Freiburg RNA Tools
BrainDead - Results
BIF
IFF
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-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
hsa-miR-323b-5p 1.000 101.000 0.867
hsa-miR-4778-3p 1.000 102.000 0.865
hsa-miR-935 1.000 103.000 0.865
hsa-miR-1537-3p 1.000 104.000 0.865
hsa-miR-3152-5p 1.000 105.000 0.865
hsa-miR-4328 1.000 106.000 0.864
hsa-miR-15a-5p 1.000 107.000 0.863
hsa-miR-548an 1.000 108.000 0.863
hsa-miR-8068 1.000 109.000 0.863
hsa-miR-187-3p 1.000 110.000 0.862
hsa-miR-662 1.000 111.000 0.861
hsa-miR-3065-3p 1.000 112.000 0.861
hsa-miR-570-5p 1.000 113.000 0.861
hsa-miR-548ai 1.000 114.000 0.861
hsa-miR-6772-3p 1.000 115.000 0.860
hsa-miR-1468-5p 1.000 116.000 0.860
hsa-miR-892c-3p 1.000 117.000 0.860
hsa-miR-548f-5p 1.000 118.000 0.859
hsa-miR-548ah-5p 1.000 119.000 0.859
hsa-miR-767-3p 1.000 120.000 0.858
hsa-miR-7978 1.000 121.000 0.858
hsa-miR-3614-3p 1.000 122.000 0.858
hsa-miR-6854-3p 1.000 123.000 0.858
hsa-miR-450a-5p 1.000 124.000 0.857
hsa-miR-302f 1.000 125.000 0.857
hsa-miR-4500 1.000 126.000 0.856
hsa-miR-6499-3p 1.000 127.000 0.855
hsa-miR-3655 1.000 128.000 0.854
hsa-miR-3173-5p 1.000 129.000 0.853
hsa-miR-4790-5p 1.000 130.000 0.853
hsa-miR-6780a-3p 1.000 131.000 0.853
hsa-miR-6876-3p 1.000 132.000 0.853
hsa-miR-548b-5p 1.000 133.000 0.851
hsa-miR-19a-5p 1.000 134.000 0.851
hsa-miR-130a-5p 1.000 135.000 0.849
hsa-miR-376b-5p 1.000 136.000 0.849
hsa-miR-122b-5p 1.000 137.000 0.849
hsa-miR-744-3p 1.000 138.000 0.848
hsa-miR-6795-3p 1.000 139.000 0.845
hsa-miR-4640-3p 1.000 140.000 0.843
hsa-miR-4676-3p 1.000 141.000 0.843
hsa-miR-3613-5p 1.000 142.000 0.843
hsa-miR-4477a 1.000 143.000 0.841
hsa-miR-4678 1.000 144.000 0.841
hsa-let-7a-2-3p 1.000 145.000 0.840
hsa-miR-892a 1.000 146.000 0.840
hsa-miR-571 1.000 147.000 0.840
hsa-miR-5586-5p 1.000 148.000 0.838
hsa-miR-6810-3p 1.000 149.000 0.838
hsa-miR-6818-3p 1.000 150.000 0.838
hsa-miR-6828-3p 1.000 151.000 0.838
hsa-miR-6868-3p 1.000 152.000 0.838
hsa-miR-301b-5p 1.000 153.000 0.838
hsa-miR-548at-3p 1.000 154.000 0.838
hsa-miR-4662a-5p 1.000 155.000 0.836
hsa-miR-136-5p 1.000 156.000 0.835
hsa-miR-30d-3p 1.000 157.000 0.835
hsa-miR-4720-3p 1.000 158.000 0.835
hsa-miR-548h-5p 1.000 159.000 0.834
hsa-miR-548m 1.000 160.000 0.833
hsa-miR-601 1.000 161.000 0.833
hsa-miR-505-3p 1.000 162.000 0.832
hsa-miR-125a-3p 1.000 163.000 0.830
hsa-miR-4775 1.000 164.000 0.829
hsa-miR-29c-5p 1.000 165.000 0.829
