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-759 -1.000 886.000 0.488
hsa-miR-760 -1.000 1325.000 0.320
hsa-miR-761 -1.000 2489.000 0.068
hsa-miR-762 -1.000 1749.000 0.200
hsa-miR-764 1.000 395.000 0.712
hsa-miR-765 -1.000 2456.000 0.072
hsa-miR-766-3p -1.000 1403.000 0.289
hsa-miR-766-5p -1.000 2257.000 0.106
hsa-miR-767-3p 1.000 120.000 0.858
hsa-miR-767-5p 1.000 16.000 0.933
hsa-miR-769-3p 1.000 733.000 0.556
hsa-miR-769-5p 1.000 527.000 0.654
hsa-miR-770-5p -1.000 1644.000 0.234
hsa-miR-7702 1.000 752.000 0.552
hsa-miR-7703 1.000 747.000 0.553
hsa-miR-7704 -1.000 1909.000 0.172
hsa-miR-7705 -1.000 1092.000 0.409
hsa-miR-7706 -1.000 1999.000 0.157
hsa-miR-7843-3p -1.000 1540.000 0.259
hsa-miR-7843-5p -1.000 1179.000 0.377
hsa-miR-7844-5p -1.000 1637.000 0.234
hsa-miR-7845-5p -1.000 2481.000 0.070
hsa-miR-7846-3p -1.000 2618.000 0.044
hsa-miR-7847-3p -1.000 2077.000 0.142
hsa-miR-7848-3p -1.000 963.000 0.448
hsa-miR-7849-3p 1.000 276.000 0.774
hsa-miR-7850-5p 1.000 77.000 0.883
hsa-miR-7851-3p -1.000 1089.000 0.412
hsa-miR-7852-3p 1.000 783.000 0.533
hsa-miR-7853-5p -1.000 1709.000 0.216
hsa-miR-7854-3p -1.000 2166.000 0.123
hsa-miR-7855-5p -1.000 1085.000 0.415
hsa-miR-7856-5p -1.000 1123.000 0.394
hsa-miR-7973 -1.000 1564.000 0.250
hsa-miR-7974 -1.000 1211.000 0.364
hsa-miR-7975 -1.000 1650.000 0.232
hsa-miR-7976 1.000 398.000 0.712
hsa-miR-7977 -1.000 1794.000 0.191
hsa-miR-7978 1.000 121.000 0.858
hsa-miR-802 -1.000 924.000 0.465
hsa-miR-8052 -1.000 1213.000 0.364
hsa-miR-8053 -1.000 1452.000 0.283
hsa-miR-8054 -1.000 2630.000 0.038
hsa-miR-8055 1.000 823.000 0.513
hsa-miR-8056 1.000 601.000 0.628
hsa-miR-8057 -1.000 2081.000 0.141
hsa-miR-8058 1.000 415.000 0.705
hsa-miR-8059 -1.000 2423.000 0.078
hsa-miR-8060 -1.000 2452.000 0.073
hsa-miR-8061 1.000 216.000 0.803
hsa-miR-8062 1.000 775.000 0.536
hsa-miR-8063 -1.000 2573.000 0.056
hsa-miR-8064 -1.000 1147.000 0.386
hsa-miR-8065 1.000 608.000 0.625
hsa-miR-8066 1.000 688.000 0.580
hsa-miR-8067 -1.000 1265.000 0.344
hsa-miR-8068 1.000 109.000 0.863
hsa-miR-8069 -1.000 1130.000 0.392
hsa-miR-8070 1.000 291.000 0.766
hsa-miR-8071 -1.000 2364.000 0.088
hsa-miR-8072 -1.000 1871.000 0.178
hsa-miR-8073 -1.000 1624.000 0.236
hsa-miR-8074 -1.000 1625.000 0.236
hsa-miR-8075 -1.000 1005.000 0.431
hsa-miR-8076 1.000 644.000 0.608
hsa-miR-8077 1.000 456.000 0.687
hsa-miR-8078 -1.000 1542.000 0.257
hsa-miR-8079 -1.000 1661.000 0.228
hsa-miR-8080 -1.000 2117.000 0.134
hsa-miR-8081 -1.000 992.000 0.435
hsa-miR-8082 -1.000 2065.000 0.144
hsa-miR-8083 -1.000 1360.000 0.309
hsa-miR-8084 -1.000 2512.000 0.065
hsa-miR-8085 -1.000 1375.000 0.300
hsa-miR-8086 -1.000 1662.000 0.228
hsa-miR-8087 -1.000 1906.000 0.172
hsa-miR-8088 -1.000 2621.000 0.042
hsa-miR-8089 -1.000 1696.000 0.220
hsa-miR-8485 -1.000 2057.000 0.145
hsa-miR-873-3p -1.000 1012.000 0.429
hsa-miR-873-5p -1.000 845.000 0.500
hsa-miR-874-3p -1.000 1638.000 0.234
hsa-miR-874-5p -1.000 2469.000 0.072
hsa-miR-875-3p 1.000 270.000 0.777
hsa-miR-875-5p 1.000 98.000 0.870
hsa-miR-876-3p -1.000 940.000 0.458
hsa-miR-876-5p 1.000 367.000 0.730
hsa-miR-877-3p -1.000 1050.000 0.419
hsa-miR-877-5p -1.000 2568.000 0.057
hsa-miR-885-3p -1.000 1759.000 0.198
hsa-miR-885-5p -1.000 1049.000 0.419
hsa-miR-887-3p -1.000 2267.000 0.105
hsa-miR-887-5p 1.000 329.000 0.746
hsa-miR-888-3p 1.000 621.000 0.620
hsa-miR-888-5p -1.000 1791.000 0.192
hsa-miR-889-3p 1.000 725.000 0.561
hsa-miR-889-5p -1.000 1901.000 0.173
hsa-miR-890 1.000 407.000 0.709
hsa-miR-891a-3p 1.000 170.000 0.825
hsa-miR-891a-5p -1.000 2146.000 0.128
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