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-4524a-5p -1.000 1666.000 0.228
hsa-miR-4524b-3p -1.000 1188.000 0.374
hsa-miR-4524b-5p -1.000 1490.000 0.273
hsa-miR-4525 1.000 515.000 0.659
hsa-miR-4526 -1.000 1481.000 0.276
hsa-miR-4527 -1.000 1963.000 0.165
hsa-miR-4528 1.000 416.000 0.705
hsa-miR-4529-3p 1.000 651.000 0.605
hsa-miR-4529-5p -1.000 2365.000 0.088
hsa-miR-4530 -1.000 1857.000 0.182
hsa-miR-4531 -1.000 2431.000 0.075
hsa-miR-4533 1.000 738.000 0.556
hsa-miR-4534 -1.000 1948.000 0.167
hsa-miR-4535 -1.000 2238.000 0.109
hsa-miR-4536-3p -1.000 2042.000 0.148
hsa-miR-4536-5p -1.000 2405.000 0.082
hsa-miR-4537 -1.000 1397.000 0.290
hsa-miR-4538 -1.000 1124.000 0.394
hsa-miR-4539 -1.000 1985.000 0.160
hsa-miR-454-3p -1.000 2437.000 0.074
hsa-miR-454-5p 1.000 569.000 0.645
hsa-miR-4540 1.000 92.000 0.871
hsa-miR-455-3p -1.000 2381.000 0.085
hsa-miR-455-5p 1.000 249.000 0.787
hsa-miR-4632-3p -1.000 1412.000 0.289
hsa-miR-4632-5p -1.000 2053.000 0.145
hsa-miR-4633-3p -1.000 1890.000 0.175
hsa-miR-4633-5p -1.000 1889.000 0.175
hsa-miR-4634 -1.000 2133.000 0.131
hsa-miR-4635 -1.000 2118.000 0.133
hsa-miR-4636 1.000 245.000 0.788
hsa-miR-4637 -1.000 2205.000 0.115
hsa-miR-4638-3p -1.000 1883.000 0.176
hsa-miR-4638-5p -1.000 2453.000 0.073
hsa-miR-4639-3p 1.000 390.000 0.713
hsa-miR-4639-5p -1.000 1184.000 0.376
hsa-miR-4640-3p 1.000 140.000 0.843
hsa-miR-4640-5p -1.000 1728.000 0.209
hsa-miR-4641 1.000 391.000 0.713
hsa-miR-4642 -1.000 1732.000 0.208
hsa-miR-4643 -1.000 1454.000 0.283
hsa-miR-4644 -1.000 2600.000 0.050
hsa-miR-4645-3p 1.000 301.000 0.763
hsa-miR-4645-5p -1.000 1205.000 0.365
hsa-miR-4646-3p 1.000 313.000 0.753
hsa-miR-4646-5p -1.000 2199.000 0.115
hsa-miR-4647 -1.000 1943.000 0.167
hsa-miR-4648 -1.000 1867.000 0.181
hsa-miR-4649-3p -1.000 942.000 0.456
hsa-miR-4649-5p -1.000 1900.000 0.174
hsa-miR-4650-3p -1.000 2123.000 0.132
hsa-miR-4650-5p 1.000 522.000 0.657
hsa-miR-4651 -1.000 1627.000 0.235
hsa-miR-4652-3p 1.000 225.000 0.800
hsa-miR-4652-5p -1.000 2157.000 0.125
hsa-miR-4653-3p 1.000 811.000 0.522
hsa-miR-4653-5p -1.000 1230.000 0.357
hsa-miR-4654 -1.000 1316.000 0.322
hsa-miR-4655-3p -1.000 1480.000 0.276
hsa-miR-4655-5p -1.000 2204.000 0.115
hsa-miR-4656 -1.000 958.000 0.448
hsa-miR-4657 -1.000 2024.000 0.150
hsa-miR-4658 -1.000 1896.000 0.174
hsa-miR-4659a-3p -1.000 1314.000 0.324
hsa-miR-4659a-5p -1.000 2350.000 0.092
hsa-miR-4659b-3p -1.000 890.000 0.487
hsa-miR-4659b-5p -1.000 1243.000 0.352
hsa-miR-466 -1.000 2280.000 0.103
hsa-miR-4660 -1.000 2533.000 0.061
hsa-miR-4661-3p -1.000 2371.000 0.087
hsa-miR-4661-5p -1.000 953.000 0.450
hsa-miR-4662a-3p -1.000 2125.000 0.132
hsa-miR-4662a-5p 1.000 155.000 0.836
hsa-miR-4662b -1.000 2126.000 0.132
hsa-miR-4663 -1.000 1724.000 0.211
hsa-miR-4664-3p 1.000 417.000 0.705
hsa-miR-4664-5p 1.000 542.000 0.650
hsa-miR-4665-3p -1.000 1972.000 0.163
hsa-miR-4665-5p -1.000 1471.000 0.279
hsa-miR-4666a-3p 1.000 271.000 0.776
hsa-miR-4666a-5p 1.000 680.000 0.584
hsa-miR-4666b 1.000 780.000 0.534
hsa-miR-4667-3p 1.000 790.000 0.531
hsa-miR-4667-5p -1.000 2505.000 0.066
hsa-miR-4668-3p 1.000 183.000 0.821
hsa-miR-4668-5p -1.000 1099.000 0.405
hsa-miR-4669 -1.000 2162.000 0.124
hsa-miR-4670-3p -1.000 1260.000 0.345
hsa-miR-4670-5p -1.000 938.000 0.458
hsa-miR-4671-3p -1.000 1258.000 0.347
hsa-miR-4671-5p -1.000 2374.000 0.086
hsa-miR-4672 -1.000 1828.000 0.187
hsa-miR-4673 -1.000 1864.000 0.182
hsa-miR-4674 -1.000 1752.000 0.200
hsa-miR-4675 -1.000 1596.000 0.245
hsa-miR-4676-3p 1.000 141.000 0.843
hsa-miR-4676-5p -1.000 1877.000 0.176
hsa-miR-4677-3p -1.000 2189.000 0.117
hsa-miR-4677-5p 1.000 196.000 0.814
hsa-miR-4678 1.000 144.000 0.841
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