The miRNA Enrichment Analysis and Annotation Tool (miEAA) is a service provided by the Chair for Clinical Bioinformatics at Saarland University. Basically, miEAA is a multi-species microRNA enrichment analysis tool. For more information, see their website or published paper.
Before Performing enrichment analysis on a miRNA set, note that based on your input miRNA type (either all mature or precursor, not a mixture of both!) and the species, there will be different sets of supported enrichment categories.
Thus, it is recommended to retrieve a list of possible enrichment categories that you may use:
## A list of available enrichment categories for: ## mature human miRNA: rba_mieaa_cats(mirna_type = "mature", species = 9606) ## precursor human miRNA rba_mieaa_cats(mirna_type = "precursor", species = 9606) ## precursor zebrafish miRNA rba_mieaa_cats(mirna_type = "mature", species = "Danio rerio")
There are two approaches to do this, we will start with the simpler one.
Just fill the arguments of
to the function’s manual; As you can see in the function’s arguments,
you have a lot of controls over your enrichment request, but you need to
## 1 We create a variable with our miRNAs' mature IDs <- c("hsa-miR-20b-5p", "hsa-miR-144-5p", "hsa-miR-17-5p", "hsa-miR-20a-5p", mirs "hsa-miR-222-3p", "hsa-miR-106a-5p", "hsa-miR-93-5p", "hsa-miR-126-3p", "hsa-miR-363-3p", "hsa-miR-302c-3p", "hsa-miR-374b-5p", "hsa-miR-18a-5p", "hsa-miR-548d-3p", "hsa-miR-135a-3p", "hsa-miR-558", "hsa-miR-130b-5p", "hsa-miR-148a-3p") ## 2a We can perform enrichment analysis on our miRNA set without limiting the analysis to any categories <- rba_mieaa_enrich(test_set = mirs, mieaa_all mirna_type = "mature", test_type = "ORA", species = 9606) #> -- Step 1/3: Submitting Enrichment request: #> No categories were supplied, Requesting enrichment using all of the 28 available categories for species 'Homo sapiens'. #> Submitting ORA enrichment request for 17 miRNA IDs of species Homo sapiens to miEAA servers. #> #> -- Step 2/3: Checking for Submitted enrichment job's status every 5 seconds. #> Your submitted job ID is: 96b5dcb3-7416-45da-8934-0cc40067c54d #> .... #> #> -- Step 3/3: Retrieving the results of the finished enrichment job. #> Retrieving results of submitted enrichment request with ID: 96b5dcb3-7416-45da-8934-0cc40067c54d ## 2b Or, We can limit the enrichment to certain datasets (enrichment categories) <- rba_mieaa_enrich(test_set = mirs, mieaa_kegg mirna_type = "mature", test_type = "ORA", species = 9606, categories = c("miRWalk_Diseases_mature", "miRWalk_Organs_mature") )#> -- Step 1/3: Submitting Enrichment request: #> Submitting ORA enrichment request for 17 miRNA IDs of species Homo sapiens to miEAA servers. #> #> -- Step 2/3: Checking for Submitted enrichment job's status every 5 seconds. #> Your submitted job ID is: ab0fb7b4-ddff-40ce-8b26-8f2bb2ee7233 #> . #> #> -- Step 3/3: Retrieving the results of the finished enrichment job. #> Retrieving results of submitted enrichment request with ID: ab0fb7b4-ddff-40ce-8b26-8f2bb2ee7233
As stated before,
rba_mieaa_enrich() is a wrapper
function, meaning that it executes the following sequence of
## 1 Submit enrichment request to miEAA <- rba_mieaa_enrich_submit(test_set = mirs, request mirna_type = "mature", test_type = "ORA", species = 9606, categories = c("miRWalk_Diseases_mature", "miRWalk_Organs_mature") )## 2 check for job's running status rba_mieaa_enrich_status(job_id = request$job_id) ## 3 If the job has completed, retrieve the results <- rba_mieaa_enrich_results(job_id = request$job_id)results
Please Note: Other services supported by rbioapi also provide Over-representation analysis tools. Please see the vignette article Do with rbioapi: Over-Representation (Enrichment) Analysis in R (link to the documentation site) for an in-depth review.
miEAA only recognizes miRBASE version 22 accessions. You can use
rba_mieaa_convert_version() to convert miRNA accession
between different miRBASE versions. Also, as stated before, miEAA
differentiate between precursor and mature miRNA accessions, to convert
between these 2 accession types, use
To cite miEAA (Please see https://ccb-compute2.cs.uni-saarland.de/mieaa2/):
To cite rbioapi: (Free access link to the article)
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