FishGET is an evolutionarily-supported database of species covering two whole genome duplication (WGD) events. We committed to collect and organize a large number of pair-end data of ray-finned fish for unified analysis, which will lead to more complete reference transcriptome, and provided gene / RNA expression profile in different experiment type and tissues during the entire development. The figure on the right shows the overview of the data analysis process.
Cite: Cheng Guo, You Duan, Weidong Ye et al. FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization. iScience. 10.1016/j.isci.2023.106539.
Chart
Chart with 23 data points.
End of interactive chart.
RELATED SPECIES
FishGET covers 8 species, which are classified into model, economic, ornamental and ornamental fish according to several article introduction.
DATA SOURCE
We downloaded 97 bioprojects from SRA and GSA, of which 93 were used for analysis and 4 used for article information storage only.
EXPERIMENT TYPE
We manually classified 97 bioprojects according to experiment types (eg: baseline: 32 bioprojects). And we organized the relevant information of 79 articles.
TRANSCRIPTOME
About 55% gene / RNA come from the genome GTF file, and about 45% non-coding gene / lncRNA come from the FishGET assembly pipeline.
EXPRESSION PROFILE
93 bioprojects cover 1317 samples. Users can perform cross-bioproject visualizations for comparative analysis.
ANNOTATION
Including co-expression network, NR / KEGG / GO, neighboring location, lncRNA type identification and homologous annotation.
DISTRIBUTION OF BIOPROJECTS
The phylogenetic relationships among the ray-finned fishes in FishGET are shown in the figure below left. This 8 fishes span two different whole genome duplication events found in teleost fish. Including teleost-specific WGD event (the first red star) and salmonid-specific WGD event (the second red star).
The distribution of bioprojects in FishGET is shown in the following figure on the right. The number of bioprojects and samples of each species are shown in the stacked bar figure, and the experiment types covered by each species are shown in the pie figure.
Chart
Combination chart with 11 data series.
The chart has 1 X axis displaying categories.
The chart has 1 Y axis displaying values. Range: 0 to 450.