miRBooking-scan explore miRBooking

The miRBooking-scan Web service provides an exploratory view of reference microtargetomes computed by miRBooking.

Not interested in HELA-GINGERAS? Choose a different cell line.

HELA-GINGERAS

RNA-Seq - ENCSR000CRQ

You're now looking into HELA-GINGERAS cell line. We need more detail such as:

  • link to a reference dataset (i.e. GEO)
  • miRBooking parameters used for the computation
  • initial quantifications

Here's how you can reproduce this:

mirbooking --targets=GCF_000001405.25_GRCh37.p13_rna.fna --mirnas=mature.fa --cds-regions=[...] --score-table=scores --log-base=512 --threshold=0.0179 --quantities=hela-gingeras.tsv

Download this view:

curl -H Accept:text/tab-separated-values http://major.iric.ca/~poirigui/cgi-bin/mirbooking-scan/app.cgi/cell-lines/hela-gingeras

target_accession position mirna_accession target_name target_quantity location vacancy mirna_name mirna_quantity probability occupancy silencing
NM_001402.5 10 MIMAT0000098 EEF1A1 5113.77 5'UTR 4895.77 hsa-miR-100-5p 798.658 0.018 101 0.186
NM_001402.5 10 MIMAT0000097 EEF1A1 5113.77 5'UTR 4895.77 hsa-miR-99a-5p 2265.15 0.018 117 0.216
NM_001402.5 198 MIMAT0000077 EEF1A1 5113.77 CDS 4443.77 hsa-miR-22-3p 753.932 0.019 103 0.2
NM_001402.5 198 MIMAT0001341 EEF1A1 5113.77 CDS 4443.77 hsa-miR-424-5p 2238.16 0.019 116 0.219
NM_001402.5 198 MIMAT0000068 EEF1A1 5113.77 CDS 4443.77 hsa-miR-15a-5p 6286.37 0.019 135 0.255
NM_001402.5 198 MIMAT0000417 EEF1A1 5113.77 CDS 4443.77 hsa-miR-15b-5p 6512.89 0.019 135 0.255
NM_001402.5 198 MIMAT0000069 EEF1A1 5113.77 CDS 4443.77 hsa-miR-16-5p 112020.0 0.019 181 0.342
NM_001402.5 217 MIMAT0000085 EEF1A1 5113.77 CDS 4443.77 hsa-miR-28-5p 362.301 0.031 150 0.465
NM_001402.5 249 MIMAT0000693 EEF1A1 5113.77 CDS 4577.77 hsa-miR-30e-3p 267.916 0.052 240 1.252
NM_001402.5 249 MIMAT0000088 EEF1A1 5113.77 CDS 4577.77 hsa-miR-30a-3p 998.012 0.052 296 1.545
NM_001402.5 288 MIMAT0004697 EEF1A1 5113.77 CDS 5032.77 hsa-miR-151a-5p 312.642 0.018 81 0.146
NM_001402.5 411 MIMAT0001341 EEF1A1 5113.77 CDS 2537.77 hsa-miR-424-5p 2238.16 0.085 539 4.591
NM_001402.5 411 MIMAT0000068 EEF1A1 5113.77 CDS 2537.77 hsa-miR-15a-5p 6286.37 0.085 611 5.204
NM_001402.5 411 MIMAT0000417 EEF1A1 5113.77 CDS 2537.77 hsa-miR-15b-5p 6512.89 0.085 614 5.229
NM_001402.5 411 MIMAT0000069 EEF1A1 5113.77 CDS 2537.77 hsa-miR-16-5p 112020.0 0.085 812 6.916
NM_001402.5 417 MIMAT0000086 EEF1A1 5113.77 CDS 2537.77 hsa-miR-29a-3p 714.822 0.019 101 0.189
NM_001402.5 417 MIMAT0000100 EEF1A1 5113.77 CDS 2537.77 hsa-miR-29b-3p 2516.15 0.019 120 0.224
NM_001402.5 536 MIMAT0000080 EEF1A1 5113.77 CDS 4361.77 hsa-miR-24-3p 5456.39 0.107 752 8.01
NM_001402.5 587 MIMAT0000093 EEF1A1 5113.77 CDS 4619.77 hsa-miR-93-5p 1518.29 0.018 110 0.201
NM_001402.5 587 MIMAT0000070 EEF1A1 5113.77 CDS 4619.77 hsa-miR-17-5p 1550.47 0.018 111 0.203
NM_001402.5 587 MIMAT0000075 EEF1A1 5113.77 CDS 4619.77 hsa-miR-20a-5p 6644.6 0.018 132 0.241
