Question: compare expression between the same gene in different organisms?
0
gravatar for luckilyduck
11 months ago by
luckilyduck0 wrote:

I'm an undergrad taking a genomics course where I'm doing a mini research project on a gene (APOE). For one of my hypothesis, I would like to compare the expression of APOE between different organisms and see what the differences are and if it is significant. Eventually I want to also compare the folding as well and see what the differences in the transport functions are. I'm lacking in the genetics and genomics subject (and really regretting taking this course) so I'm a bit unsure of how to execute this and obtain this data?

My thoughts were to possibly obtain the cDNA (humans) and run a BLAST (blastx?) against the other organisms and compare the values from there? I'm not really sure though if this is correct and what values would be significant for what I'm looking for (query?).

If anyone knows anything about this, please give some guidance! Anything at all will help, even literature recommendations on something similar to what I am doing would be tremendous help!

ADD COMMENTlink modified 11 months ago by Dattatray Mongad340 • written 11 months ago by luckilyduck0
2

One tip - " ask questions!! ". I strongly suggest to talk to your supervisor and understand the project. Ask questions, ask often, ask questions that you think are "stupid" (asking stupid questions is a wise man's approach). Ask until the picture is clear, set small goals at first, break the task, seek help but explore on your own.

ADD REPLYlink modified 11 months ago • written 11 months ago by lakhujanivijay4.5k

I would like to compare the expression of APOE between different organisms and see what the differences are and if it is significant.

Apologies in advance if this following advice is going to sound pessimistic but you are proposing fairly difficult projects.

If you do find expression data for APOE comparing it across organisms is like comparing orange to apples. You could do it but I am not sure if the results would tell you anything useful.

Eventually I want to also compare the folding as well and see what the differences in the transport functions are.

How are you planning to do this? Protein folding is not the easiest of the topics and how it may affect transport would be even more challenging.

My thoughts were to possibly obtain the cDNA (humans) and run a BLAST (blastx?) against the other organisms and compare the values from there?

Are you thinking about finding possible changes in amino acids (rather than actual expression) to see how the gene may have evolved over time in different organism? This aspect may be doable.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax74k

This is an option of an approach I wanted to take however I really have no idea how to approach it. I also thought it may have been more difficult, but taking your advice into consideration I'll definitely see if I can try that instead if it is more doable. I went on UniProt and did a sequence alignment to compare active sites. Would this data be relevant?

Thank you so much for your response!

ADD REPLYlink written 11 months ago by luckilyduck0

For one of my hypothesis, I would like to compare the expression of APOE between different organisms

What's the hypothesis, then? :-)

ADD REPLYlink written 11 months ago by WouterDeCoster42k
1
gravatar for Dattatray Mongad
11 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad340 wrote:

In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or proteome data. Top of that, the expression values changes with respect to condition of organism (disease Vs normal). It is impossible to get expression level of particular gene in all other organisms (because of lack of data).

However, still if you want to do, you have to dig up literature and data for that. which is extremely difficult.

For folding purpose, you can do molecular modelling and simulations, if the strucure of APOE is available on PDB for different organisms.

Final remarks: your rationale is very vague, can you clearly communicate what exactly you aim is?

ADD COMMENTlink written 11 months ago by Dattatray Mongad340
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1298 users visited in the last hour