Freiburg RNA Tools
BrainDead - Results
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BrainDead 4526878

Input and runtime details for job 4526878 (precomputed example)

Training data

? Class-annotated RNAs in FASTA[.fa]

Model parameters

? k-mers of interest
AA,AGA,AGGU,AGU,AGUU,CU,GAA,GAGG,GG,GGG,GU,GUU,UGA,UGU,UU,UUG,UUGU,UUU
? k-mer features reflect
number of occurrences (feature is number >= 0)
? Max. energy ranked stable-3
? Machine learning model
Support Vector Classification using RBF kernel

Candidate data

? Candidate RNAs in FASTA[.fa]

Job ID 4526878 (server version trunk)

?Job Submitted & Queued@ Wed Feb 10 15:00:26 CET 2021
?BrainDead Started@ Wed Feb 10 15:16:53 CET 2021
?BrainDead Finished & Post-Processing@ Wed Feb 10 15:16:53 CET 2021
?Post-Processing Finished@ Wed Feb 10 15:17:07 CET 2021
?Job Completed@ Wed Feb 10 15:17:11 CET 2021
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4526878&toolName=BrainDead ( 30 days expiry )

Description of the job

miRNAs as ligands for microglia activation

This example summarizes our study that investigates the ability of mature miRNAs to act as immune receptor ligands. The ability of extracellular miRNAs to directly activate receptors is a recently discovered new field of operation of miRNAs beside their classic role in post-transcriptional gene regulation. The small RNAs available within the example's training data were experimentally tested for their potential to activate murine microglia cells in vitro. They are pre-classified as +/-1 when found activating or non-activating, resp., using fold change analyses based TNF-alpha concentration measurements. The example's training data set comprises both the original training data (top group) as well as the experimentally verified candidate sequences (middle and bottom group) from our initial BrainDead main publication (see list of references within Help page). For details on the selected k-mers, please refer to the manuscript. The candidate set covers all mature human miRNAs from mirBase v22.1.

? Output download complete results [zip]

