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: https://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-10399-5p -1.000 901.000 0.479
hsa-miR-1258 -1.000 902.000 0.479
hsa-miR-550b-3p -1.000 903.000 0.479
hsa-miR-3668 -1.000 904.000 0.478
hsa-miR-7161-3p -1.000 905.000 0.476
hsa-miR-548aw -1.000 906.000 0.476
hsa-miR-507 -1.000 907.000 0.475
hsa-miR-4729 -1.000 908.000 0.475
hsa-miR-3169 -1.000 909.000 0.474
hsa-miR-1910-5p -1.000 910.000 0.474
hsa-miR-4310 -1.000 911.000 0.474
hsa-miR-18b-5p -1.000 912.000 0.472
hsa-miR-106b-3p -1.000 913.000 0.472
hsa-miR-6822-5p -1.000 914.000 0.471
hsa-miR-1304-5p -1.000 915.000 0.471
hsa-miR-5000-3p -1.000 916.000 0.471
hsa-miR-4700-5p -1.000 917.000 0.470
hsa-miR-4510 -1.000 918.000 0.469
hsa-miR-6500-5p -1.000 919.000 0.469
hsa-miR-320a-3p -1.000 920.000 0.467
hsa-miR-320b -1.000 921.000 0.467
hsa-miR-320c -1.000 922.000 0.467
hsa-miR-20b-3p -1.000 923.000 0.466
hsa-miR-802 -1.000 924.000 0.465
hsa-miR-208a-3p -1.000 925.000 0.465
hsa-miR-6774-5p -1.000 926.000 0.464
hsa-miR-30c-1-3p -1.000 927.000 0.464
hsa-miR-101-2-5p -1.000 928.000 0.463
hsa-miR-9901 -1.000 929.000 0.463
hsa-miR-4708-5p -1.000 930.000 0.463
hsa-miR-6886-5p -1.000 931.000 0.463
hsa-miR-1246 -1.000 932.000 0.463
hsa-miR-619-5p -1.000 933.000 0.463
hsa-miR-4710 -1.000 934.000 0.462
hsa-miR-363-3p -1.000 935.000 0.462
hsa-miR-2682-3p -1.000 936.000 0.460
hsa-miR-6784-5p -1.000 937.000 0.459
hsa-miR-4670-5p -1.000 938.000 0.458
hsa-miR-582-3p -1.000 939.000 0.458
hsa-miR-876-3p -1.000 940.000 0.458
hsa-miR-3074-5p -1.000 941.000 0.457
hsa-miR-4649-3p -1.000 942.000 0.456
hsa-miR-6855-5p -1.000 943.000 0.455
hsa-miR-548as-5p -1.000 944.000 0.455
hsa-miR-542-3p -1.000 945.000 0.454
hsa-miR-16-1-3p -1.000 946.000 0.453
hsa-miR-22-3p -1.000 947.000 0.453
hsa-miR-6841-3p -1.000 948.000 0.452
hsa-miR-6892-3p -1.000 949.000 0.452
hsa-miR-512-3p -1.000 950.000 0.451
hsa-miR-216a-5p -1.000 951.000 0.450
hsa-miR-216b-5p -1.000 952.000 0.450
hsa-miR-4661-5p -1.000 953.000 0.450
hsa-miR-372-5p -1.000 954.000 0.450
hsa-miR-660-3p -1.000 955.000 0.449
hsa-miR-1914-5p -1.000 956.000 0.449
hsa-miR-4330 -1.000 957.000 0.449
hsa-miR-4656 -1.000 958.000 0.448
hsa-miR-4467 -1.000 959.000 0.448
hsa-miR-5588-5p -1.000 960.000 0.448
hsa-miR-647 -1.000 961.000 0.448
hsa-miR-3191-5p -1.000 962.000 0.448
hsa-miR-7848-3p -1.000 963.000 0.448
hsa-miR-4684-5p -1.000 964.000 0.448
hsa-miR-23a-5p -1.000 965.000 0.448
hsa-miR-6735-3p -1.000 966.000 0.447
hsa-miR-3118 -1.000 967.000 0.447
hsa-miR-4282 -1.000 968.000 0.446
hsa-miR-224-5p -1.000 969.000 0.446
hsa-miR-5698 -1.000 970.000 0.446
hsa-miR-4326 -1.000 971.000 0.445
hsa-miR-6825-3p -1.000 972.000 0.444
hsa-miR-27b-3p -1.000 973.000 0.443
hsa-miR-497-3p -1.000 974.000 0.443
hsa-miR-3195 -1.000 975.000 0.443
hsa-miR-6827-5p -1.000 976.000 0.442
hsa-miR-155-5p -1.000 977.000 0.442
hsa-miR-15b-3p -1.000 978.000 0.442
hsa-miR-4524a-3p -1.000 979.000 0.440
hsa-miR-617 -1.000 980.000 0.439
hsa-miR-31-3p -1.000 981.000 0.437
hsa-miR-3064-3p -1.000 982.000 0.437
hsa-miR-548ay-3p -1.000 983.000 0.437
hsa-miR-6082 -1.000 984.000 0.436
hsa-miR-6762-5p -1.000 985.000 0.436
hsa-miR-6813-3p -1.000 986.000 0.436
hsa-miR-520g-5p -1.000 987.000 0.436
hsa-miR-3682-3p -1.000 988.000 0.436
hsa-miR-4713-5p -1.000 989.000 0.435
hsa-miR-4795-3p -1.000 990.000 0.435
hsa-miR-12116 -1.000 991.000 0.435
hsa-miR-8081 -1.000 992.000 0.435
hsa-miR-517a-3p -1.000 993.000 0.435
hsa-miR-517b-3p -1.000 994.000 0.435
hsa-miR-1271-5p -1.000 995.000 0.434
hsa-miR-3674 -1.000 996.000 0.434
hsa-miR-2114-5p -1.000 997.000 0.434
hsa-miR-519d-5p -1.000 998.000 0.434
hsa-miR-6847-5p -1.000 999.000 0.433
hsa-miR-203b-3p -1.000 1000.000 0.433
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