hsa-miR-654-3p 1.000 166.000 0.826
hsa-miR-3922-3p 1.000 167.000 0.825
hsa-miR-619-3p 1.000 168.000 0.825
hsa-miR-449a 1.000 169.000 0.825
hsa-miR-891a-3p 1.000 170.000 0.825
hsa-miR-424-5p 1.000 171.000 0.824
hsa-miR-548ag 1.000 172.000 0.824
hsa-miR-4783-3p 1.000 173.000 0.823
hsa-miR-622 1.000 174.000 0.822
hsa-miR-548at-5p 1.000 175.000 0.821
hsa-miR-4280 1.000 176.000 0.821
hsa-miR-204-5p 1.000 177.000 0.821
hsa-miR-211-5p 1.000 178.000 0.821
hsa-miR-4753-3p 1.000 179.000 0.821
hsa-miR-5010-3p 1.000 180.000 0.821
hsa-miR-6782-3p 1.000 181.000 0.821
hsa-miR-6780b-3p 1.000 182.000 0.821
hsa-miR-4668-3p 1.000 183.000 0.821
hsa-miR-302b-3p 1.000 184.000 0.821
hsa-miR-586 1.000 185.000 0.820
hsa-miR-3689a-5p 1.000 186.000 0.819
hsa-miR-3689b-5p 1.000 187.000 0.819
hsa-miR-3689e 1.000 188.000 0.819
hsa-miR-548au-3p 1.000 189.000 0.818
hsa-miR-6715b-5p 1.000 190.000 0.817
hsa-miR-3168 1.000 191.000 0.816
hsa-miR-4305 1.000 192.000 0.816
hsa-miR-92a-2-5p 1.000 193.000 0.816
hsa-miR-122-5p 1.000 194.000 0.816
hsa-miR-1285-5p 1.000 195.000 0.814
hsa-miR-4677-5p 1.000 196.000 0.814
hsa-miR-5699-3p 1.000 197.000 0.814
hsa-miR-138-2-3p 1.000 198.000 0.814
hsa-miR-4273 1.000 199.000 0.814
hsa-miR-4520-5p 1.000 200.000 0.814
hsa-miR-3150b-3p 1.000 201.000 0.813
hsa-miR-597-3p 1.000 202.000 0.813
hsa-miR-2052 1.000 203.000 0.811
hsa-miR-6501-5p 1.000 204.000 0.811
hsa-miR-141-5p 1.000 205.000 0.810
hsa-miR-4325 1.000 206.000 0.810
hsa-miR-551a 1.000 207.000 0.809
hsa-miR-551b-3p 1.000 208.000 0.809
hsa-miR-548d-5p 1.000 209.000 0.809
hsa-miR-548ad-5p 1.000 210.000 0.809
hsa-miR-548ae-5p 1.000 211.000 0.809
hsa-miR-548ay-5p 1.000 212.000 0.809
hsa-miR-4312 1.000 213.000 0.805
hsa-miR-2117 1.000 214.000 0.804
hsa-miR-142-3p 1.000 215.000 0.804
hsa-miR-8061 1.000 216.000 0.803
hsa-miR-4307 1.000 217.000 0.803
hsa-miR-495-5p 1.000 218.000 0.801
hsa-miR-6840-3p 1.000 219.000 0.801
hsa-miR-4999-5p 1.000 220.000 0.801
hsa-miR-618 1.000 221.000 0.801
hsa-miR-199b-5p 1.000 222.000 0.801
hsa-miR-146b-3p 1.000 223.000 0.800
hsa-miR-3136-3p 1.000 224.000 0.800
hsa-miR-4652-3p 1.000 225.000 0.800
hsa-miR-219a-1-3p 1.000 226.000 0.798
hsa-miR-2113 1.000 227.000 0.798
hsa-miR-6837-3p 1.000 228.000 0.797
hsa-miR-499a-5p 1.000 229.000 0.797
hsa-miR-219a-5p 1.000 230.000 0.796
hsa-miR-4447 1.000 231.000 0.796
hsa-miR-1265 1.000 232.000 0.796
hsa-miR-548ba 1.000 233.000 0.796
hsa-miR-2681-3p 1.000 234.000 0.795
