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-6510-3p 1.000 701.000 0.572
hsa-miR-6746-3p 1.000 702.000 0.572
hsa-miR-6849-3p 1.000 703.000 0.572
hsa-miR-6500-3p 1.000 704.000 0.572
hsa-miR-125a-5p 1.000 705.000 0.571
hsa-miR-3182 1.000 706.000 0.570
hsa-miR-3667-3p 1.000 707.000 0.570
hsa-miR-513b-5p 1.000 708.000 0.569
hsa-miR-1322 1.000 709.000 0.568
hsa-miR-3151-3p 1.000 710.000 0.568
hsa-miR-3192-3p 1.000 711.000 0.568
hsa-miR-4728-3p 1.000 712.000 0.568
hsa-miR-4750-3p 1.000 713.000 0.568
hsa-miR-4758-3p 1.000 714.000 0.568
hsa-miR-6730-3p 1.000 715.000 0.568
hsa-miR-6821-3p 1.000 716.000 0.568
hsa-miR-7114-3p 1.000 717.000 0.568
hsa-miR-4704-5p 1.000 718.000 0.568
hsa-miR-519e-5p 1.000 719.000 0.567
hsa-miR-3912-5p 1.000 720.000 0.566
hsa-miR-4495 1.000 721.000 0.566
hsa-miR-3713 1.000 722.000 0.565
hsa-miR-5696 1.000 723.000 0.564
hsa-miR-4701-5p 1.000 724.000 0.564
hsa-miR-889-3p 1.000 725.000 0.561
hsa-miR-642b-5p 1.000 726.000 0.560
hsa-miR-518c-3p 1.000 727.000 0.560
hsa-miR-3165 1.000 728.000 0.560
hsa-miR-6507-3p 1.000 729.000 0.559
hsa-miR-194-3p 1.000 730.000 0.559
hsa-miR-3160-5p 1.000 731.000 0.559
hsa-miR-609 1.000 732.000 0.557
hsa-miR-769-3p 1.000 733.000 0.556
hsa-miR-4522 1.000 734.000 0.556
hsa-miR-629-3p 1.000 735.000 0.556
hsa-miR-6791-3p 1.000 736.000 0.556
hsa-miR-6824-3p 1.000 737.000 0.556
hsa-miR-4533 1.000 738.000 0.556
hsa-miR-635 1.000 739.000 0.554
hsa-miR-3664-3p 1.000 740.000 0.554
hsa-miR-614 1.000 741.000 0.554
hsa-miR-29c-3p 1.000 742.000 0.554
hsa-miR-431-5p 1.000 743.000 0.554
hsa-let-7g-3p 1.000 744.000 0.554
hsa-miR-521 1.000 745.000 0.554
hsa-miR-6824-5p 1.000 746.000 0.553
hsa-miR-7703 1.000 747.000 0.553
hsa-miR-6772-5p 1.000 748.000 0.553
hsa-miR-5590-5p 1.000 749.000 0.553
hsa-miR-448 1.000 750.000 0.553
hsa-miR-191-3p 1.000 751.000 0.553
hsa-miR-7702 1.000 752.000 0.552
hsa-miR-329-3p 1.000 753.000 0.552
hsa-miR-655-3p 1.000 754.000 0.552
hsa-miR-6770-3p 1.000 755.000 0.551
hsa-miR-6130 1.000 756.000 0.551
hsa-miR-3689f 1.000 757.000 0.549
hsa-miR-7112-3p 1.000 758.000 0.549
hsa-miR-199a-5p 1.000 759.000 0.549
hsa-miR-2115-5p 1.000 760.000 0.548
hsa-miR-4764-3p 1.000 761.000 0.548
hsa-miR-10527-5p 1.000 762.000 0.547
hsa-miR-3689d 1.000 763.000 0.547
hsa-miR-4483 1.000 764.000 0.546
hsa-miR-6853-3p 1.000 765.000 0.546
hsa-miR-6740-5p 1.000 766.000 0.543
hsa-miR-92a-1-5p 1.000 767.000 0.542
hsa-miR-93-5p 1.000 768.000 0.542
hsa-miR-514a-3p 1.000 769.000 0.540
hsa-miR-6857-3p 1.000 770.000 0.540
hsa-miR-12131 1.000 771.000 0.540
hsa-miR-6877-3p 1.000 772.000 0.539
hsa-miR-1292-3p 1.000 773.000 0.538
hsa-miR-383-5p 1.000 774.000 0.537
hsa-miR-8062 1.000 775.000 0.536
hsa-miR-6133 1.000 776.000 0.536
hsa-miR-4685-5p 1.000 777.000 0.536
hsa-miR-1911-5p 1.000 778.000 0.535
hsa-miR-3681-5p 1.000 779.000 0.535
hsa-miR-4666b 1.000 780.000 0.534
hsa-miR-3129-5p 1.000 781.000 0.534
hsa-miR-218-2-3p 1.000 782.000 0.533
hsa-miR-7852-3p 1.000 783.000 0.533
hsa-miR-506-5p 1.000 784.000 0.532
hsa-miR-1915-5p 1.000 785.000 0.532
hsa-miR-3188 1.000 786.000 0.531
hsa-miR-501-5p 1.000 787.000 0.531
hsa-miR-1238-3p 1.000 788.000 0.531
hsa-miR-4297 1.000 789.000 0.531
hsa-miR-4667-3p 1.000 790.000 0.531
hsa-miR-6760-3p 1.000 791.000 0.531
hsa-miR-6773-3p 1.000 792.000 0.531
hsa-miR-6889-3p 1.000 793.000 0.531
hsa-miR-9898 1.000 794.000 0.531
hsa-miR-552-3p 1.000 795.000 0.530
hsa-miR-4736 1.000 796.000 0.530
hsa-miR-6749-5p 1.000 797.000 0.529
hsa-miR-23c 1.000 798.000 0.528
hsa-miR-585-3p 1.000 799.000 0.527
hsa-miR-5008-3p 1.000 800.000 0.527
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