STATISTICS


1. Transcriptome

The transcript sources of Danio rerio are ensembl, LncRBase V.2, ZFLNC.

  • According to the over.chain files downloaded from UCSC, we transformed genome versions of transcriptome obtained from LncRBase and ZFLNC into GRCz11, and then merge them by gffcompare to obtain final transcriptome of Danio rerio.
  • The histogram below shows the distribution of coding / non-coding / unknow / misc genes in chromosomes. Only chromosomes with more than 1000 genes are shown.
  • The gene types of Danio rerio are mainly coding and non-coding.

2. LncRNA type


LncRNA type information was obtained from GTF files from three sources.

  • The bar chart above shows the distribution of each lncRNA type in chromosomes. Only chromosomes with more than 750 lncRNAs are shown.

  • The pie chart on the left shows the proportion of each lncRNA type.

  • The most proportion lncRNA types on each chromosome are inter gene.

3. Function

The number of genes with GO / KEGG annotation on each chromosome is shown in the figure above. (Only chromosomes with more than 100 annotated information are shown.)

In terms of functional annotations, the GO annotation of Danio rerio are briefly displayed here.

Details of GO and other annotations are available on each gene's / RNA's details page.

The figure on the left shows GO ID that has been annotated at least 600 times.

4. Bioproject (PRJEB12982)

The bioroject from SRA is used for expression profile construction and annotation.

  • We downloaded a high resolution Danio rerio embryo development bioproject (White, R. J.) for analysis.
  • PRJEB12982 covers 18 stages of Danio rerio embryonic development.
  • This bioproject is the largest baseline in FishGET. The sample number is up to 360.

Bioroject details can be easily browsed by a folded tree on the expression page .