Freiburg RNA Tools
BrainDead - Results
BIF
IFF
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-4324 -1.000 1601.000 0.242
hsa-miR-6855-3p -1.000 1602.000 0.242
hsa-miR-513a-5p -1.000 1603.000 0.241
hsa-miR-138-1-3p -1.000 1604.000 0.241
hsa-miR-5089-5p -1.000 1605.000 0.241
hsa-miR-6753-5p -1.000 1606.000 0.240
hsa-miR-379-3p -1.000 1607.000 0.240
hsa-miR-5011-3p -1.000 1608.000 0.240
hsa-miR-6504-5p -1.000 1609.000 0.240
hsa-miR-5009-5p -1.000 1610.000 0.240
hsa-miR-5684 -1.000 1611.000 0.240
hsa-miR-323a-3p -1.000 1612.000 0.239
hsa-miR-4793-5p -1.000 1613.000 0.239
hsa-miR-6086 -1.000 1614.000 0.239
hsa-miR-3975 -1.000 1615.000 0.238
hsa-miR-504-5p -1.000 1616.000 0.238
hsa-miR-5682 -1.000 1617.000 0.238
hsa-miR-3944-3p -1.000 1618.000 0.238
hsa-miR-642a-3p -1.000 1619.000 0.238
hsa-miR-3164 -1.000 1620.000 0.238
hsa-miR-548j-5p -1.000 1621.000 0.237
hsa-miR-548ap-5p -1.000 1622.000 0.237
hsa-miR-548av-5p -1.000 1623.000 0.237
hsa-miR-8073 -1.000 1624.000 0.236
hsa-miR-8074 -1.000 1625.000 0.236
hsa-miR-149-3p -1.000 1626.000 0.235
hsa-miR-4651 -1.000 1627.000 0.235
hsa-miR-5196-3p -1.000 1628.000 0.235
hsa-miR-7108-3p -1.000 1629.000 0.235
hsa-miR-10401-3p -1.000 1630.000 0.235
hsa-miR-1301-3p -1.000 1631.000 0.235
hsa-miR-4257 -1.000 1632.000 0.235
hsa-miR-1302 -1.000 1633.000 0.234
hsa-miR-302e -1.000 1634.000 0.234
hsa-miR-4999-3p -1.000 1635.000 0.234
hsa-miR-200a-3p -1.000 1636.000 0.234
hsa-miR-7844-5p -1.000 1637.000 0.234
hsa-miR-874-3p -1.000 1638.000 0.234
hsa-miR-4486 -1.000 1639.000 0.234
hsa-miR-10400-3p -1.000 1640.000 0.234
hsa-miR-6084 -1.000 1641.000 0.234
hsa-miR-324-3p -1.000 1642.000 0.234
hsa-miR-616-5p -1.000 1643.000 0.234
hsa-miR-770-5p -1.000 1644.000 0.234
hsa-miR-3909 -1.000 1645.000 0.233
hsa-miR-432-5p -1.000 1646.000 0.233
hsa-miR-5192 -1.000 1647.000 0.232
hsa-miR-484 -1.000 1648.000 0.232
hsa-miR-3130-5p -1.000 1649.000 0.232
hsa-miR-7975 -1.000 1650.000 0.232
hsa-miR-3973 -1.000 1651.000 0.231
hsa-miR-499b-3p -1.000 1652.000 0.231
hsa-miR-28-5p -1.000 1653.000 0.231
hsa-miR-6766-5p -1.000 1654.000 0.230
hsa-miR-4421 -1.000 1655.000 0.229
hsa-miR-11181-5p -1.000 1656.000 0.229
hsa-miR-485-3p -1.000 1657.000 0.229
hsa-miR-1263 -1.000 1658.000 0.228
hsa-miR-1909-5p -1.000 1659.000 0.228
hsa-miR-4252 -1.000 1660.000 0.228
hsa-miR-8079 -1.000 1661.000 0.228
hsa-miR-8086 -1.000 1662.000 0.228
hsa-miR-3196 -1.000 1663.000 0.228
hsa-miR-4497 -1.000 1664.000 0.228
hsa-miR-4501 -1.000 1665.000 0.228
hsa-miR-4524a-5p -1.000 1666.000 0.228
hsa-miR-4485-5p -1.000 1667.000 0.228
hsa-miR-4321 -1.000 1668.000 0.227
hsa-miR-18a-3p -1.000 1669.000 0.227
hsa-miR-3648 -1.000 1670.000 0.227
hsa-miR-6778-5p -1.000 1671.000 0.226
hsa-miR-299-3p -1.000 1672.000 0.226
hsa-miR-4474-5p -1.000 1673.000 0.226
hsa-miR-3977 -1.000 1674.000 0.225
hsa-miR-423-3p -1.000 1675.000 0.225
hsa-miR-4737 -1.000 1676.000 0.225
hsa-miR-6744-5p -1.000 1677.000 0.225
hsa-miR-2277-5p -1.000 1678.000 0.225
hsa-miR-610 -1.000 1679.000 0.224
hsa-miR-3194-5p -1.000 1680.000 0.224
hsa-miR-4450 -1.000 1681.000 0.224
hsa-miR-185-3p -1.000 1682.000 0.224
hsa-miR-7114-5p -1.000 1683.000 0.223
hsa-miR-99b-5p -1.000 1684.000 0.223
hsa-miR-4680-5p -1.000 1685.000 0.223
hsa-miR-4762-5p -1.000 1686.000 0.223
hsa-miR-128-2-5p -1.000 1687.000 0.222
hsa-miR-5694 -1.000 1688.000 0.222
hsa-miR-365a-5p -1.000 1689.000 0.221
hsa-miR-96-3p -1.000 1690.000 0.221
hsa-miR-6514-5p -1.000 1691.000 0.220
hsa-miR-590-5p -1.000 1692.000 0.220
hsa-miR-378j -1.000 1693.000 0.220
hsa-miR-147b-5p -1.000 1694.000 0.220
hsa-miR-3907 -1.000 1695.000 0.220
hsa-miR-8089 -1.000 1696.000 0.220
hsa-miR-5004-5p -1.000 1697.000 0.218
hsa-miR-1304-3p -1.000 1698.000 0.218
hsa-miR-892b -1.000 1699.000 0.218
hsa-miR-5089-3p -1.000 1700.000 0.218
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

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

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