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-194-5p -1.000 1854.000 0.184
hsa-miR-195-3p -1.000 1150.000 0.385
hsa-miR-195-5p -1.000 1993.000 0.158
hsa-miR-196a-1-3p -1.000 1793.000 0.191
hsa-miR-196a-3p -1.000 2322.000 0.094
hsa-miR-196a-5p 1.000 352.000 0.737
hsa-miR-196b-3p -1.000 1048.000 0.419
hsa-miR-196b-5p 1.000 302.000 0.763
hsa-miR-197-3p -1.000 1047.000 0.419
hsa-miR-197-5p -1.000 2539.000 0.060
hsa-miR-1972 -1.000 2114.000 0.134
hsa-miR-1973 -1.000 1923.000 0.170
hsa-miR-1976 1.000 665.000 0.596
hsa-miR-198 -1.000 1994.000 0.158
hsa-miR-199a-3p 1.000 628.000 0.615
hsa-miR-199a-5p 1.000 759.000 0.549
hsa-miR-199b-3p 1.000 629.000 0.615
hsa-miR-199b-5p 1.000 222.000 0.801
hsa-miR-19a-3p -1.000 1167.000 0.380
hsa-miR-19a-5p 1.000 134.000 0.851
hsa-miR-19b-1-5p 1.000 46.000 0.907
hsa-miR-19b-2-5p 1.000 45.000 0.911
hsa-miR-19b-3p -1.000 1168.000 0.380
hsa-miR-200a-3p -1.000 1636.000 0.234
hsa-miR-200a-5p -1.000 2095.000 0.138
hsa-miR-200b-3p -1.000 1905.000 0.173
hsa-miR-200b-5p -1.000 1916.000 0.171
hsa-miR-200c-3p -1.000 2134.000 0.130
hsa-miR-200c-5p 1.000 76.000 0.883
hsa-miR-202-3p -1.000 2516.000 0.064
hsa-miR-202-5p 1.000 363.000 0.731
hsa-miR-203a-3p 1.000 529.000 0.653
hsa-miR-203a-5p 1.000 328.000 0.747
hsa-miR-203b-3p -1.000 1000.000 0.433
hsa-miR-203b-5p -1.000 884.000 0.489
hsa-miR-204-3p -1.000 2637.000 0.033
hsa-miR-204-5p 1.000 177.000 0.821
hsa-miR-205-3p -1.000 1007.000 0.431
hsa-miR-205-5p -1.000 1201.000 0.368
hsa-miR-2052 1.000 203.000 0.811
hsa-miR-2053 1.000 50.000 0.902
hsa-miR-2054 1.000 612.000 0.624
hsa-miR-206 -1.000 2069.000 0.142
hsa-miR-208a-3p -1.000 925.000 0.465
hsa-miR-208a-5p 1.000 520.000 0.657
hsa-miR-208b-3p 1.000 383.000 0.717
hsa-miR-208b-5p 1.000 625.000 0.618
hsa-miR-20a-3p -1.000 1796.000 0.191
hsa-miR-20a-5p -1.000 2027.000 0.150
hsa-miR-20b-3p -1.000 923.000 0.466
hsa-miR-20b-5p -1.000 2023.000 0.151
hsa-miR-21-3p -1.000 1814.000 0.189
hsa-miR-21-5p 1.000 100.000 0.868
hsa-miR-210-3p 1.000 464.000 0.684
hsa-miR-210-5p -1.000 1400.000 0.289
hsa-miR-211-3p -1.000 2586.000 0.054
hsa-miR-211-5p 1.000 178.000 0.821
hsa-miR-2110 -1.000 2446.000 0.073
hsa-miR-2113 1.000 227.000 0.798
hsa-miR-2114-3p -1.000 1758.000 0.199
hsa-miR-2114-5p -1.000 997.000 0.434
hsa-miR-2115-3p -1.000 2566.000 0.057
hsa-miR-2115-5p 1.000 760.000 0.548
hsa-miR-2116-3p -1.000 2570.000 0.057
hsa-miR-2116-5p 1.000 446.000 0.693
hsa-miR-2117 1.000 214.000 0.804
hsa-miR-212-3p -1.000 1971.000 0.163
hsa-miR-212-5p -1.000 1090.000 0.410
hsa-miR-214-3p -1.000 2318.000 0.095
hsa-miR-214-5p 1.000 617.000 0.623
hsa-miR-215-3p -1.000 880.000 0.492
hsa-miR-215-5p -1.000 1967.000 0.163
hsa-miR-216a-3p -1.000 2455.000 0.072
hsa-miR-216a-5p -1.000 951.000 0.450
hsa-miR-216b-3p -1.000 1281.000 0.338
hsa-miR-216b-5p -1.000 952.000 0.450
hsa-miR-217-3p 1.000 541.000 0.650
hsa-miR-217-5p -1.000 1959.000 0.165
hsa-miR-218-1-3p -1.000 1559.000 0.251
hsa-miR-218-2-3p 1.000 782.000 0.533
hsa-miR-218-5p 1.000 479.000 0.678
hsa-miR-219a-1-3p 1.000 226.000 0.798
hsa-miR-219a-2-3p -1.000 1702.000 0.217
hsa-miR-219a-5p 1.000 230.000 0.796
hsa-miR-219b-3p -1.000 1240.000 0.353
hsa-miR-219b-5p -1.000 1132.000 0.391
hsa-miR-22-3p -1.000 947.000 0.453
hsa-miR-22-5p 1.000 672.000 0.590
hsa-miR-221-3p 1.000 421.000 0.705
hsa-miR-221-5p -1.000 1348.000 0.312
hsa-miR-222-3p -1.000 2235.000 0.109
hsa-miR-222-5p -1.000 1177.000 0.377
hsa-miR-223-3p 1.000 68.000 0.889
hsa-miR-223-5p 1.000 86.000 0.875
hsa-miR-224-3p -1.000 2202.000 0.115
hsa-miR-224-5p -1.000 969.000 0.446
hsa-miR-2276-3p -1.000 2070.000 0.142
hsa-miR-2276-5p -1.000 851.000 0.500
hsa-miR-2277-3p 1.000 590.000 0.635
hsa-miR-2277-5p -1.000 1678.000 0.225
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