hsa-miR-122b-3p 1.000 235.000 0.795
hsa-miR-515-3p 1.000 236.000 0.794
hsa-miR-3059-5p 1.000 237.000 0.792
hsa-miR-656-5p 1.000 238.000 0.792
hsa-miR-27a-3p 1.000 239.000 0.791
hsa-miR-584-3p 1.000 240.000 0.791
hsa-miR-135b-5p 1.000 241.000 0.790
hsa-miR-34c-5p 1.000 242.000 0.790
hsa-miR-25-3p 1.000 243.000 0.789
hsa-miR-489-5p 1.000 244.000 0.788
hsa-miR-4636 1.000 245.000 0.788
hsa-miR-1266-3p 1.000 246.000 0.788
hsa-miR-301a-5p 1.000 247.000 0.787
hsa-miR-4694-5p 1.000 248.000 0.787
hsa-miR-455-5p 1.000 249.000 0.787
hsa-miR-4715-5p 1.000 250.000 0.786
hsa-miR-369-3p 1.000 251.000 0.786
hsa-miR-3064-5p 1.000 252.000 0.785
hsa-miR-581 1.000 253.000 0.785
hsa-miR-624-5p 1.000 254.000 0.784
hsa-miR-584-5p 1.000 255.000 0.784
hsa-miR-653-5p 1.000 256.000 0.783
hsa-miR-1179 1.000 257.000 0.783
hsa-miR-5681b 1.000 258.000 0.783
hsa-miR-575 1.000 259.000 0.782
hsa-miR-660-5p 1.000 260.000 0.782
hsa-miR-548b-3p 1.000 261.000 0.781
hsa-miR-138-5p 1.000 262.000 0.780
hsa-miR-100-5p 1.000 263.000 0.780
hsa-miR-6830-3p 1.000 264.000 0.780
hsa-miR-134-5p 1.000 265.000 0.780
hsa-miR-552-5p 1.000 266.000 0.778
hsa-miR-12135 1.000 267.000 0.778
hsa-miR-7159-3p 1.000 268.000 0.778
hsa-miR-7107-3p 1.000 269.000 0.777
hsa-miR-875-3p 1.000 270.000 0.777
hsa-miR-4666a-3p 1.000 271.000 0.776
hsa-miR-548a-5p 1.000 272.000 0.776
hsa-miR-548ar-5p 1.000 273.000 0.776
hsa-miR-3144-3p 1.000 274.000 0.775
hsa-miR-494-5p 1.000 275.000 0.775
hsa-miR-7849-3p 1.000 276.000 0.774
hsa-miR-450b-5p 1.000 277.000 0.774
hsa-miR-3659 1.000 278.000 0.773
hsa-miR-1178-3p 1.000 279.000 0.773
hsa-miR-649 1.000 280.000 0.772
hsa-miR-598-3p 1.000 281.000 0.772
hsa-miR-335-3p 1.000 282.000 0.772
hsa-miR-6759-3p 1.000 283.000 0.772
hsa-miR-320a-5p 1.000 284.000 0.771
hsa-miR-548al 1.000 285.000 0.770
hsa-miR-125b-5p 1.000 286.000 0.770
hsa-miR-2467-5p 1.000 287.000 0.769
hsa-miR-361-3p 1.000 288.000 0.769
hsa-miR-563 1.000 289.000 0.769
hsa-miR-384 1.000 290.000 0.767
hsa-miR-8070 1.000 291.000 0.766
hsa-miR-548o-3p 1.000 292.000 0.765
hsa-miR-548ah-3p 1.000 293.000 0.765
hsa-miR-548ar-3p 1.000 294.000 0.765
hsa-miR-548av-3p 1.000 295.000 0.765
hsa-miR-5707 1.000 296.000 0.765
hsa-miR-548ab 1.000 297.000 0.765
hsa-miR-382-5p 1.000 298.000 0.764
hsa-miR-6838-3p 1.000 299.000 0.763
hsa-miR-4714-5p 1.000 300.000 0.763
hsa-miR-4645-3p 1.000 301.000 0.763
hsa-miR-196b-5p 1.000 302.000 0.763
hsa-miR-1205 1.000 303.000 0.762
