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-574-3p -1.000 1401.000 0.289
hsa-miR-1224-3p -1.000 1402.000 0.289
hsa-miR-766-3p -1.000 1403.000 0.289
hsa-miR-1228-3p -1.000 1404.000 0.289
hsa-miR-1229-3p -1.000 1405.000 0.289
hsa-miR-1260a -1.000 1406.000 0.289
hsa-miR-1281 -1.000 1407.000 0.289
hsa-miR-1913 -1.000 1408.000 0.289
hsa-miR-3162-3p -1.000 1409.000 0.289
hsa-miR-1260b -1.000 1410.000 0.289
hsa-miR-3620-3p -1.000 1411.000 0.289
hsa-miR-4632-3p -1.000 1412.000 0.289
hsa-miR-4722-3p -1.000 1413.000 0.289
hsa-miR-4749-3p -1.000 1414.000 0.289
hsa-miR-4763-5p -1.000 1415.000 0.289
hsa-miR-4769-3p -1.000 1416.000 0.289
hsa-miR-4787-3p -1.000 1417.000 0.289
hsa-miR-5011-5p -1.000 1418.000 0.289
hsa-miR-6727-3p -1.000 1419.000 0.289
hsa-miR-6728-3p -1.000 1420.000 0.289
hsa-miR-6729-3p -1.000 1421.000 0.289
hsa-miR-6736-3p -1.000 1422.000 0.289
hsa-miR-6752-3p -1.000 1423.000 0.289
hsa-miR-6761-3p -1.000 1424.000 0.289
hsa-miR-6769a-3p -1.000 1425.000 0.289
hsa-miR-6787-3p -1.000 1426.000 0.289
hsa-miR-6792-3p -1.000 1427.000 0.289
hsa-miR-6804-3p -1.000 1428.000 0.289
hsa-miR-6858-3p -1.000 1429.000 0.289
hsa-miR-6890-3p -1.000 1430.000 0.289
hsa-miR-7113-3p -1.000 1431.000 0.289
hsa-miR-6823-5p -1.000 1432.000 0.288
hsa-miR-450a-2-3p -1.000 1433.000 0.288
hsa-miR-548k -1.000 1434.000 0.288
hsa-miR-431-3p -1.000 1435.000 0.288
hsa-miR-6165 -1.000 1436.000 0.287
hsa-miR-6800-5p -1.000 1437.000 0.287
hsa-miR-373-5p -1.000 1438.000 0.287
hsa-miR-6815-5p -1.000 1439.000 0.287
hsa-miR-4696 -1.000 1440.000 0.286
hsa-miR-518b -1.000 1441.000 0.285
hsa-miR-6134 -1.000 1442.000 0.285
hsa-miR-4255 -1.000 1443.000 0.285
hsa-miR-29a-3p -1.000 1444.000 0.284
hsa-miR-4690-3p -1.000 1445.000 0.284
hsa-miR-3942-3p -1.000 1446.000 0.284
hsa-miR-4774-5p -1.000 1447.000 0.284
hsa-miR-605-3p -1.000 1448.000 0.284
hsa-miR-362-3p -1.000 1449.000 0.283
hsa-miR-382-3p -1.000 1450.000 0.283
hsa-miR-18b-3p -1.000 1451.000 0.283
hsa-miR-8053 -1.000 1452.000 0.283
hsa-miR-371b-5p -1.000 1453.000 0.283
hsa-miR-4643 -1.000 1454.000 0.283
hsa-miR-6831-3p -1.000 1455.000 0.283
hsa-miR-526a-5p -1.000 1456.000 0.283
hsa-miR-520c-5p -1.000 1457.000 0.283
hsa-miR-518d-5p -1.000 1458.000 0.283
hsa-miR-520d-5p -1.000 1459.000 0.282
hsa-miR-518a-5p -1.000 1460.000 0.282
hsa-miR-527 -1.000 1461.000 0.282
hsa-miR-6074 -1.000 1462.000 0.282
hsa-miR-573 -1.000 1463.000 0.282
hsa-miR-151a-3p -1.000 1464.000 0.282
hsa-miR-520g-3p -1.000 1465.000 0.282
hsa-miR-3187-3p -1.000 1466.000 0.281
hsa-miR-1470 -1.000 1467.000 0.281
hsa-miR-1271-3p -1.000 1468.000 0.280
hsa-miR-568 -1.000 1469.000 0.280
hsa-miR-6839-5p -1.000 1470.000 0.280
hsa-miR-4665-5p -1.000 1471.000 0.279
hsa-miR-6802-5p -1.000 1472.000 0.279
hsa-miR-6829-3p -1.000 1473.000 0.278
hsa-miR-6825-5p -1.000 1474.000 0.278
hsa-miR-129-5p -1.000 1475.000 0.278
hsa-miR-3194-3p -1.000 1476.000 0.277
hsa-miR-4264 -1.000 1477.000 0.277
hsa-miR-5704 -1.000 1478.000 0.277
hsa-miR-3685 -1.000 1479.000 0.276
hsa-miR-4655-3p -1.000 1480.000 0.276
hsa-miR-4526 -1.000 1481.000 0.276
hsa-miR-1199-5p -1.000 1482.000 0.276
hsa-miR-4523 -1.000 1483.000 0.276
hsa-miR-513c-3p -1.000 1484.000 0.274
hsa-miR-3663-3p -1.000 1485.000 0.274
hsa-miR-6794-5p -1.000 1486.000 0.273
hsa-miR-30c-5p -1.000 1487.000 0.273
hsa-miR-30b-5p -1.000 1488.000 0.273
hsa-miR-3678-5p -1.000 1489.000 0.273
hsa-miR-4524b-5p -1.000 1490.000 0.273
hsa-miR-6732-3p -1.000 1491.000 0.273
hsa-miR-6771-3p -1.000 1492.000 0.273
hsa-miR-6776-3p -1.000 1493.000 0.273
hsa-miR-6779-3p -1.000 1494.000 0.273
hsa-miR-6819-3p -1.000 1495.000 0.273
hsa-miR-4767 -1.000 1496.000 0.272
hsa-miR-5579-5p -1.000 1497.000 0.272
hsa-miR-4292 -1.000 1498.000 0.272
hsa-miR-3134 -1.000 1499.000 0.271
hsa-miR-1288-3p -1.000 1500.000 0.270
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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Feeds the job parameters to the input page to resubmit the job.

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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