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-921 -1.000 2101.000 0.137
hsa-miR-631 -1.000 2102.000 0.136
hsa-miR-10393-5p -1.000 2103.000 0.136
hsa-miR-648 -1.000 2104.000 0.136
hsa-miR-4284 -1.000 2105.000 0.135
hsa-miR-4505 -1.000 2106.000 0.135
hsa-miR-1343-3p -1.000 2107.000 0.135
hsa-miR-559 -1.000 2108.000 0.135
hsa-miR-4703-5p -1.000 2109.000 0.135
hsa-miR-4735-3p -1.000 2110.000 0.135
hsa-miR-664a-5p -1.000 2111.000 0.134
hsa-miR-7159-5p -1.000 2112.000 0.134
hsa-miR-4454 -1.000 2113.000 0.134
hsa-miR-1972 -1.000 2114.000 0.134
hsa-miR-5691 -1.000 2115.000 0.134
hsa-miR-6868-5p -1.000 2116.000 0.134
hsa-miR-8080 -1.000 2117.000 0.134
hsa-miR-4635 -1.000 2118.000 0.133
hsa-miR-548q -1.000 2119.000 0.133
hsa-miR-4790-3p -1.000 2120.000 0.133
hsa-miR-6512-3p -1.000 2121.000 0.132
hsa-miR-3142 -1.000 2122.000 0.132
hsa-miR-4650-3p -1.000 2123.000 0.132
hsa-miR-1266-5p -1.000 2124.000 0.132
hsa-miR-4662a-3p -1.000 2125.000 0.132
hsa-miR-4662b -1.000 2126.000 0.132
hsa-miR-4300 -1.000 2127.000 0.131
hsa-miR-1295b-3p -1.000 2128.000 0.131
hsa-miR-143-3p -1.000 2129.000 0.131
hsa-miR-4263 -1.000 2130.000 0.131
hsa-miR-3135b -1.000 2131.000 0.131
hsa-miR-3178 -1.000 2132.000 0.131
hsa-miR-4634 -1.000 2133.000 0.131
hsa-miR-200c-3p -1.000 2134.000 0.130
hsa-miR-6792-5p -1.000 2135.000 0.130
hsa-miR-193b-3p -1.000 2136.000 0.130
hsa-miR-4475 -1.000 2137.000 0.130
hsa-miR-3183 -1.000 2138.000 0.130
hsa-miR-4311 -1.000 2139.000 0.129
hsa-miR-3688-3p -1.000 2140.000 0.129
hsa-miR-6894-5p -1.000 2141.000 0.129
hsa-miR-2467-3p -1.000 2142.000 0.129
hsa-miR-3605-5p -1.000 2143.000 0.129
hsa-miR-10397-3p -1.000 2144.000 0.129
hsa-miR-4740-3p -1.000 2145.000 0.128
hsa-miR-891a-5p -1.000 2146.000 0.128
hsa-miR-6830-5p -1.000 2147.000 0.128
hsa-miR-6748-5p -1.000 2148.000 0.128
hsa-miR-519c-3p -1.000 2149.000 0.128
hsa-miR-6870-5p -1.000 2150.000 0.128
hsa-miR-6515-5p -1.000 2151.000 0.127
hsa-miR-3960 -1.000 2152.000 0.127
hsa-miR-4747-3p -1.000 2153.000 0.126
hsa-miR-589-3p -1.000 2154.000 0.126
hsa-miR-411-5p -1.000 2155.000 0.126
hsa-miR-12129 -1.000 2156.000 0.126
hsa-miR-4652-5p -1.000 2157.000 0.125
hsa-miR-520h -1.000 2158.000 0.125
hsa-miR-3148 -1.000 2159.000 0.125
hsa-miR-7157-3p -1.000 2160.000 0.124
hsa-miR-496 -1.000 2161.000 0.124
hsa-miR-4669 -1.000 2162.000 0.124
hsa-miR-1275 -1.000 2163.000 0.124
hsa-miR-671-5p -1.000 2164.000 0.124
hsa-miR-4763-3p -1.000 2165.000 0.123
hsa-miR-7854-3p -1.000 2166.000 0.123
hsa-miR-3928-3p -1.000 2167.000 0.122
hsa-miR-3688-5p -1.000 2168.000 0.122
hsa-miR-421 -1.000 2169.000 0.122
hsa-miR-577 -1.000 2170.000 0.122
hsa-miR-136-3p -1.000 2171.000 0.122
hsa-miR-374b-5p -1.000 2172.000 0.121
hsa-miR-6837-5p -1.000 2173.000 0.121
hsa-miR-143-5p -1.000 2174.000 0.120
hsa-miR-4776-5p -1.000 2175.000 0.120
hsa-miR-4504 -1.000 2176.000 0.120
hsa-miR-10524-5p -1.000 2177.000 0.120
hsa-miR-10226 -1.000 2178.000 0.119
hsa-miR-338-5p -1.000 2179.000 0.119
hsa-miR-3609 -1.000 2180.000 0.119
hsa-miR-345-3p -1.000 2181.000 0.119
hsa-miR-1255a -1.000 2182.000 0.118
hsa-miR-1306-5p -1.000 2183.000 0.118
hsa-miR-6816-3p -1.000 2184.000 0.118
hsa-miR-3157-5p -1.000 2185.000 0.118
hsa-miR-99a-3p -1.000 2186.000 0.118
hsa-miR-514a-5p -1.000 2187.000 0.117
hsa-miR-378f -1.000 2188.000 0.117
hsa-miR-4677-3p -1.000 2189.000 0.117
hsa-miR-4738-3p -1.000 2190.000 0.117
hsa-miR-5093 -1.000 2191.000 0.117
hsa-miR-520a-5p -1.000 2192.000 0.117
hsa-miR-10398-3p -1.000 2193.000 0.117
hsa-miR-1272 -1.000 2194.000 0.116
hsa-miR-1199-3p -1.000 2195.000 0.116
hsa-miR-4281 -1.000 2196.000 0.116
hsa-miR-3151-5p -1.000 2197.000 0.115
hsa-miR-1273h-5p -1.000 2198.000 0.115
hsa-miR-4646-5p -1.000 2199.000 0.115
hsa-miR-141-3p -1.000 2200.000 0.115
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