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-2909 1.000 801.000 0.526
hsa-miR-512-5p 1.000 802.000 0.526
hsa-miR-125b-1-3p 1.000 803.000 0.525
hsa-miR-193b-5p 1.000 804.000 0.525
hsa-miR-4803 1.000 805.000 0.525
hsa-miR-4439 1.000 806.000 0.525
hsa-miR-6805-3p 1.000 807.000 0.523
hsa-miR-6882-3p 1.000 808.000 0.523
hsa-miR-6894-3p 1.000 809.000 0.523
hsa-miR-103a-2-5p 1.000 810.000 0.523
hsa-miR-4653-3p 1.000 811.000 0.522
hsa-miR-4276 1.000 812.000 0.522
hsa-miR-548e-3p 1.000 813.000 0.520
hsa-miR-5685 1.000 814.000 0.520
hsa-miR-1248 1.000 815.000 0.519
hsa-miR-3186-5p 1.000 816.000 0.519
hsa-miR-1843 1.000 817.000 0.518
hsa-miR-634 1.000 818.000 0.517
hsa-miR-3156-3p 1.000 819.000 0.517
hsa-miR-3672 1.000 820.000 0.514
hsa-miR-3147 1.000 821.000 0.513
hsa-miR-3660 1.000 822.000 0.513
hsa-miR-8055 1.000 823.000 0.513
hsa-miR-513b-3p 1.000 824.000 0.512
hsa-miR-4789-3p 1.000 825.000 0.511
hsa-miR-548h-3p 1.000 826.000 0.510
hsa-miR-548z 1.000 827.000 0.510
hsa-miR-3611 1.000 828.000 0.510
hsa-miR-3942-5p 1.000 829.000 0.509
hsa-miR-3664-5p 1.000 830.000 0.509
hsa-miR-4789-5p 1.000 831.000 0.507
hsa-miR-548e-5p 1.000 832.000 0.506
hsa-miR-519a-3p 1.000 833.000 0.506
hsa-miR-3923 1.000 834.000 0.505
hsa-miR-539-3p 1.000 835.000 0.505
hsa-miR-6822-3p 1.000 836.000 0.505
hsa-miR-6864-3p 1.000 837.000 0.505
hsa-miR-15a-3p -1.000 838.000 0.500
hsa-miR-98-3p -1.000 839.000 0.500
hsa-miR-339-5p -1.000 840.000 0.500
hsa-miR-92b-3p -1.000 841.000 0.500
hsa-miR-659-3p -1.000 842.000 0.500
hsa-miR-541-5p -1.000 843.000 0.500
hsa-miR-190b-3p 1.000 844.000 0.500
hsa-miR-873-5p -1.000 845.000 0.500
hsa-miR-937-3p -1.000 846.000 0.500
hsa-miR-1293 -1.000 847.000 0.500
hsa-miR-1250-3p -1.000 848.000 0.500
hsa-miR-548n 1.000 849.000 0.500
hsa-miR-1277-3p 1.000 850.000 0.500
hsa-miR-2276-5p -1.000 851.000 0.500
hsa-miR-548x-3p -1.000 852.000 0.500
hsa-miR-4258 -1.000 853.000 0.500
hsa-miR-4275 -1.000 854.000 0.500
hsa-miR-3606-3p -1.000 855.000 0.500
hsa-miR-3617-5p -1.000 856.000 0.500
hsa-miR-3657 -1.000 857.000 0.500
hsa-miR-548ad-3p -1.000 858.000 0.500
hsa-miR-548ae-3p -1.000 859.000 0.500
hsa-miR-548aj-3p -1.000 860.000 0.500
hsa-miR-4482-3p -1.000 861.000 0.500
hsa-miR-4699-3p -1.000 862.000 0.500
hsa-miR-4707-5p -1.000 863.000 0.500
hsa-miR-4776-3p -1.000 864.000 0.500
hsa-miR-5001-3p -1.000 865.000 0.500
hsa-miR-548ap-3p -1.000 866.000 0.500
hsa-miR-5190 -1.000 867.000 0.500
hsa-miR-5589-5p -1.000 868.000 0.500
hsa-miR-6509-3p -1.000 869.000 0.500
hsa-miR-6751-3p -1.000 870.000 0.500
hsa-miR-6793-5p -1.000 871.000 0.500
hsa-miR-6814-3p 1.000 872.000 0.500
hsa-miR-6815-3p 1.000 873.000 0.500
hsa-miR-6871-3p -1.000 874.000 0.500
hsa-miR-548ao-3p -1.000 875.000 0.495
hsa-miR-181b-5p -1.000 876.000 0.494
hsa-miR-6733-3p -1.000 877.000 0.494
hsa-miR-4472 -1.000 878.000 0.493
hsa-miR-4735-5p -1.000 879.000 0.493
hsa-miR-215-3p -1.000 880.000 0.492
hsa-miR-1238-5p -1.000 881.000 0.492
hsa-miR-30c-2-3p -1.000 882.000 0.490
hsa-miR-6884-5p -1.000 883.000 0.489
hsa-miR-203b-5p -1.000 884.000 0.489
hsa-miR-576-5p -1.000 885.000 0.488
hsa-miR-759 -1.000 886.000 0.488
hsa-miR-412-5p -1.000 887.000 0.488
hsa-miR-145-5p -1.000 888.000 0.488
hsa-miR-1587 -1.000 889.000 0.487
hsa-miR-4659b-3p -1.000 890.000 0.487
hsa-miR-3529-5p -1.000 891.000 0.487
hsa-miR-10399-3p -1.000 892.000 0.486
hsa-miR-570-3p -1.000 893.000 0.486
hsa-miR-6762-3p -1.000 894.000 0.485
hsa-miR-6848-3p -1.000 895.000 0.485
hsa-miR-548ao-5p -1.000 896.000 0.485
hsa-miR-4770 -1.000 897.000 0.484
hsa-miR-670-5p -1.000 898.000 0.483
hsa-miR-574-5p -1.000 899.000 0.481
hsa-miR-5088-3p -1.000 900.000 0.481
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