1. Transcriptome

The transcriptome of Oncorhynchus mykiss is from the FishGET assembly pipeline and genome gtf file.

  • The histogram 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 Oncorhynchus mykiss are mainly coding and non-coding.

2. LncRNA type

LncRNA type identification was performed by self-written Python scripts.

  • The bar chart above shows the distribution of each lncRNA type in chromosomes. Only chromosomes with more than 3400 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 Oncorhynchus mykiss 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 200 times.

4. Distribution of bioprojects / samples by experiment type

The data of Oncorhynchus mykiss contains 24 bioprojects (400 samples) from SRA.

  • 18 bioprojects were found corresponding 23 articles.
  • 22 bioprojects (379 samples) were used for transcript assembly, expression profile construction and annotation.
  • 2 bioprojects were only used for article information storage. Click the charts below to trigger the dynamic effect.
  • All bioprojects were manually organized and divided into 7 experiment types to help users conduct comparative analysis.
  • The bioprojects mainly focuses on the baseline, challenge and chemical.

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