Neural functions in cancer: Data analyses and database construction
Recent studies have revealed that neural functions are involved in possibly every aspect of a cancer development, serving as bridges connecting microenvironmental stressors, activities of intracellular subsystems, and cell survival. Elucidation of the functional roles played by the neural system cou...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-02-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1062052/full |
| _version_ | 1811165276558852096 |
|---|---|
| author | Renbo Tan Renbo Tan Feilong Wang Feilong Wang Yi Zhou Zhenyu Huang Zhenyu Huang Zheng An Ying Xu Ying Xu |
| author_facet | Renbo Tan Renbo Tan Feilong Wang Feilong Wang Yi Zhou Zhenyu Huang Zhenyu Huang Zheng An Ying Xu Ying Xu |
| author_sort | Renbo Tan |
| collection | DOAJ |
| description | Recent studies have revealed that neural functions are involved in possibly every aspect of a cancer development, serving as bridges connecting microenvironmental stressors, activities of intracellular subsystems, and cell survival. Elucidation of the functional roles played by the neural system could provide the missing links in developing a systems-level understanding of cancer biology. However, the existing information is highly fragmented and scattered across the literature and internet databases, making it difficult for cancer researchers to use. We have conducted computational analyses of transcriptomic data of cancer tissues in TCGA and tissues of healthy organs in GTEx, aiming to demonstrate how the functional roles by the neural genes could be derived and what non-neural functions they are associated with, across different stages of 26 cancer types. Several novel discoveries are made, including i) the expressions of certain neural genes can predict the prognosis of a cancer patient; ii) cancer metastasis tends to involve specific neural functions; iii) cancers of low survival rates involve more neural interactions than those with high survival rates; iv) more malignant cancers involve more complex neural functions; and v) neural functions are probably induced to alleviate stresses and help the associated cancer cells to survive. A database, called NGC, is developed for organizing such derived neural functions and associations, along with gene expressions and functional annotations collected from public databases, aiming to provide an integrated and publicly available information resource to enable cancer researchers to take full advantage of the relevant information in their research, facilitated by tools provided by NGC. |
| first_indexed | 2024-04-10T15:35:46Z |
| format | Article |
| id | doaj.art-8bfab93cfb004882b825c97e5ae4ebae |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T15:35:46Z |
| publishDate | 2023-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-8bfab93cfb004882b825c97e5ae4ebae2023-02-13T07:18:10ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-02-011410.3389/fgene.2023.10620521062052Neural functions in cancer: Data analyses and database constructionRenbo Tan0Renbo Tan1Feilong Wang2Feilong Wang3Yi Zhou4Zhenyu Huang5Zhenyu Huang6Zheng An7Ying Xu8Ying Xu9Key Laboratory of Symbolic Computation and knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, ChinaCancer Systems Biology Center, China-Japan Union Hospital of Jilin University, Changchun, ChinaKey Laboratory of Symbolic Computation and knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, ChinaCancer Systems Biology Center, China-Japan Union Hospital of Jilin University, Changchun, ChinaComputational Systems Biology Lab, Department of Biochemistry and Molecular Biology, And Institute of Bioinformatics, University of Georgia, Athens, GA, United StatesKey Laboratory of Symbolic Computation and knowledge Engineering, College of Computer Science and Technology, Jilin University, Changchun, ChinaCancer Systems Biology Center, China-Japan Union Hospital of Jilin University, Changchun, ChinaComputational Systems Biology Lab, Department of Biochemistry and Molecular Biology, And Institute of Bioinformatics, University of Georgia, Athens, GA, United StatesCancer Systems Biology Center, China-Japan Union Hospital of Jilin University, Changchun, ChinaComputational Systems Biology Lab, Department of Biochemistry and Molecular Biology, And Institute of Bioinformatics, University of Georgia, Athens, GA, United StatesRecent studies have revealed that neural functions are involved in possibly every aspect of a cancer development, serving as bridges connecting microenvironmental stressors, activities of intracellular subsystems, and cell survival. Elucidation of the functional roles played by the neural system could provide the missing links in developing a systems-level understanding of cancer biology. However, the existing information is highly fragmented and scattered across the literature and internet databases, making it difficult for cancer researchers to use. We have conducted computational analyses of transcriptomic data of cancer tissues in TCGA and tissues of healthy organs in GTEx, aiming to demonstrate how the functional roles by the neural genes could be derived and what non-neural functions they are associated with, across different stages of 26 cancer types. Several novel discoveries are made, including i) the expressions of certain neural genes can predict the prognosis of a cancer patient; ii) cancer metastasis tends to involve specific neural functions; iii) cancers of low survival rates involve more neural interactions than those with high survival rates; iv) more malignant cancers involve more complex neural functions; and v) neural functions are probably induced to alleviate stresses and help the associated cancer cells to survive. A database, called NGC, is developed for organizing such derived neural functions and associations, along with gene expressions and functional annotations collected from public databases, aiming to provide an integrated and publicly available information resource to enable cancer researchers to take full advantage of the relevant information in their research, facilitated by tools provided by NGC.https://www.frontiersin.org/articles/10.3389/fgene.2023.1062052/fullneural functionspan-cancermetastasistranscriptomic datadatabase |
| spellingShingle | Renbo Tan Renbo Tan Feilong Wang Feilong Wang Yi Zhou Zhenyu Huang Zhenyu Huang Zheng An Ying Xu Ying Xu Neural functions in cancer: Data analyses and database construction Frontiers in Genetics neural functions pan-cancer metastasis transcriptomic data database |
| title | Neural functions in cancer: Data analyses and database construction |
| title_full | Neural functions in cancer: Data analyses and database construction |
| title_fullStr | Neural functions in cancer: Data analyses and database construction |
| title_full_unstemmed | Neural functions in cancer: Data analyses and database construction |
| title_short | Neural functions in cancer: Data analyses and database construction |
| title_sort | neural functions in cancer data analyses and database construction |
| topic | neural functions pan-cancer metastasis transcriptomic data database |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1062052/full |
| work_keys_str_mv | AT renbotan neuralfunctionsincancerdataanalysesanddatabaseconstruction AT renbotan neuralfunctionsincancerdataanalysesanddatabaseconstruction AT feilongwang neuralfunctionsincancerdataanalysesanddatabaseconstruction AT feilongwang neuralfunctionsincancerdataanalysesanddatabaseconstruction AT yizhou neuralfunctionsincancerdataanalysesanddatabaseconstruction AT zhenyuhuang neuralfunctionsincancerdataanalysesanddatabaseconstruction AT zhenyuhuang neuralfunctionsincancerdataanalysesanddatabaseconstruction AT zhengan neuralfunctionsincancerdataanalysesanddatabaseconstruction AT yingxu neuralfunctionsincancerdataanalysesanddatabaseconstruction AT yingxu neuralfunctionsincancerdataanalysesanddatabaseconstruction |