Investigating In A Gene/Protein ?

Question

[Giselle]

Hi there,

my name is Giselle and I am and microbiology undergrad student. Please forgive my english, i am from Italy.

I wanted to ask : How would you investigate in a gene/protein on the computer ? I know the experimental site, how to do that. But i want to get as much information I can get before starting with my experiments.

The Gene is called FADA1 in Corynebacterium jeikeium.

[Larry_Parnell]

Although a basic question, it is excellent because it is exactly how scientific investigation should begin - with a computational search for all that is known about the gene of interest.

Answer 1

[Neilfws]

Hi Giselle,

If you want to ask "what is known about this gene?", you need to start with a good genome database. Here are a couple of useful resources.

First, the Integrated Microbial Genomes resource from the JGI. You can search this site in many ways. I would suggest choosing "gene search" from the menu, enter "FADA1", select the option "Gene symbol" and then select Corynebacterium jeikeium from the list of organisms. This should take you to a page of summary information for that gene. It will show you how the gene has been annotated with things like putative function, pathways and protein domains.

IMG is a very powerful resource which can take some time to learn, but it is worth the effort; it is one of the best sources of annotation for microbial genes.

You can also try the NCBI website. Here, you can choose to search "all databases" with the gene symbol and/or organism name. You should find the genome project information for this organism and a summary gene page for FADA1. You can also download gene, protein and genome sequences from this site.

I hope this helps you to get started.

Answer 2

[Larry_Parnell]

The NCBI link that Neil provides will also give you links to the PubMed papers that contain your gene within the title, abstract, etc. Those articles will help to provide knowledge on the biological function(s) of FADA1.

You should also try to gather info on FADA1 from related species. Often, we learn a lot by looking at data from related organisms, especially when the relevant experiments have not or cannot be done in the organism of interest (often is so in human).

I would search for this gene at KEGG to learn in which pathways it functions. That may also give you information about substrate and product. Try EcoCyc if there is a homolog or ortholog in E. coli. This may offer more or complementary info to KEGG.

I'd also use a common internet search tool like Yahoo or Google to see what other pages outside of well known biomedical research websites are available. For example, there are many websites that are maintained by single labs and these have a focus on a small set of genes or a gene family. Look for something similar.

Lastly, I would offer that you should search for gene expression data to learn what conditions alter or not the expression of FADA1, either in your organism or in similar ones. One place to start with this is GEO at NCBI.

Answer 3

[Mary]

Another thing I would do in general when looking for information on a gene would be to see if there is a community of researchers for that organism, and see if they have a database. Often the organism-specific databases contain deep knowledge on genes from that species. But they don't all have a community database.

In this case I don't see one for this organism. But I would look at something like this to see if there was one:

http://www.ebi.ac.uk/2can/genomes/bacteria/Corynebacterium_jeikeium.html

And check the Genomes Online Database (GOLD) to see if there was a project around that species. http://www.genomesonline.org/

And today I'm trying the brand new BioProject search--have no idea what I'm going to find: http://www.ncbi.nlm.nih.gov/bioproject

[Larry_Parnell]

+1! As this is what I was (trying) to get at with the suggestion of searching the internet. This is a good idea for the gene, gene family or the organism.

Answer 4

[Darked89]

You may also try:

http://theseed.uchicago.edu/FIG/index.cgi

Just put FADA1 in this part of the page:

Searching for Genes or Functional Roles Using Text Search Pattern: FADA1

and you will get FADA1 in 6 species. You can investigate further from there.

Answer 5

[Georg Summer]

Try Uniprot. You can search for FADA1 and will get all proteins that have FADA1 somewhere in their description/info. Typically most of the hits will be from different organisms but you can limit the search to a specific organism by FADA1 and organism:"Corynebacterium jeikeium".

Although not the case for FADA1 you might find reviewed Proteins at the beginning of the search results (reviewed = stared proteins). These entries replace/combine the unreviewed entries (given that there are more than one protein entry for the same protein).

At the end of each protein description in uniprot you can find a often large area that links to different databases (from gene db to protein modeling) and a change log for the entry. This change log can be useful to explain why a protein has suddenly a different name.