hsa-miR-4802-5p 1.000 304.000 0.762
hsa-miR-337-3p 1.000 305.000 0.760
hsa-miR-9986 1.000 306.000 0.760
hsa-miR-4445-5p 1.000 307.000 0.757
hsa-miR-148b-5p 1.000 308.000 0.757
hsa-miR-2682-5p 1.000 309.000 0.756
hsa-miR-3605-3p 1.000 310.000 0.754
hsa-miR-493-5p 1.000 311.000 0.753
hsa-miR-1236-3p 1.000 312.000 0.753
hsa-miR-4646-3p 1.000 313.000 0.753
hsa-miR-6774-3p 1.000 314.000 0.753
hsa-miR-6811-3p 1.000 315.000 0.753
hsa-miR-9851-5p 1.000 316.000 0.753
hsa-miR-758-3p 1.000 317.000 0.752
hsa-miR-371a-3p 1.000 318.000 0.752
hsa-miR-299-5p 1.000 319.000 0.752
hsa-miR-4738-5p 1.000 320.000 0.751
hsa-miR-4464 1.000 321.000 0.751
hsa-miR-433-5p 1.000 322.000 0.751
hsa-miR-148b-3p 1.000 323.000 0.751
hsa-miR-4742-3p 1.000 324.000 0.750
hsa-miR-557 1.000 325.000 0.750
hsa-miR-6808-3p 1.000 326.000 0.749
hsa-miR-3680-5p 1.000 327.000 0.748
hsa-miR-203a-5p 1.000 328.000 0.747
hsa-miR-887-5p 1.000 329.000 0.746
hsa-miR-3974 1.000 330.000 0.746
hsa-miR-378a-5p 1.000 331.000 0.746
hsa-miR-4714-3p 1.000 332.000 0.746
hsa-miR-1244 1.000 333.000 0.745
hsa-miR-452-5p 1.000 334.000 0.744
hsa-miR-4477b 1.000 335.000 0.742
hsa-miR-329-5p 1.000 336.000 0.742
hsa-miR-3921 1.000 337.000 0.742
hsa-miR-6790-5p 1.000 338.000 0.742
hsa-miR-5580-5p 1.000 339.000 0.741
hsa-miR-511-5p 1.000 340.000 0.741
hsa-miR-623 1.000 341.000 0.741
hsa-miR-6073 1.000 342.000 0.741
hsa-miR-370-5p 1.000 343.000 0.740
hsa-miR-4460 1.000 344.000 0.740
hsa-miR-4679 1.000 345.000 0.739
hsa-miR-4682 1.000 346.000 0.739
hsa-miR-33a-3p 1.000 347.000 0.739
hsa-miR-425-5p 1.000 348.000 0.739
hsa-miR-135a-5p 1.000 349.000 0.738
hsa-miR-758-5p 1.000 350.000 0.738
hsa-miR-3149 1.000 351.000 0.738
hsa-miR-196a-5p 1.000 352.000 0.737
hsa-miR-3682-5p 1.000 353.000 0.737
hsa-miR-6514-3p 1.000 354.000 0.737
hsa-miR-6827-3p 1.000 355.000 0.737
hsa-miR-6852-3p 1.000 356.000 0.737
hsa-miR-639 1.000 357.000 0.737
hsa-miR-6502-5p 1.000 358.000 0.736
hsa-miR-4329 1.000 359.000 0.734
hsa-miR-4680-3p 1.000 360.000 0.734
hsa-miR-513c-5p 1.000 361.000 0.733
hsa-miR-139-3p 1.000 362.000 0.733
hsa-miR-202-5p 1.000 363.000 0.731
hsa-miR-4277 1.000 364.000 0.731
hsa-miR-4278 1.000 365.000 0.730
hsa-miR-627-3p 1.000 366.000 0.730
hsa-miR-876-5p 1.000 367.000 0.730
hsa-miR-5047 1.000 368.000 0.730
hsa-miR-7151-5p 1.000 369.000 0.729
hsa-miR-302a-3p 1.000 370.000 0.729
hsa-miR-6813-5p 1.000 371.000 0.728
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