Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions.
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions.
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DOI：
10.3390/genes13030480
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发表时间：
2022-03-08
期刊：
影响因子：
3.5
通讯作者：
Wang Z
中科院分区：
文献类型：
--
作者：
Zhao C;Liu T;Wang Z
拓扑相关结构域(TADS)是基因组的结构和功能单位。然而，存在于相同或不同TADS中的蛋白质编码基因的功能还没有得到充分的研究。我们比较了同一TAD和不同TAD之间的蛋白质编码基因的功能相似性，以及同一GAP区(两个连续TAD之间的区域)和不同GAP区域之间的蛋白质编码基因的功能相似性。我们发现，来自相同TAD或GAP区域的蛋白质编码基因更有可能共享相似的蛋白质功能，并且这一趋势在TADS中比GAP区域更明显。我们进一步构建了两种类型的基因-基因空间相互作用网络：第一种类型是基于Hi-C接触的，第二种类型是基于Hi-C接触和处于同一TAD中的关系。利用图形自动编码器学习网络拓扑结构，重构两类网络，并根据相邻基因/节点的功能预测中心基因/节点的功能。研究发现，第二种类型的网络具有更好的性能。此外，我们检测了基于Hi-C接触的远程空间交互区域，并计算了来自这些区域的基因对的功能相似性。
Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same TAD and between different TADs, and also in the same gap region (the region between two consecutive TADs) and between different gap regions. We found that the protein-coding genes from the same TAD or gap region are more likely to share similar protein functions, and this trend is more obvious with TADs than the gap regions. We further created two types of gene–gene spatial interaction networks: the first type is based on Hi-C contacts, whereas the second type is based on both Hi-C contacts and the relationship of being in the same TAD. A graph auto-encoder was applied to learn the network topology, reconstruct the two types of networks, and predict the functions of the central genes/nodes based on the functions of the neighboring genes/nodes. It was found that better performance was achieved with the second type of network. Furthermore, we detected long-range spatially-interactive regions based on Hi-C contacts and calculated the functional similarities of the gene pairs from these regions.
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影响因子：
14.9
作者：
Howe KL;Achuthan P;Allen J;Allen J;Alvarez-Jarreta J;Amode MR;Armean IM;Azov AG;Bennett R;Bhai J;Billis K;Boddu S;Charkhchi M;Cummins C;Da Rin Fioretto L;Davidson C;Dodiya K;El Houdaigui B;Fatima R;Gall A;Garcia Giron C;Grego T;Guijarro-Clarke C;Haggerty L;Hemrom A;Hourlier T;Izuogu OG;Juettemann T;Kaikala V;Kay M;Lavidas I;Le T;Lemos D;Gonzalez Martinez J;Marugán JC;Maurel T;McMahon AC;Mohanan S;Moore B;Muffato M;Oheh DN;Paraschas D;Parker A;Parton A;Prosovetskaia I;Sakthivel MP;Salam AIA;Schmitt BM;Schuilenburg H;Sheppard D;Steed E;Szpak M;Szuba M;Taylor K;Thormann A;Threadgold G;Walts B;Winterbottom A;Chakiachvili M;Chaubal A;De Silva N;Flint B;Frankish A;Hunt SE;IIsley GR;Langridge N;Loveland JE;Martin FJ;Mudge JM;Morales J;Perry E;Ruffier M;Tate J;Thybert D;Trevanion SJ;Cunningham F;Yates AD;Zerbino DR;Flicek P
通讯作者：
Flicek P
影响因子：
4.4
作者：
Cao R;Cheng J
通讯作者：
Cheng J
DOI：
10.1186/1748-7188-9-14
发表时间：
2014
期刊：
Algorithms for molecular biology : AMB
影响因子：
--
作者：
Filippova D;Patro R;Duggal G;Kingsford C
通讯作者：
Kingsford C
进化断点的紧密 3D 接近性支持了空间同线性的概念。
影响因子：
4.4
作者：
Véron AS;Lemaitre C;Gautier C;Lacroix V;Sagot MF
通讯作者：
Sagot MF
影响因子：
9.3
作者：
Durand NC;Shamim MS;Machol I;Rao SS;Huntley MH;Lander ES;Aiden EL
通讯作者：
Aiden EL