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-6727-5p -1.000 1801.000 0.190
hsa-miR-10396a-5p -1.000 1802.000 0.190
hsa-miR-10400-5p -1.000 1803.000 0.190
hsa-miR-10396b-5p -1.000 1804.000 0.190
hsa-miR-638 -1.000 1805.000 0.190
hsa-miR-3620-5p -1.000 1806.000 0.190
hsa-miR-4734 -1.000 1807.000 0.190
hsa-miR-5587-5p -1.000 1808.000 0.190
hsa-miR-6724-5p -1.000 1809.000 0.190
hsa-miR-6756-5p -1.000 1810.000 0.190
hsa-miR-4743-5p -1.000 1811.000 0.189
hsa-miR-4718 -1.000 1812.000 0.189
hsa-miR-7106-3p -1.000 1813.000 0.189
hsa-miR-21-3p -1.000 1814.000 0.189
hsa-miR-4692 -1.000 1815.000 0.189
hsa-miR-625-5p -1.000 1816.000 0.189
hsa-miR-3176 -1.000 1817.000 0.188
hsa-miR-6720-5p -1.000 1818.000 0.188
hsa-miR-5591-3p -1.000 1819.000 0.188
hsa-miR-3135a -1.000 1820.000 0.188
hsa-miR-3691-5p -1.000 1821.000 0.188
hsa-miR-4691-3p -1.000 1822.000 0.188
hsa-miR-3945 -1.000 1823.000 0.187
hsa-miR-339-3p -1.000 1824.000 0.187
hsa-miR-1286 -1.000 1825.000 0.187
hsa-miR-6127 -1.000 1826.000 0.187
hsa-miR-1295a -1.000 1827.000 0.187
hsa-miR-4672 -1.000 1828.000 0.187
hsa-miR-6791-5p -1.000 1829.000 0.187
hsa-miR-1343-5p -1.000 1830.000 0.187
hsa-miR-4787-5p -1.000 1831.000 0.187
hsa-miR-6789-5p -1.000 1832.000 0.187
hsa-miR-4313 -1.000 1833.000 0.186
hsa-miR-6858-5p -1.000 1834.000 0.186
hsa-miR-525-3p -1.000 1835.000 0.186
hsa-miR-1915-3p -1.000 1836.000 0.186
hsa-miR-6842-5p -1.000 1837.000 0.185
hsa-miR-5186 -1.000 1838.000 0.185
hsa-miR-6862-5p -1.000 1839.000 0.185
hsa-miR-7160-3p -1.000 1840.000 0.185
hsa-miR-3199 -1.000 1841.000 0.185
hsa-miR-6718-5p -1.000 1842.000 0.185
hsa-miR-524-5p -1.000 1843.000 0.185
hsa-miR-7161-5p -1.000 1844.000 0.184
hsa-miR-3612 -1.000 1845.000 0.184
hsa-miR-1827 -1.000 1846.000 0.184
hsa-miR-4694-3p -1.000 1847.000 0.184
hsa-miR-4719 -1.000 1848.000 0.184
hsa-miR-4723-3p -1.000 1849.000 0.184
hsa-miR-5195-5p -1.000 1850.000 0.184
hsa-miR-12125 -1.000 1851.000 0.184
hsa-miR-6731-5p -1.000 1852.000 0.184
hsa-miR-6786-5p -1.000 1853.000 0.184
hsa-miR-194-5p -1.000 1854.000 0.184
hsa-miR-5100 -1.000 1855.000 0.183
hsa-miR-5687 -1.000 1856.000 0.183
hsa-miR-4530 -1.000 1857.000 0.182
hsa-miR-4689 -1.000 1858.000 0.182
hsa-miR-615-5p -1.000 1859.000 0.182
hsa-miR-3677-3p -1.000 1860.000 0.182
hsa-miR-12121 -1.000 1861.000 0.182
hsa-miR-3171 -1.000 1862.000 0.182
hsa-miR-1908-3p -1.000 1863.000 0.182
hsa-miR-4673 -1.000 1864.000 0.182
hsa-miR-6869-3p -1.000 1865.000 0.182
hsa-miR-381-3p -1.000 1866.000 0.181
hsa-miR-4648 -1.000 1867.000 0.181
hsa-miR-6795-5p -1.000 1868.000 0.180
hsa-miR-3686 -1.000 1869.000 0.179
hsa-miR-651-3p -1.000 1870.000 0.179
hsa-miR-8072 -1.000 1871.000 0.178
hsa-miR-16-5p -1.000 1872.000 0.178
hsa-miR-6765-3p -1.000 1873.000 0.178
hsa-miR-1251-5p -1.000 1874.000 0.178
hsa-miR-580-5p -1.000 1875.000 0.177
hsa-miR-542-5p -1.000 1876.000 0.177
hsa-miR-4676-5p -1.000 1877.000 0.176
hsa-miR-4503 -1.000 1878.000 0.176
hsa-miR-3153 -1.000 1879.000 0.176
hsa-miR-1307-5p -1.000 1880.000 0.176
hsa-miR-4418 -1.000 1881.000 0.176
hsa-miR-4515 -1.000 1882.000 0.176
hsa-miR-4638-3p -1.000 1883.000 0.176
hsa-miR-101-3p -1.000 1884.000 0.175
hsa-miR-3616-5p -1.000 1885.000 0.175
hsa-miR-6851-5p -1.000 1886.000 0.175
hsa-miR-1301-5p -1.000 1887.000 0.175
hsa-miR-1203 -1.000 1888.000 0.175
hsa-miR-4633-5p -1.000 1889.000 0.175
hsa-miR-4633-3p -1.000 1890.000 0.175
hsa-miR-6749-3p -1.000 1891.000 0.175
hsa-miR-6722-5p -1.000 1892.000 0.175
hsa-miR-3158-5p -1.000 1893.000 0.175
hsa-miR-3666 -1.000 1894.000 0.175
hsa-miR-6734-5p -1.000 1895.000 0.174
hsa-miR-4658 -1.000 1896.000 0.174
hsa-miR-498-3p -1.000 1897.000 0.174
hsa-miR-1183 -1.000 1898.000 0.174
hsa-miR-424-3p -1.000 1899.000 0.174
hsa-miR-4649-5p -1.000 1900.000 0.174
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