Functional Annotation of Tomato Transcriptome

Question

[kevluv93]

I know this question has been asked and answered many times, but I'm having trouble with making a gene function annotation on a series of differentially expressed genes for my tomato transcriptomes (Solanum Lycopersicum).

Our genomics group sent to me a series of top differentially expressed genes in my tomato experiment, with each gene having an annotation from the sol genomics network. The gene IDs look like this:

Solyc11g020960
Solyc04g081710
Solyc07g043000

I just need to classify them by their general function. I already have their protein products annotated in my dataset, I need to see what function and pathways they belong to. Naturally I started using DAVID but it doesn't seem to recognize these Gene IDs regardless of what identifier I choose. Also DAVID hasn't been updated in the last 5 years, which is also concerning. Tomato plants are a very well annotated organism, but I can't seem to find any online gene function annotation tools which have their metabolic pathways.

Any advice on how to get these gene functions annotated in a user-friendly way? The end goal is to find out what pathways these genes belong to and what functions they control, and display these findings in a useful way where I can read them.

Thank you and have a great day!

Answer 1

[Gary]

You can try PANTHER (http://www.pantherdb.org/). It can identify Solanum Lycopersicum.

[kevluv93]

PANTHER is working pretty fantastically. I uploaded my gene IDs and it's giving me GO and charts representing functions. I'll see if I can extract this data and add it to my gene ID chart to make things better. I'll update as I go, right now PANTHER seems to be a great way to do GO.

[kevluv93]

I was successful in using PANTHER, thanks for the advice

[BioCh'ti]

Hi Kevluv, could you let me know what kind of identifiers you used for the tomato analysis? Moreover, did you noticed any consistency over the different analyses you conducted with Panther, Agrigo or Blast2Go? I mean, did you get almost the same BP, MF or CP significantly over represented?

[kevluv93]

I used the ITAG2.4 Loci IDs from the sol genomics database for my tomato transcriptome. (ex solyc12g011350). I ended up using blast2go, AgriGO, and Plant MetGenMap. I can't get PANTHER's statistical gene enrichment function to work for some reason, idk why. I used these three programs and the outputs were never the same. Blast2go reported no GO term enrichment, even after using the tomato database as the background. AgriGO reported enrichment, but very little and usually in one category like "molecular functions". So, according to AgriGO, I have no enrichment in other categories such as cellular components or biological processes. Plant MetGenMap seemed to produce the most hits for gene enrichment. I will note though, Plant MetGenMap did report every hit that AgriGO reported as enriched. I'm not quite sure what to trust, but I'm kind of leaning towards Plant MetGenMap.

Answer 2

[Antonio R. Franco]

The free version of Blast2Go can do what you want

It will run any type of Blast, and annotate your sequences with GO, EC enzyme number, InterPro domains, and KEGG patways

The free version will do, but the PRO version will allow you to do it faster and using more possibilities. You can use local databases, which can speed your searching

You have the chance to try the PRO version for some days for free

[kevluv93]

I'll definitely give it a try. I was iffy about blast2go because the pro version cost a lot of money. I'll be back with results. Any other programs that come to mind that could give me gene functions based on my gene IDs? I've been trying to convert my gene IDs to a more typical type of gene ID such as UniProt (because the tomato genes did get sent to other databases). But I'll let everyone know how blast2go basic went

[kevluv93]

Okay so I downloaded blast2go basic and immediately saw an issue: blast2go basic will not let you upload textfiles of gene IDs in the basic version. In order to upload a set of Gene IDs you have to select the "Load GeneSymbol Lists" function, but that's only available on the Blast2go pro version. I can get a free trial, but that'll take time.

Answer 3

[Mary]

Have a look at AgriGo: http://bioinfo.cau.edu.cn/agriGO/