FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

Heng Li; Wanting Zhang; Keyi Ren; Hong Yang; Lei Zhang; Waqar Younas; Yingyin Cheng; Yaping Wang; Mijuan Shi; Xiao-Qin Xia

doi:10.1016/j.jgg.2024.09.019

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

doi: 10.1016/j.jgg.2024.09.019

Heng Li^1,2,
Wanting Zhang³,
Keyi Ren^4,5,
Hong Yang^6,7,
Lei Zhang^6,7,
Waqar Younas^6,7,
Yingyin Cheng⁸,
Yaping Wang^9,10,
Mijuan Shi^9,10, ,,
Xiao-Qin Xia^9,10, ,

1. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
2. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
3. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
4. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
5. College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China;
6. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
7. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
8. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
9. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
10. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China

基金项目:

This work was supported by the National Key R&D Program of China (2021YFD1200804 and 2018YFD0901201) and the Strategic Priority Research Program of the Chinese Academy of Sciences (Precision Seed Design and Breeding) (XDA24010206).

详细信息

通讯作者:
Mijuan Shi,E-mail:shimijuan@ihb.ac.cn

Xiao-Qin Xia,E-mail:xqxia@ihb.ac.cn

计量
- 文章访问数: 11
- HTML全文浏览量: 5
- PDF下载量: 0
- 被引次数: 0
出版历程
- 收稿日期: 2024-04-03
- 网络出版日期: 2025-06-05
- 刊出日期: 2024-10-09

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

Heng Li^1,2,
Wanting Zhang³,
Keyi Ren^4,5,
Hong Yang^6,7,
Lei Zhang^6,7,
Waqar Younas^6,7,
Yingyin Cheng⁸,
Yaping Wang^9,10,
Mijuan Shi^{9,10
, ,},
Xiao-Qin Xia^{9,10
, ,}

1. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
2. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
3. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
4. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
5. College of Fisheries and Life Science, Dalian Ocean University, Dalian, Liaoning 116023, China;
6. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
7. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China;
8. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
9. Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China;
10. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China

Funds:

摘要

HTML全文

参考文献(15)

Binder, J.X., Pletscher-Frankild, S., Tsafou, K., Stolte, C., O'Donoghue, S.I., Schneider, R., Jensen, L.J., 2014. Compartments: unification and visualization of protein subcellular localization evidence. Database 2014, bau012.

Diesh, C., Stevens, G.J., Xie, P., De Jesus Martinez, T., Hershberg, E.A., Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., et al., 2023. Jbrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol. 24, 74.

Food and Agriculture Organization of the United Nations., 2020. The State of World Fisheries and Aquaculture 2020: Sustainability in Action. F. A. O.

Gasteiger, E., Jung, E., Bairoch, A., 2001. Swiss-prot: connecting biomolecular knowledge via a protein database. Curr. Issues Mol. Biol. 3, 47-55.

Guo, C., Duan, Y., Ye, W., Zhang, W., Cheng, Y., Shi, M., Xia, X.Q., 2023a. FishGET: a fish gene expression and transcriptome database with improved accuracy and visualization. iScience. 26, 106539.

Guo, C., Ye, W., Cao, D., Shi, M., Zhang, W., Cheng, Y., Wang, Y., Xia, X.Q., 2024. Unraveling the stereoscopic gene transcriptional landscape of zebrafish using fishsed, a fish spatial expression database with multispecies scalability. Sci. China Life Sci. 67, 843-846.

Guo, C., Ye, W., Shi, M., Duan, Y., Zhang, W., Cheng, Y., Xia, X.Q., 2023b. Fishsct: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. Sci. China Life Sci. 66, 2185-2188.

Hayward, N.K., Wilmott, J.S., Waddell, N., Johansson, P.A., Field, M.A., Nones, K., Patch, A.M., Kakavand, H., Alexandrov, L.B., Burke, H., et al., 2017. Whole-genome landscapes of major melanoma subtypes. Nature 545, 175-180.

Kramer, A.C., Gurdziel, K.,Thummel, R., 2021. A comparative analysis of gene and protein expression throughout a full 28-day retinal regeneration time-course in adult zebrafish. Front. Cell Dev. Biol. 9, 741514.

Kumar, S., Suleski, M., Craig, J.M., Kasprowicz, A.E., Sanderford, M., Li, M., Stecher, G.,Hedges, S.B., 2022. Timetree 5: an expanded resource for species divergence times. Mol. Biol. Evol. 39.

Li, H., Shi, M., Ren, K., Zhang, L., Ye, W., Zhang, W., Cheng, Y., Xia, X.Q., 2023. Visual omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. Bioinformatics 39.

Papatheodorou, I., Moreno, P., Manning, J., Fuentes, A.M., George, N., Fexova, S., Fonseca, N.A., Fullgrabe, A., Green, M., Huang, N., et al., 2020. Expression atlas update: from tissues to single cells. Nucleic Acids Res. 48, D77-d83.

Pasquier, J., Cabau, C., Nguyen, T., Jouanno, E., Severac, D., Braasch, I., Journot, L., Pontarotti, P., Klopp, C., Postlethwait, J.H., et al., 2016. Gene evolution and gene expression after whole genome duplication in fish: the phylofish database. BMC Genom. 17, 368.

Sprague, J., Doerry, E., Douglas, S., Westerfield, M., 2001. The zebrafish information network (zfin): a resource for genetic, genomic and developmental research. Nucleic Acids Res. 29, 87-90.

Szklarczyk, D., Kirsch, R., Koutrouli, M., Nastou, K., Mehryary, F., Hachilif, R., Gable, A.L., Fang, T., Doncheva, N.T., Pyysalo, S., et al., 2023. The string database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638-d646.

施引文献

资源附件(0)

访问统计

点击查看大图

计量

文章访问数: 11
HTML全文浏览量: 5
PDF下载量: 0
被引次数: 0

姓名
邮箱
手机号码
标题
留言内容
验证码

留言板

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

doi: 10.1016/j.jgg.2024.09.019

通讯作者:
Mijuan Shi,E-mail:shimijuan@ihb.ac.cn

Xiao-Qin Xia,E-mail:xqxia@ihb.ac.cn

计量

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

计量

目录

留言板

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

doi: 10.1016/j.jgg.2024.09.019

通讯作者: Mijuan Shi,E-mail:shimijuan@ihb.ac.cn Xiao-Qin Xia,E-mail:xqxia@ihb.ac.cn

计量

出版历程

FishCODE: a web-based information platform for comprehensive omics data exploration in fish research

计量

出版历程

目录

通讯作者:
Mijuan Shi,E-mail:shimijuan@ihb.ac.cn

Xiao-Qin Xia,E-mail:xqxia@ihb.ac.cn