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-8056 1.000 601.000 0.628
hsa-miR-4443 1.000 602.000 0.627
hsa-miR-376c-5p 1.000 603.000 0.626
hsa-miR-487a-5p 1.000 604.000 0.626
hsa-miR-487b-5p 1.000 605.000 0.626
hsa-miR-6843-3p 1.000 606.000 0.626
hsa-miR-1250-5p 1.000 607.000 0.626
hsa-miR-8065 1.000 608.000 0.625
hsa-miR-4511 1.000 609.000 0.624
hsa-miR-432-3p 1.000 610.000 0.624
hsa-miR-548f-3p 1.000 611.000 0.624
hsa-miR-2054 1.000 612.000 0.624
hsa-miR-4764-5p 1.000 613.000 0.624
hsa-miR-3119 1.000 614.000 0.624
hsa-miR-3928-5p 1.000 615.000 0.624
hsa-miR-150-5p 1.000 616.000 0.623
hsa-miR-214-5p 1.000 617.000 0.623
hsa-miR-5000-5p 1.000 618.000 0.623
hsa-miR-518d-3p 1.000 619.000 0.622
hsa-miR-6854-5p 1.000 620.000 0.621
hsa-miR-888-3p 1.000 621.000 0.620
hsa-miR-548a-3p 1.000 622.000 0.619
hsa-miR-3115 1.000 623.000 0.619
hsa-miR-6834-5p 1.000 624.000 0.618
hsa-miR-208b-5p 1.000 625.000 0.618
hsa-miR-4707-3p 1.000 626.000 0.617
hsa-miR-532-5p 1.000 627.000 0.616
hsa-miR-199a-3p 1.000 628.000 0.615
hsa-miR-199b-3p 1.000 629.000 0.615
hsa-miR-548p 1.000 630.000 0.613
hsa-miR-4272 1.000 631.000 0.613
hsa-miR-126-5p 1.000 632.000 0.612
hsa-miR-1233-3p 1.000 633.000 0.612
hsa-miR-3622a-3p 1.000 634.000 0.612
hsa-miR-5708 1.000 635.000 0.612
hsa-miR-6859-3p 1.000 636.000 0.612
hsa-miR-4752 1.000 637.000 0.612
hsa-miR-4695-3p 1.000 638.000 0.611
hsa-miR-6797-3p 1.000 639.000 0.611
hsa-miR-6823-3p 1.000 640.000 0.611
hsa-let-7d-3p 1.000 641.000 0.611
hsa-miR-517c-3p 1.000 642.000 0.609
hsa-miR-409-3p 1.000 643.000 0.608
hsa-miR-8076 1.000 644.000 0.608
hsa-miR-4440 1.000 645.000 0.607
hsa-miR-302d-5p 1.000 646.000 0.607
hsa-miR-1284 1.000 647.000 0.607
hsa-miR-4755-5p 1.000 648.000 0.607
hsa-miR-29b-1-5p 1.000 649.000 0.606
hsa-miR-2681-5p 1.000 650.000 0.606
hsa-miR-4529-3p 1.000 651.000 0.605
hsa-miR-642a-5p 1.000 652.000 0.605
hsa-miR-32-3p 1.000 653.000 0.605
hsa-miR-4315 1.000 654.000 0.604
hsa-miR-100-3p 1.000 655.000 0.602
hsa-miR-4804-5p 1.000 656.000 0.601
hsa-miR-3192-5p 1.000 657.000 0.601
hsa-miR-1247-5p 1.000 658.000 0.600
hsa-miR-27a-5p 1.000 659.000 0.600
hsa-miR-365b-5p 1.000 660.000 0.599
hsa-miR-4457 1.000 661.000 0.598
hsa-miR-1269b 1.000 662.000 0.597
hsa-miR-6817-3p 1.000 663.000 0.597
hsa-miR-636 1.000 664.000 0.596
hsa-miR-1976 1.000 665.000 0.596
hsa-miR-6879-3p 1.000 666.000 0.596
hsa-miR-3145-3p 1.000 667.000 0.595
hsa-miR-4766-5p 1.000 668.000 0.594
hsa-miR-4425 1.000 669.000 0.594
hsa-miR-3972 1.000 670.000 0.593
hsa-miR-12114 1.000 671.000 0.591
hsa-miR-22-5p 1.000 672.000 0.590
hsa-miR-548s 1.000 673.000 0.590
hsa-miR-4756-3p 1.000 674.000 0.590
hsa-miR-553 1.000 675.000 0.589
hsa-miR-133a-3p 1.000 676.000 0.587
hsa-miR-133b 1.000 677.000 0.587
hsa-miR-5087 1.000 678.000 0.587
hsa-miR-4283 1.000 679.000 0.586
hsa-miR-4666a-5p 1.000 680.000 0.584
hsa-miR-377-3p 1.000 681.000 0.584
hsa-miR-6895-3p 1.000 682.000 0.584
hsa-miR-4259 1.000 683.000 0.583
hsa-miR-6754-5p 1.000 684.000 0.583
hsa-miR-146a-3p 1.000 685.000 0.583
hsa-miR-1180-3p 1.000 686.000 0.583
hsa-miR-3938 1.000 687.000 0.583
hsa-miR-8066 1.000 688.000 0.580
hsa-miR-5197-5p 1.000 689.000 0.580
hsa-miR-148a-5p 1.000 690.000 0.579
hsa-miR-4750-5p 1.000 691.000 0.579
hsa-miR-4720-5p 1.000 692.000 0.577
hsa-miR-644a 1.000 693.000 0.575
hsa-miR-433-3p 1.000 694.000 0.575
hsa-miR-519b-3p 1.000 695.000 0.574
hsa-miR-561-3p 1.000 696.000 0.574
hsa-miR-6871-5p 1.000 697.000 0.574
hsa-miR-367-3p 1.000 698.000 0.574
hsa-miR-578 1.000 699.000 0.573
hsa-miR-675-3p 1.000 700.000 0.572
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