技术研究项目(NMDYB18017)；内蒙古自治区个体化用药工程技术研究中心开放课题(MDK2019088) |
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| Identification of hub genes and key pathways in chicken embryo skin development based on gene regulatory network |
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Husile1,3,Wudubala2,3,CHEN Yujie1,3,Ll Chun2,3,HUO Hongyan1,3,BAI Haihua1,WU Jianghong2,3*
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| (1.College of Life Sciences and Food Engineering, Inner Mongolia University for Nationalities, Tongliao 028000, China;2.College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao 028000, China;3.Key Laboratory of Bioinformatics, Inner Mongolia University for Nationalities, Tongliao 028000, China) |
| Abstract: |
| In order to explore the changes of skin regulatory patterns during vertebrate embryonic development, chicken embryo was used as study model. The RNA-Seq data of skin tissues from day 6 to 21 of embryonic development from the SRA database of NCBI were adopted for cluster analysis. The hub gene set was gradually mined based on the network topological attributes at three levels of gene coexpression network, signal pathway and protein interaction network. The change of interaction network of hub genes at different developmental stages was analyzed. The results showed that: 1)The development of chicken embryo skin could be divided into five stages at the gene level, which were 6-9 days, 10-12 days, 13-14 days, 15-17 days and 18-21 days. 2)The functional enrichment analysis showed that the skin differentiation was low and the plasticity was strong in the early stage of development, the middle stage was the key stage of skin hair follicle development, and the last four days was the establishment stage of skin extracellular matrix. There was a strict sequence pattern in the molecular development process. 3)The molecular regulatory process of chicken embryo skin development at the level of gene regulatory network were explored and screened. In conclusion, the key genes involved in different developmental modules are proposed according to the network topology attribute binding protein interaction database, which provides new perspectives and analysis methods for the analysis of transcriptome sequencing data and the molecular mechanism of vertebrate skin development. |
| Key words: chicken embryo skin development gene regulatory network protein interaction network sequential development model |