Downloads

Predictions for candidate RNAs

Predicted class

Sort by selecting a column name.
RNA id class rank prob(1)
hsa-miR-500b-3p -1.000 2301.000 0.098
hsa-miR-6071 -1.000 2302.000 0.098
hsa-miR-509-5p -1.000 2303.000 0.098
hsa-miR-135a-2-3p -1.000 2304.000 0.098
hsa-miR-4739 -1.000 2305.000 0.098
hsa-miR-1908-5p -1.000 2306.000 0.097
hsa-miR-3117-5p -1.000 2307.000 0.097
hsa-miR-3125 -1.000 2308.000 0.097
hsa-miR-9903 -1.000 2309.000 0.097
hsa-miR-7155-3p -1.000 2310.000 0.097
hsa-miR-518f-3p -1.000 2311.000 0.096
hsa-miR-526a-3p -1.000 2312.000 0.096
hsa-miR-516a-5p -1.000 2313.000 0.096
hsa-miR-6783-5p -1.000 2314.000 0.096
hsa-miR-5585-3p -1.000 2315.000 0.096
hsa-miR-4681 -1.000 2316.000 0.096
hsa-miR-6529-5p -1.000 2317.000 0.096
hsa-miR-214-3p -1.000 2318.000 0.095
hsa-miR-1-3p -1.000 2319.000 0.095
hsa-miR-510-3p -1.000 2320.000 0.094
hsa-miR-4795-5p -1.000 2321.000 0.094
hsa-miR-196a-3p -1.000 2322.000 0.094
hsa-miR-3161 -1.000 2323.000 0.094
hsa-miR-6814-5p -1.000 2324.000 0.094
hsa-miR-4476 -1.000 2325.000 0.094
hsa-miR-124-3p -1.000 2326.000 0.094
hsa-miR-181b-3p -1.000 2327.000 0.094
hsa-miR-181b-2-3p -1.000 2328.000 0.094
hsa-miR-6796-3p -1.000 2329.000 0.094
hsa-miR-4465 -1.000 2330.000 0.094
hsa-miR-6797-5p -1.000 2331.000 0.094
hsa-miR-4496 -1.000 2332.000 0.093
hsa-miR-92b-5p -1.000 2333.000 0.093
hsa-miR-4433a-3p -1.000 2334.000 0.093
hsa-miR-4433b-3p -1.000 2335.000 0.093
hsa-miR-451b -1.000 2336.000 0.093
hsa-miR-520b-3p -1.000 2337.000 0.093
hsa-miR-520c-3p -1.000 2338.000 0.093
hsa-miR-6509-5p -1.000 2339.000 0.093
hsa-miR-7158-3p -1.000 2340.000 0.093
hsa-miR-1268a -1.000 2341.000 0.093
hsa-miR-4517 -1.000 2342.000 0.093
hsa-miR-105-5p -1.000 2343.000 0.093
hsa-miR-1276 -1.000 2344.000 0.093
hsa-miR-1273c -1.000 2345.000 0.093
hsa-miR-5091 -1.000 2346.000 0.093
hsa-miR-7154-5p -1.000 2347.000 0.092
hsa-miR-133a-5p -1.000 2348.000 0.092
hsa-miR-5703 -1.000 2349.000 0.092
hsa-miR-4659a-5p -1.000 2350.000 0.092
hsa-miR-3141 -1.000 2351.000 0.092
hsa-miR-330-3p -1.000 2352.000 0.091
hsa-miR-6750-5p -1.000 2353.000 0.091
hsa-miR-4742-5p -1.000 2354.000 0.091
hsa-miR-4270 -1.000 2355.000 0.090
hsa-miR-487b-3p -1.000 2356.000 0.090
hsa-miR-6773-5p -1.000 2357.000 0.090
hsa-miR-488-5p -1.000 2358.000 0.090
hsa-miR-606 -1.000 2359.000 0.089
hsa-miR-4693-3p -1.000 2360.000 0.089
hsa-miR-3163 -1.000 2361.000 0.089
hsa-miR-3150a-5p -1.000 2362.000 0.088
hsa-miR-6793-3p -1.000 2363.000 0.088
hsa-miR-8071 -1.000 2364.000 0.088
hsa-miR-4529-5p -1.000 2365.000 0.088
hsa-miR-3529-3p -1.000 2366.000 0.088
hsa-miR-4723-5p -1.000 2367.000 0.088
hsa-miR-517-5p -1.000 2368.000 0.088
hsa-miR-3683 -1.000 2369.000 0.088
hsa-miR-595 -1.000 2370.000 0.087
hsa-miR-4661-3p -1.000 2371.000 0.087
hsa-miR-4683 -1.000 2372.000 0.087
hsa-miR-3166 -1.000 2373.000 0.086
hsa-miR-4671-5p -1.000 2374.000 0.086
hsa-miR-4777-3p -1.000 2375.000 0.086
hsa-miR-1910-3p -1.000 2376.000 0.086
hsa-miR-4725-3p -1.000 2377.000 0.086
hsa-miR-6850-5p -1.000 2378.000 0.086
hsa-miR-6499-5p -1.000 2379.000 0.085
hsa-miR-3191-3p -1.000 2380.000 0.085
hsa-miR-455-3p -1.000 2381.000 0.085
hsa-miR-3202 -1.000 2382.000 0.085
hsa-miR-2355-5p -1.000 2383.000 0.085
hsa-miR-4711-5p -1.000 2384.000 0.085
hsa-miR-892c-5p -1.000 2385.000 0.085
hsa-miR-12128 -1.000 2386.000 0.085
hsa-miR-4800-5p -1.000 2387.000 0.085
hsa-miR-9902 -1.000 2388.000 0.084
hsa-miR-6887-5p -1.000 2389.000 0.084
hsa-miR-6889-5p -1.000 2390.000 0.084
hsa-miR-10523-5p -1.000 2391.000 0.084
hsa-miR-502-3p -1.000 2392.000 0.083
hsa-miR-146b-5p -1.000 2393.000 0.083
hsa-miR-4782-5p -1.000 2394.000 0.083
hsa-miR-6812-5p -1.000 2395.000 0.083
hsa-miR-5580-3p -1.000 2396.000 0.083
hsa-miR-1291 -1.000 2397.000 0.083
hsa-miR-335-5p -1.000 2398.000 0.083
hsa-miR-495-3p -1.000 2399.000 0.083
hsa-miR-605-5p -1.000 2400.000 0.083
Rows: 1-100 101-200 201-300 301-400 401-500 501-600 601-700 701-800 801-900 901-1000 1001-1100 1101-1200 1201-1300 1301-1400 1401-1500 1501-1600 1601-1700 1701-1800 1801-1900 1901-2000 2001-2100 2101-2200 2201-2300 2301-2400 2401-2500 2501-2600 2601-2656 all

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When using BrainDead please cite :

Results are computed with BrainDead version 1.0.1 using IntaRNA 3.1.5 and Vienna RNA package 2.4.14