Previously, I identified several genes with GO terms associated with an adaptive immune response. A writeup to each of these is described in the link, but here’s the suspects:
- Q92956 (TNR14_HUMAN): Tumor necrosis factor receptor, interacts with CD160
- O95971 (BY55_HUMAN): CD160 antigen. Likely plays role in both anti-viral innate immune response along with adaptive immune response
- P60033 (CD81_HUMAN): CD81 antigen. Whole bunch of roles, inc. structural component, enables receptor complex assembly upon encounter with pathogens, and more.
- NOTE: P35762 (CD81_MOUSE) was also present in the crab transcriptome.
Alright, so we’ve got genes linked to adaptive immunity! This raises two key questions.
- Are these genes actually related to adaptive immunity?
- Are these genes correctly identified?
- Are these genes at a significant expression level?
1 and 2 are the big ones - the presence alone of adaptive immune-related genes would be a neat little finding. But 3 is also important to this system specifically. Let’s go through each.
Are the genes related to adaptive immunity?
TNR14_HUMAN: Did some searching, looks like there are a few papers describing it as potentially having a role in innate immune response (I think, wow it’s a tough read), such as this. Plus it also has the GO term associated with innate immune response.
- Conclusion: NOT definitively adaptive-response
BY55_HUMAN: That same paper also examined CD160, and found that it is also linked to innate immune response. Plus a few others - it’s pretty well-established. Plus again, also has the GO term associated with innate immune response.
- Conclusion: NOT definitively adaptive-response
CD81_HUMAN: No clear demonstrations I could find of its involvement in innate immune response. However, it also has [about a billion other roles]https://www.uniprot.org/uniprot/P60033), including protein stability regulation, receptor internalization, protein localization, and a bunch more.
- Conclusion: NOT definitively adaptive-response
Alright, well that’s a bummer. For the sake of completeness and because it’s quick, let’s look at whether the genes were correctly IDed. Here’s the e-values of each transcript matching a gene described above (plus CD81_MOUSE).
Are the genes correctly identified?
| Transcript_ID | Gene_ID | e-value |
|---|---|---|
| TRINITY_DN277121_c0_g1_i2 | TNR14_HUMAN | 1.2e-171 |
| TRINITY_DN277121_c0_g1_i1 | TNR14_HUMAN | 2.3e-103 |
| TRINITY_DN472921_c0_g1_i1 | BY55_HUMAN | 1.5e-18 |
| TRINITY_DN633565_c0_g1_i1 | CD81_HUMAN | 1.5e-65 |
| TRINITY_DN39038_c3_g1_i2 | CD81_MOUSE | 2.6e-131 |
| TRINITY_DN39038_c3_g1_i1 | CD81_MOUSE | 1.7e-130 |
The BY55_HUMAN e-value looks a liiitle bit questionable, but all others are pretty dang solid. I’d feel confident in saying that genes were, in fact, IDed correctly
Alright, we just won’t worry about Question 3 at this point - in light of Question 2, it’s probably irrelevant. Ah well, onto the next thing!