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-6873-5p -1.000 2524.000 0.062
hsa-miR-6874-3p 1.000 38.000 0.925
hsa-miR-6874-5p -1.000 2614.000 0.045
hsa-miR-6875-3p -1.000 1769.000 0.196
hsa-miR-6875-5p -1.000 1922.000 0.170
hsa-miR-6876-3p 1.000 132.000 0.853
hsa-miR-6876-5p -1.000 1115.000 0.398
hsa-miR-6877-3p 1.000 772.000 0.539
hsa-miR-6877-5p -1.000 2638.000 0.033
hsa-miR-6878-3p 1.000 432.000 0.700
hsa-miR-6878-5p -1.000 2520.000 0.062
hsa-miR-6879-3p 1.000 666.000 0.596
hsa-miR-6879-5p -1.000 2556.000 0.059
hsa-miR-6880-3p -1.000 1068.000 0.419
hsa-miR-6880-5p -1.000 2620.000 0.043
hsa-miR-6881-3p 1.000 576.000 0.643
hsa-miR-6881-5p -1.000 2480.000 0.070
hsa-miR-6882-3p 1.000 808.000 0.523
hsa-miR-6882-5p -1.000 2530.000 0.061
hsa-miR-6883-3p -1.000 1069.000 0.419
hsa-miR-6883-5p -1.000 2054.000 0.145
hsa-miR-6884-3p 1.000 577.000 0.643
hsa-miR-6884-5p -1.000 883.000 0.489
hsa-miR-6885-3p 1.000 393.000 0.713
hsa-miR-6885-5p -1.000 2209.000 0.113
hsa-miR-6886-3p -1.000 1070.000 0.419
hsa-miR-6886-5p -1.000 931.000 0.463
hsa-miR-6887-3p 1.000 510.000 0.661
hsa-miR-6887-5p -1.000 2389.000 0.084
hsa-miR-6888-3p 1.000 7.000 0.948
hsa-miR-6888-5p -1.000 2425.000 0.077
hsa-miR-6889-3p 1.000 793.000 0.531
hsa-miR-6889-5p -1.000 2390.000 0.084
hsa-miR-6890-3p -1.000 1430.000 0.289
hsa-miR-6890-5p -1.000 2518.000 0.063
hsa-miR-6891-3p 1.000 511.000 0.661
hsa-miR-6891-5p -1.000 1944.000 0.167
hsa-miR-6892-3p -1.000 949.000 0.452
hsa-miR-6892-5p -1.000 2476.000 0.071
hsa-miR-6893-3p -1.000 1071.000 0.419
hsa-miR-6893-5p -1.000 1570.000 0.249
hsa-miR-6894-3p 1.000 809.000 0.523
hsa-miR-6894-5p -1.000 2141.000 0.129
hsa-miR-6895-3p 1.000 682.000 0.584
hsa-miR-6895-5p -1.000 2565.000 0.058
hsa-miR-7-1-3p -1.000 2483.000 0.070
hsa-miR-7-2-3p -1.000 1952.000 0.166
hsa-miR-7-5p 1.000 487.000 0.671
hsa-miR-708-3p -1.000 1290.000 0.336
hsa-miR-708-5p -1.000 2011.000 0.153
hsa-miR-7106-3p -1.000 1813.000 0.189
hsa-miR-7106-5p -1.000 1721.000 0.212
hsa-miR-7107-3p 1.000 269.000 0.777
hsa-miR-7107-5p -1.000 2294.000 0.099
hsa-miR-7108-3p -1.000 1629.000 0.235
hsa-miR-7108-5p -1.000 1283.000 0.338
hsa-miR-7109-3p -1.000 1590.000 0.247
hsa-miR-7109-5p -1.000 1951.000 0.167
hsa-miR-711 -1.000 2553.000 0.059
hsa-miR-7110-3p -1.000 1072.000 0.419
hsa-miR-7110-5p -1.000 2608.000 0.047
hsa-miR-7111-3p -1.000 1073.000 0.419
hsa-miR-7111-5p -1.000 2416.000 0.080
hsa-miR-7112-3p 1.000 758.000 0.549
hsa-miR-7112-5p -1.000 1976.000 0.163
hsa-miR-7113-3p -1.000 1431.000 0.289
hsa-miR-7113-5p -1.000 1304.000 0.332
hsa-miR-7114-3p 1.000 717.000 0.568
hsa-miR-7114-5p -1.000 1683.000 0.223
hsa-miR-7150 -1.000 2247.000 0.108
hsa-miR-7151-3p -1.000 2220.000 0.111
hsa-miR-7151-5p 1.000 369.000 0.729
hsa-miR-7152-3p -1.000 2002.000 0.156
hsa-miR-7152-5p -1.000 1088.000 0.413
hsa-miR-7153-3p 1.000 451.000 0.691
hsa-miR-7153-5p -1.000 2256.000 0.106
hsa-miR-7154-3p 1.000 580.000 0.640
hsa-miR-7154-5p -1.000 2347.000 0.092
hsa-miR-7155-3p -1.000 2310.000 0.097
hsa-miR-7155-5p -1.000 1526.000 0.266
hsa-miR-7156-3p -1.000 2498.000 0.067
hsa-miR-7156-5p 1.000 378.000 0.721
hsa-miR-7157-3p -1.000 2160.000 0.124
hsa-miR-7157-5p -1.000 1578.000 0.248
hsa-miR-7158-3p -1.000 2340.000 0.093
hsa-miR-7158-5p -1.000 1937.000 0.169
hsa-miR-7159-3p 1.000 268.000 0.778
hsa-miR-7159-5p -1.000 2112.000 0.134
hsa-miR-7160-3p -1.000 1840.000 0.185
hsa-miR-7160-5p 1.000 579.000 0.642
hsa-miR-7161-3p -1.000 905.000 0.476
hsa-miR-7161-5p -1.000 1844.000 0.184
hsa-miR-7162-3p -1.000 1962.000 0.165
hsa-miR-7162-5p 1.000 512.000 0.661
hsa-miR-718 -1.000 1598.000 0.244
hsa-miR-744-3p 1.000 138.000 0.848
hsa-miR-744-5p -1.000 2201.000 0.115
hsa-miR-7515 -1.000 2634.000 0.036
hsa-miR-758-3p 1.000 317.000 0.752
hsa-miR-758-5p 1.000 350.000 0.738
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