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 interestAA,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-9-5p 1.000 1.000 0.957
hsa-miR-190a-5p 1.000 2.000 0.955
hsa-miR-130b-5p 1.000 3.000 0.953
hsa-miR-153-5p 1.000 4.000 0.951
hsa-miR-4793-3p 1.000 5.000 0.951
hsa-miR-4288 1.000 6.000 0.950
hsa-miR-6888-3p 1.000 7.000 0.948
hsa-miR-30a-3p 1.000 8.000 0.945
hsa-let-7g-5p 1.000 9.000 0.942
hsa-miR-4716-5p 1.000 10.000 0.940
hsa-miR-6826-3p 1.000 11.000 0.940
hsa-let-7a-5p 1.000 12.000 0.938
hsa-miR-3925-3p 1.000 13.000 0.937
hsa-miR-544b 1.000 14.000 0.934
hsa-miR-5701 1.000 15.000 0.933
hsa-miR-767-5p 1.000 16.000 0.933
hsa-miR-4732-3p 1.000 17.000 0.930
hsa-miR-98-5p 1.000 18.000 0.930
hsa-miR-340-3p 1.000 19.000 0.930
hsa-miR-381-5p 1.000 20.000 0.930
hsa-miR-410-5p 1.000 21.000 0.930
hsa-let-7f-5p 1.000 22.000 0.930
hsa-miR-30e-3p 1.000 23.000 0.930
hsa-let-7e-5p 1.000 24.000 0.930
hsa-miR-124-5p 1.000 25.000 0.930
hsa-miR-375-3p 1.000 26.000 0.930
hsa-let-7b-5p 1.000 27.000 0.930
hsa-let-7c-5p 1.000 28.000 0.930
hsa-miR-181a-3p 1.000 29.000 0.930
hsa-miR-548d-3p 1.000 30.000 0.929
hsa-miR-5584-3p 1.000 31.000 0.929
hsa-miR-548bb-3p 1.000 32.000 0.929
hsa-miR-338-3p 1.000 33.000 0.928
hsa-miR-181a-2-3p 1.000 34.000 0.926
hsa-miR-943 1.000 35.000 0.926
hsa-miR-30b-3p 1.000 36.000 0.926
hsa-miR-152-5p 1.000 37.000 0.925
hsa-miR-6874-3p 1.000 38.000 0.925
hsa-miR-132-5p 1.000 39.000 0.922
hsa-miR-942-5p 1.000 40.000 0.920
hsa-miR-497-5p 1.000 41.000 0.920
hsa-miR-676-3p 1.000 42.000 0.917
hsa-miR-409-5p 1.000 43.000 0.914
hsa-miR-4423-5p 1.000 44.000 0.912
hsa-miR-19b-2-5p 1.000 45.000 0.911
hsa-miR-19b-1-5p 1.000 46.000 0.907
hsa-miR-374b-3p 1.000 47.000 0.904
hsa-miR-579-5p 1.000 48.000 0.904
hsa-let-7i-5p 1.000 49.000 0.904
hsa-miR-2053 1.000 50.000 0.902
hsa-miR-154-5p 1.000 51.000 0.901
hsa-miR-105-3p 1.000 52.000 0.900
hsa-miR-599 1.000 53.000 0.899
hsa-miR-302d-3p 1.000 54.000 0.899
hsa-miR-1264 1.000 55.000 0.898
hsa-miR-4308 1.000 56.000 0.896
hsa-miR-544a 1.000 57.000 0.896
hsa-miR-4765 1.000 58.000 0.895
hsa-miR-593-3p 1.000 59.000 0.895
hsa-let-7d-5p 1.000 60.000 0.894
hsa-miR-549a-5p 1.000 61.000 0.894
hsa-miR-6751-5p 1.000 62.000 0.894
hsa-miR-374c-3p 1.000 63.000 0.893
hsa-miR-548as-3p 1.000 64.000 0.893
hsa-miR-1294 1.000 65.000 0.892
hsa-miR-6856-3p 1.000 66.000 0.891
hsa-miR-6844 1.000 67.000 0.890
hsa-miR-223-3p 1.000 68.000 0.889
hsa-miR-29a-5p 1.000 69.000 0.888
hsa-miR-548v 1.000 70.000 0.887
hsa-miR-1537-5p 1.000 71.000 0.887
hsa-miR-548am-3p 1.000 72.000 0.887
hsa-miR-548y 1.000 73.000 0.885
hsa-miR-3678-3p 1.000 74.000 0.885
hsa-miR-449c-3p 1.000 75.000 0.884
hsa-miR-200c-5p 1.000 76.000 0.883
hsa-miR-7850-5p 1.000 77.000 0.883
hsa-miR-4295 1.000 78.000 0.882
hsa-miR-2355-3p 1.000 79.000 0.881
hsa-miR-6739-3p 1.000 80.000 0.879
hsa-miR-6755-3p 1.000 81.000 0.879
hsa-miR-26a-2-3p 1.000 82.000 0.878
hsa-miR-449b-5p 1.000 83.000 0.877
hsa-miR-653-3p 1.000 84.000 0.877
hsa-miR-4703-3p 1.000 85.000 0.876
hsa-miR-223-5p 1.000 86.000 0.875
hsa-miR-548az-5p 1.000 87.000 0.874
hsa-miR-6851-3p 1.000 88.000 0.873
hsa-miR-548g-5p 1.000 89.000 0.872
hsa-miR-548x-5p 1.000 90.000 0.872
hsa-miR-548aj-5p 1.000 91.000 0.872
hsa-miR-4540 1.000 92.000 0.871
hsa-miR-371b-3p 1.000 93.000 0.871
hsa-miR-582-5p 1.000 94.000 0.871
hsa-miR-1226-3p 1.000 95.000 0.870
hsa-miR-4301 1.000 96.000 0.870
hsa-miR-6766-3p 1.000 97.000 0.870
hsa-miR-875-5p 1.000 98.000 0.870
hsa-miR-1282 1.000 99.000 0.869
hsa-miR-21-5p 1.000 100.000 0.868
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