FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species
The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research a...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022002963 |
| _version_ | 1797978195322994688 |
|---|---|
| author | Suxu Tan Wenwen Wang Wencai Jie Jinding Liu |
| author_facet | Suxu Tan Wenwen Wang Wencai Jie Jinding Liu |
| author_sort | Suxu Tan |
| collection | DOAJ |
| description | The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp. |
| first_indexed | 2024-04-11T05:19:06Z |
| format | Article |
| id | doaj.art-07f93d60b5f74f118c03a8fb6e217e1d |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:06Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-07f93d60b5f74f118c03a8fb6e217e1d2022-12-24T04:53:25ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012036763684FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish speciesSuxu Tan0Wenwen Wang1Wencai Jie2Jinding Liu3Department of Animal Science, Michigan State University, East Lansing, MI 48824, USASchool of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USAInstitute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, ChinaDepartment of Animal Science, Michigan State University, East Lansing, MI 48824, USA; Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Corresponding author at: Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food industry. Furthermore, there is a lack of online platform to analyze users’ new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, including gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize experiments and tools to perform differential/specific expression and alternative splicing analysis, co-expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript- and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample information, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo.njau.edu.cn/fishExp.http://www.sciencedirect.com/science/article/pii/S2001037022002963Alternative splicingGene expressionFishDatabaseAnalysis platform |
| spellingShingle | Suxu Tan Wenwen Wang Wencai Jie Jinding Liu FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species Computational and Structural Biotechnology Journal Alternative splicing Gene expression Fish Database Analysis platform |
| title | FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| title_full | FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| title_fullStr | FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| title_full_unstemmed | FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| title_short | FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| title_sort | fishexp a comprehensive database and analysis platform for gene expression and alternative splicing of fish species |
| topic | Alternative splicing Gene expression Fish Database Analysis platform |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022002963 |
| work_keys_str_mv | AT suxutan fishexpacomprehensivedatabaseandanalysisplatformforgeneexpressionandalternativesplicingoffishspecies AT wenwenwang fishexpacomprehensivedatabaseandanalysisplatformforgeneexpressionandalternativesplicingoffishspecies AT wencaijie fishexpacomprehensivedatabaseandanalysisplatformforgeneexpressionandalternativesplicingoffishspecies AT jindingliu fishexpacomprehensivedatabaseandanalysisplatformforgeneexpressionandalternativesplicingoffishspecies |