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-4645-3p 1.000 301.000 0.763
hsa-miR-196b-5p 1.000 302.000 0.763
hsa-miR-1205 1.000 303.000 0.762
hsa-miR-4802-5p 1.000 304.000 0.762
hsa-miR-337-3p 1.000 305.000 0.760
hsa-miR-9986 1.000 306.000 0.760
hsa-miR-4445-5p 1.000 307.000 0.757
hsa-miR-148b-5p 1.000 308.000 0.757
hsa-miR-2682-5p 1.000 309.000 0.756
hsa-miR-3605-3p 1.000 310.000 0.754
hsa-miR-493-5p 1.000 311.000 0.753
hsa-miR-1236-3p 1.000 312.000 0.753
hsa-miR-4646-3p 1.000 313.000 0.753
hsa-miR-6774-3p 1.000 314.000 0.753
hsa-miR-6811-3p 1.000 315.000 0.753
hsa-miR-9851-5p 1.000 316.000 0.753
hsa-miR-758-3p 1.000 317.000 0.752
hsa-miR-371a-3p 1.000 318.000 0.752
hsa-miR-299-5p 1.000 319.000 0.752
hsa-miR-4738-5p 1.000 320.000 0.751
hsa-miR-4464 1.000 321.000 0.751
hsa-miR-433-5p 1.000 322.000 0.751
hsa-miR-148b-3p 1.000 323.000 0.751
hsa-miR-4742-3p 1.000 324.000 0.750
hsa-miR-557 1.000 325.000 0.750
hsa-miR-6808-3p 1.000 326.000 0.749
hsa-miR-3680-5p 1.000 327.000 0.748
hsa-miR-203a-5p 1.000 328.000 0.747
hsa-miR-887-5p 1.000 329.000 0.746
hsa-miR-3974 1.000 330.000 0.746
hsa-miR-378a-5p 1.000 331.000 0.746
hsa-miR-4714-3p 1.000 332.000 0.746
hsa-miR-1244 1.000 333.000 0.745
hsa-miR-452-5p 1.000 334.000 0.744
hsa-miR-4477b 1.000 335.000 0.742
hsa-miR-329-5p 1.000 336.000 0.742
hsa-miR-3921 1.000 337.000 0.742
hsa-miR-6790-5p 1.000 338.000 0.742
hsa-miR-5580-5p 1.000 339.000 0.741
hsa-miR-511-5p 1.000 340.000 0.741
hsa-miR-623 1.000 341.000 0.741
hsa-miR-6073 1.000 342.000 0.741
hsa-miR-370-5p 1.000 343.000 0.740
hsa-miR-4460 1.000 344.000 0.740
hsa-miR-4679 1.000 345.000 0.739
hsa-miR-4682 1.000 346.000 0.739
hsa-miR-33a-3p 1.000 347.000 0.739
hsa-miR-425-5p 1.000 348.000 0.739
hsa-miR-135a-5p 1.000 349.000 0.738
hsa-miR-758-5p 1.000 350.000 0.738
hsa-miR-3149 1.000 351.000 0.738
hsa-miR-196a-5p 1.000 352.000 0.737
hsa-miR-3682-5p 1.000 353.000 0.737
hsa-miR-6514-3p 1.000 354.000 0.737
hsa-miR-6827-3p 1.000 355.000 0.737
hsa-miR-6852-3p 1.000 356.000 0.737
hsa-miR-639 1.000 357.000 0.737
hsa-miR-6502-5p 1.000 358.000 0.736
hsa-miR-4329 1.000 359.000 0.734
hsa-miR-4680-3p 1.000 360.000 0.734
hsa-miR-513c-5p 1.000 361.000 0.733
hsa-miR-139-3p 1.000 362.000 0.733
hsa-miR-202-5p 1.000 363.000 0.731
hsa-miR-4277 1.000 364.000 0.731
hsa-miR-4278 1.000 365.000 0.730
hsa-miR-627-3p 1.000 366.000 0.730
hsa-miR-876-5p 1.000 367.000 0.730
hsa-miR-5047 1.000 368.000 0.730
hsa-miR-7151-5p 1.000 369.000 0.729
hsa-miR-302a-3p 1.000 370.000 0.729
hsa-miR-6813-5p 1.000 371.000 0.728
hsa-miR-3123 1.000 372.000 0.728
hsa-miR-3617-3p 1.000 373.000 0.728
hsa-miR-4796-5p 1.000 374.000 0.728
hsa-miR-6866-3p 1.000 375.000 0.728
hsa-miR-6873-3p 1.000 376.000 0.728
hsa-miR-6080 1.000 377.000 0.721
hsa-miR-7156-5p 1.000 378.000 0.721
hsa-miR-103a-1-5p 1.000 379.000 0.721
hsa-miR-140-5p 1.000 380.000 0.718
hsa-miR-3150a-3p 1.000 381.000 0.718
hsa-miR-5002-5p 1.000 382.000 0.718
hsa-miR-208b-3p 1.000 383.000 0.717
hsa-miR-33a-5p 1.000 384.000 0.716
hsa-miR-5705 1.000 385.000 0.715
hsa-miR-29b-3p 1.000 386.000 0.715
hsa-miR-4743-3p 1.000 387.000 0.714
hsa-miR-6764-3p 1.000 388.000 0.713
hsa-miR-1279 1.000 389.000 0.713
hsa-miR-4639-3p 1.000 390.000 0.713
hsa-miR-4641 1.000 391.000 0.713
hsa-miR-664b-3p 1.000 392.000 0.713
hsa-miR-6885-3p 1.000 393.000 0.713
hsa-miR-592 1.000 394.000 0.713
hsa-miR-764 1.000 395.000 0.712
hsa-miR-499b-5p 1.000 396.000 0.712
hsa-miR-29b-2-5p 1.000 397.000 0.712
hsa-miR-7976 1.000 398.000 0.712
hsa-miR-4446-5p 1.000 399.000 0.711
hsa-miR-545-3p 1.000 400.000 0.710
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