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: http://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-4773 -1.000 2601.000 0.050
hsa-miR-4428 -1.000 2602.000 0.049
hsa-miR-4716-3p -1.000 2603.000 0.049
hsa-miR-5739 -1.000 2604.000 0.049
hsa-miR-4422 -1.000 2605.000 0.048
hsa-miR-4753-5p -1.000 2606.000 0.048
hsa-miR-6511a-5p -1.000 2607.000 0.048
hsa-miR-7110-5p -1.000 2608.000 0.047
hsa-miR-3175 -1.000 2609.000 0.046
hsa-miR-4470 -1.000 2610.000 0.046
hsa-miR-3925-5p -1.000 2611.000 0.045
hsa-miR-4801 -1.000 2612.000 0.045
hsa-miR-5680 -1.000 2613.000 0.045
hsa-miR-6874-5p -1.000 2614.000 0.045
hsa-miR-6768-5p -1.000 2615.000 0.045
hsa-miR-942-3p -1.000 2616.000 0.044
hsa-miR-3146 -1.000 2617.000 0.044
hsa-miR-7846-3p -1.000 2618.000 0.044
hsa-miR-641 -1.000 2619.000 0.043
hsa-miR-6880-5p -1.000 2620.000 0.043
hsa-miR-8088 -1.000 2621.000 0.042
hsa-miR-342-3p -1.000 2622.000 0.042
hsa-miR-3185 -1.000 2623.000 0.042
hsa-miR-378g -1.000 2624.000 0.042
hsa-miR-4798-3p -1.000 2625.000 0.042
hsa-miR-1253 -1.000 2626.000 0.041
hsa-miR-376a-3p -1.000 2627.000 0.039
hsa-miR-6835-5p -1.000 2628.000 0.039
hsa-miR-4751 -1.000 2629.000 0.038
hsa-miR-8054 -1.000 2630.000 0.038
hsa-miR-3132 -1.000 2631.000 0.038
hsa-miR-6738-5p -1.000 2632.000 0.038
hsa-miR-6716-5p -1.000 2633.000 0.037
hsa-miR-7515 -1.000 2634.000 0.036
hsa-miR-4713-3p -1.000 2635.000 0.034
hsa-miR-10a-3p -1.000 2636.000 0.033
hsa-miR-204-3p -1.000 2637.000 0.033
hsa-miR-6877-5p -1.000 2638.000 0.033
hsa-miR-4746-5p -1.000 2639.000 0.033
hsa-miR-6720-3p -1.000 2640.000 0.033
hsa-miR-10b-3p -1.000 2641.000 0.033
hsa-miR-3919 -1.000 2642.000 0.031
hsa-miR-3155a -1.000 2643.000 0.031
hsa-miR-4482-5p -1.000 2644.000 0.031
hsa-miR-378i -1.000 2645.000 0.030
hsa-miR-140-3p -1.000 2646.000 0.028
hsa-miR-4516 -1.000 2647.000 0.028
hsa-miR-3156-5p -1.000 2648.000 0.028
hsa-miR-183-5p -1.000 2649.000 0.028
hsa-miR-922 -1.000 2650.000 0.028
hsa-miR-379-5p -1.000 2651.000 0.027
hsa-miR-541-3p -1.000 2652.000 0.025
hsa-miR-3198 -1.000 2653.000 0.022
hsa-miR-361-5p -1.000 2654.000 0.022
hsa-miR-422a -1.000 2655.000 0.022
hsa-miR-4727-3p -1.000 2656.000 0.020
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.

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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