NM_001402.5 587 MIMAT0000680 EEF1A1 5113.77 CDS 4619.77 hsa-miR-106b-5p 11796.5 0.018 141 0.258
NM_001402.5 634 MIMAT0000261 EEF1A1 5113.77 CDS 5012.77 hsa-miR-183-5p 560.486 0.019 101 0.197
NM_001402.5 664 MIMAT0000763 EEF1A1 5113.77 CDS 4671.77 hsa-miR-338-3p 2614.44 0.068 442 3.026
NM_001402.5 805 MIMAT0000064 EEF1A1 5113.77 CDS 4018.77 hsa-let-7c-5p 441.875 0.025 126 0.318
NM_001402.5 805 MIMAT0000062 EEF1A1 5113.77 CDS 4018.77 hsa-let-7a-5p 5442.54 0.025 178 0.449
NM_001402.5 805 MIMAT0000096 EEF1A1 5113.77 CDS 4018.77 hsa-miR-98-5p 6443.26 0.025 182 0.459
NM_001402.5 805 MIMAT0000415 EEF1A1 5113.77 CDS 4018.77 hsa-let-7i-5p 7472.99 0.025 185 0.467
NM_001402.5 805 MIMAT0000414 EEF1A1 5113.77 CDS 4018.77 hsa-let-7g-5p 14906.8 0.025 199 0.502
NM_001402.5 805 MIMAT0000067 EEF1A1 5113.77 CDS 4018.77 hsa-let-7f-5p 51336.602 0.025 225 0.568
NM_001402.5 842 MIMAT0000099 EEF1A1 5113.77 CDS 4793.77 hsa-miR-101-3p 3105.8 0.049 320 1.552
NM_001402.5 870 MIMAT0000086 EEF1A1 5113.77 CDS 4894.77 hsa-miR-29a-3p 714.822 0.019 99 0.185
NM_001402.5 870 MIMAT0000100 EEF1A1 5113.77 CDS 4894.77 hsa-miR-29b-3p 2516.15 0.019 120 0.224
NM_001402.5 1181 MIMAT0000080 EEF1A1 5113.77 CDS 4925.77 hsa-miR-24-3p 5456.39 0.027 188 0.508
NM_001402.5 1256 MIMAT0000101 EEF1A1 5113.77 CDS 4566.77 hsa-miR-103a-3p 1731.32 0.089 547 4.893
NM_001402.5 1370 MIMAT0003393 EEF1A1 5113.77 CDS 4892.77 hsa-miR-425-5p 221.047 0.058 221 1.278
NM_001402.5 1395 MIMAT0000077 EEF1A1 5113.77 CDS 4448.77 hsa-miR-22-3p 753.932 0.019 100 0.195
NM_001402.5 1395 MIMAT0001341 EEF1A1 5113.77 CDS 4448.77 hsa-miR-424-5p 2238.16 0.019 115 0.218
NM_001402.5 1395 MIMAT0000068 EEF1A1 5113.77 CDS 4448.77 hsa-miR-15a-5p 6286.37 0.019 134 0.253
NM_001402.5 1395 MIMAT0000417 EEF1A1 5113.77 CDS 4448.77 hsa-miR-15b-5p 6512.89 0.019 135 0.255
NM_001402.5 1395 MIMAT0000069 EEF1A1 5113.77 CDS 4448.77 hsa-miR-16-5p 112020.0 0.019 181 0.342
NM_001402.5 1640 MIMAT0000077 EEF1A1 5113.77 3'UTR 4988.77 hsa-miR-22-3p 753.932 0.023 125 2.869
NM_001402.5 1956 MIMAT0004493 EEF1A1 5113.77 3'UTR 4744.77 hsa-miR-20a-3p 470.084 0.073 369 26.942
NM_001402.5 1964 MIMAT0000101 EEF1A1 5113.77 3'UTR 4744.77 hsa-miR-103a-3p 1731.32 0.018 108 1.994
NM_001402.5 2001 MIMAT0000080 EEF1A1 5113.77 3'UTR 4987.77 hsa-miR-24-3p 5456.39 0.018 126 2.316
NM_001402.5 2030 MIMAT0000101 EEF1A1 5113.77 3'UTR 5007.77 hsa-miR-103a-3p 1731.32 0.018 106 1.957
NM_001402.5 2527 MIMAT0000080 EEF1A1 5113.77 3'UTR 4894.77 hsa-miR-24-3p 5456.39 0.021 144 3.005
NM_001402.5 2533 MIMAT0000424 EEF1A1 5113.77 3'UTR 4894.77 hsa-miR-128-3p 219.33 0.077 219 16.972
NM_001402.5 2684 MIMAT0000765 EEF1A1 5113.77 3'UTR 4974.77 hsa-miR-335-5p 2539.41 0.021 139 2.987
NM_001402.5 2805 MIMAT0000086 EEF1A1 5113.77 3'UTR 4898.77 hsa-miR-29a-3p 714.822 0.019 96 1.793

Cite us

Weill N, Lisi V, Scott N, Dallaire P, Pelloux J, Major F. MirBooking simulates the stoichiometric mode of action of microRNAs, Nucleic Acids Res. 2015 43(14):6730-8.