Zebrafish Genome Literacy Workshop 2023

Exercise 5 - exploring data

First we will make a BED file. Using the InterPro website to find out, what are the accessions for the protein domains "Zinc finger, C2H2C-type" and "Zinc finger, PHD-finger"?

IPR002515 and IPR019787

Use BioMart to filter zebrafish genes for genes containing those domains. How many genes are there?

116 genes.

Export the following attributes for these genes - in order - as a TSV file. Make sure you click "Unique results only".

• Chromosome/scaffold name
• Gene start (bp)
• Gene end (bp)
• Gene name

Change the filename from "mart_export.txt" to e.g. "zinc-finger-genes.bed". Go to the zebrafish "Whole genome" view by clicking on "View karyotype" on the zebrafish home page. Use "Configure this page" to upload your BED file. Customise the display so as to show the features on the right side of the chromosomes, rather than the left. Try making another BED file using BioMart and display it on the same display.

Next let's imagine we are doing a positional cloning experiment. You have found a mutant that shows skeletal muscle defects and can't swim very well. You've mapped the genomic locus to chromosome 20, somewhere between 830,000 and 3,200,000 bp. Use BioMart to find the phenotypes associated with all genes in that interval. Can you find a candidate gene?

ENSDARG00000099390 (was named lama2, laminin alpha 2, in Ensembl 109 and earlier).

Next, let's try to find zebrafish orthologues of human genes. In BioMart, choose "Human genes (GRCh38.p13)" as your dataset. Filter genes by these "Gene stable ID(s)":

ENSG00000133424
ENSG00000181027
ENSG00000106692
ENSG00000009830
ENSG00000130714
ENSG00000173540
ENSG00000162885
ENSG00000085998
ENSG00000173120

In attributes, look for the section where you can choose the following attributes:

• Gene stable ID
• Gene name
• Zebrafish gene stable ID
• Zebrafish gene name
• Zebrafish homology type
• %id. target Zebrafish gene identical to query gene
• %id. query gene identical to target Zebrafish gene
• Zebrafish orthology confidence [0 low, 1 high]

How many of the genes have a one2one relationship and how many a one2many relationship?

8 have 1:1 and 1 has 1:many.

How many of the orthologues are high confidence and how many are low?

9 are high and 1 is low.

Can you find out which phenotype most of the human genes have in common?

Muscular dystrophy.

Now do the reverse. Pick five of your favourite zebrafish genes and find human orthologues for them.