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-562 1.000 401.000 0.710
hsa-miR-6764-5p 1.000 402.000 0.710
hsa-let-7c-3p 1.000 403.000 0.710
hsa-miR-6742-3p 1.000 404.000 0.709
hsa-miR-1184 1.000 405.000 0.709
hsa-miR-1256 1.000 406.000 0.709
hsa-miR-890 1.000 407.000 0.709
hsa-miR-4712-5p 1.000 408.000 0.709
hsa-miR-548ak 1.000 409.000 0.708
hsa-miR-5590-3p 1.000 410.000 0.708
hsa-miR-548l 1.000 411.000 0.707
hsa-miR-6839-3p 1.000 412.000 0.707
hsa-miR-4782-3p 1.000 413.000 0.707
hsa-miR-548bc 1.000 414.000 0.707
hsa-miR-8058 1.000 415.000 0.705
hsa-miR-4528 1.000 416.000 0.705
hsa-miR-4664-3p 1.000 417.000 0.705
hsa-miR-6847-3p 1.000 418.000 0.705
hsa-miR-643 1.000 419.000 0.705
hsa-miR-4456 1.000 420.000 0.705
hsa-miR-221-3p 1.000 421.000 0.705
hsa-miR-3689b-3p 1.000 422.000 0.704
hsa-miR-3689c 1.000 423.000 0.704
hsa-miR-4474-3p 1.000 424.000 0.703
hsa-miR-4317 1.000 425.000 0.703
hsa-miR-4287 1.000 426.000 0.703
hsa-miR-548t-5p 1.000 427.000 0.703
hsa-miR-3652 1.000 428.000 0.700
hsa-let-7e-3p 1.000 429.000 0.700
hsa-miR-5006-3p 1.000 430.000 0.700
hsa-miR-6781-3p 1.000 431.000 0.700
hsa-miR-6878-3p 1.000 432.000 0.700
hsa-miR-95-5p 1.000 433.000 0.699
hsa-miR-5007-5p 1.000 434.000 0.699
hsa-miR-6516-5p 1.000 435.000 0.699
hsa-miR-34a-5p 1.000 436.000 0.698
hsa-miR-28-3p 1.000 437.000 0.698
hsa-miR-6818-5p 1.000 438.000 0.698
hsa-miR-1267 1.000 439.000 0.695
hsa-miR-613 1.000 440.000 0.695
hsa-miR-6852-5p 1.000 441.000 0.694
hsa-let-7f-2-3p 1.000 442.000 0.694
hsa-miR-23b-5p 1.000 443.000 0.694
hsa-miR-377-5p 1.000 444.000 0.693
hsa-miR-608 1.000 445.000 0.693
hsa-miR-2116-5p 1.000 446.000 0.693
hsa-miR-1185-5p 1.000 447.000 0.693
hsa-miR-545-5p 1.000 448.000 0.691
hsa-miR-6779-5p 1.000 449.000 0.691
hsa-miR-15b-5p 1.000 450.000 0.691
hsa-miR-7153-3p 1.000 451.000 0.691
hsa-miR-154-3p 1.000 452.000 0.690
hsa-miR-3908 1.000 453.000 0.689
hsa-miR-503-3p 1.000 454.000 0.687
hsa-miR-10395-3p 1.000 455.000 0.687
hsa-miR-8077 1.000 456.000 0.687
hsa-miR-6820-3p 1.000 457.000 0.687
hsa-miR-6846-3p 1.000 458.000 0.687
hsa-miR-5195-3p 1.000 459.000 0.686
hsa-miR-4697-3p 1.000 460.000 0.686
hsa-miR-1227-3p 1.000 461.000 0.686
hsa-miR-6767-3p 1.000 462.000 0.686
hsa-miR-1306-3p 1.000 463.000 0.684
hsa-miR-210-3p 1.000 464.000 0.684
hsa-miR-6078 1.000 465.000 0.684
hsa-miR-4453 1.000 466.000 0.684
hsa-miR-369-5p 1.000 467.000 0.683
hsa-miR-6737-3p 1.000 468.000 0.683
hsa-miR-6758-3p 1.000 469.000 0.683
hsa-miR-924 1.000 470.000 0.681
hsa-miR-548g-3p 1.000 471.000 0.681
hsa-miR-3143 1.000 472.000 0.681
hsa-miR-26a-1-3p 1.000 473.000 0.680
hsa-miR-944 1.000 474.000 0.679
hsa-miR-302c-3p 1.000 475.000 0.679
hsa-miR-323a-5p 1.000 476.000 0.679
hsa-miR-514b-3p 1.000 477.000 0.679
hsa-miR-96-5p 1.000 478.000 0.678
hsa-miR-218-5p 1.000 479.000 0.678
hsa-miR-4780 1.000 480.000 0.677
hsa-miR-181d-5p 1.000 481.000 0.675
hsa-miR-33b-5p 1.000 482.000 0.673
hsa-miR-522-3p 1.000 483.000 0.673
hsa-miR-520a-3p 1.000 484.000 0.672
hsa-miR-34b-5p 1.000 485.000 0.672
hsa-miR-6796-5p 1.000 486.000 0.671
hsa-miR-7-5p 1.000 487.000 0.671
hsa-miR-101-5p 1.000 488.000 0.671
hsa-miR-3174 1.000 489.000 0.670
hsa-miR-628-5p 1.000 490.000 0.669
hsa-miR-652-3p 1.000 491.000 0.669
hsa-miR-374a-3p 1.000 492.000 0.667
hsa-miR-4760-3p 1.000 493.000 0.666
hsa-miR-1208 1.000 494.000 0.665
hsa-miR-301b-3p 1.000 495.000 0.665
hsa-miR-550a-3p 1.000 496.000 0.664
hsa-miR-519e-3p 1.000 497.000 0.662
hsa-miR-548aq-5p 1.000 498.000 0.662
hsa-miR-12130 1.000 499.000 0.662
hsa-miR-1206 1.000 500.000 0.661
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