The miRNA Enrichment Analysis and Annotation Tool (miEAA) is a multi-species microRNA enrichment-analysis service provided by the Chair for Clinical Bioinformatics at Saarland University. For more information, see the miEAA website or its latest publication.
Before performing enrichment analysis on a miRNA set, note that the supported enrichment categories depend on both the miRNA type (mature or precursor, without mixing the two) and the species. See the miEAA integrated data sets for details.
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 = "precursor", species = "Danio rerio")There are two approaches to do this, we will start with the simpler one.
Supply the arguments of rba_mieaa_enrich() as described
in its manual. You must provide test_set,
mirna_type, test_type, and
species:
## 1 We create a variable with our miRNAs' mature IDs
mirs <- c(
"hsa-miR-20b-5p", "hsa-miR-144-5p", "hsa-miR-17-5p", "hsa-miR-20a-5p",
"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 Perform enrichment analysis without limiting it to selected categories
mieaa_all <- rba_mieaa_enrich(
test_set = mirs,
mirna_type = "mature",
test_type = "ORA",
species = 9606
)
#> -- Step 1/3: Submitting Enrichment analysis request:
#> No categories were supplied, Requesting enrichment using all of the 32 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 analysis's status every 5 seconds.
#> Your submitted job ID is: ae3fa2a0-0e69-4f91-920d-b29c174ac8cf
#> ....
#>
#> -- Step 3/3: Retrieving the results.
#> Retrieving results of submitted enrichment request with ID: ae3fa2a0-0e69-4f91-920d-b29c174ac8cf
## 2b Limit the enrichment to selected data sets (enrichment categories)
mieaa_kegg <- rba_mieaa_enrich(
test_set = mirs,
mirna_type = "mature",
test_type = "ORA",
species = 9606,
categories = "KEGG_mature"
)
#> -- Step 1/3: Submitting Enrichment analysis request:
#> Submitting ORA enrichment request for 17 miRNA IDs of species Homo sapiens to miEAA servers.
#>
#> -- Step 2/3: Checking for Submitted enrichment analysis's status every 5 seconds.
#> Your submitted job ID is: 772e1bd0-73d0-4496-bac3-af19ea36b56a
#> .
#>
#> -- Step 3/3: Retrieving the results.
#> Retrieving results of submitted enrichment request with ID: 772e1bd0-73d0-4496-bac3-af19ea36b56aAs stated before, rba_mieaa_enrich() is a wrapper
function, meaning that it executes the following sequence of
functions:
## 1 Submit enrichment request to miEAA
request <- rba_mieaa_enrich_submit(
test_set = mirs,
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$job_id)
## 3 If the job has completed, retrieve the results
results <- rba_mieaa_enrich_results(job_id = request$job_id)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 uses miRBase version 22 identifiers. Use
rba_mieaa_convert_version() to convert miRNA identifiers
between supported miRBase versions. miEAA also distinguishes mature and
precursor miRNA identifiers; use rba_mieaa_convert_type()
to convert between these identifier types.
To cite miEAA (see https://ccb-compute2.cs.uni-saarland.de/mieaa/):
To cite rbioapi:
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