Help Needed with Finding Homologous Genes between Rat and Human for Dataset Integration

Question

[dxj294]

Hello Biostars Community,

I’m relatively new to the field of bioinformatics and am looking for some guidance on how to properly map homologous genes between rat and human. I have a background in Computer Science and am currently transitioning into bioinformatics.

Here’s my current situation:

I have two datasets:

Human Genes: 30,000 genes.
Rat Genes: 3,000 genes.

To perform my analysis, I need to have both the rat and human genes in a comparable format. My goal is to integrate these datasets by mapping the rat genes to their human homologs.

What I Have Tried So Far:

Using Ensembl BioMart:
    I uploaded the list of 3,000 rat genes to Ensembl BioMart.
    I was able to find homologous human genes for 2,800 of the rat genes.
    However, I found that about 100 of the human gene columns were empty.

My Questions:

1. Is my approach correct? Given that I found homologs for most but not all rat genes, is this expected or am I missing something?
2. How can I handle the unmapped genes? Are there alternative methods or tools I should use to find homologs for the remaining rat genes?
3. Are there better strategies or tools for ensuring that I can get as complete a mapping as possible between rat and human genes?

I would appreciate any advice or suggestions, especially from those who have worked on integrating gene datasets across different species. Your insights will be incredibly valuable to me as I navigate through this.

Thank you in advance for your help!