miRBooking-scan explore miRBooking

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

Not interested in HELA? Choose a different cell line.

HELA

Expression profiling by array. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34681

You're now looking into HELA 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.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

target_accession position mirna_accession target_name target_quantity location vacancy mirna_name mirna_quantity probability occupancy silencing
NM_002046.5 1 MIMAT0005892 GAPDH 1110.29 5'UTR 1010.29 hsa-miR-1304-5p 640.865 0.087 100 0.868
NM_002046.5 3 MIMAT0002835 GAPDH 1110.29 5'UTR 1010.29 hsa-miR-526b-5p 662.97 0.065 76 0.495
NM_002046.5 21 MIMAT0004564 GAPDH 1110.29 5'UTR 916.29 hsa-miR-214-5p 582.89 0.022 26 0.058
NM_002046.5 22 MIMAT0003240 GAPDH 1110.29 5'UTR 916.29 hsa-miR-575 527.931 0.084 94 0.79
NM_002046.5 27 MIMAT0000080 GAPDH 1110.29 5'UTR 916.29 hsa-miR-24-3p 26827.5 0.107 194 2.066
NM_002046.5 29 MIMAT0002174 GAPDH 1110.29 5'UTR 916.29 hsa-miR-484 1183.33 0.111 140 1.55
NM_002046.5 29 MIMAT0000450 GAPDH 1110.29 5'UTR 916.29 hsa-miR-149-5p 1457.1 0.022 29 0.063
NM_002046.5 39 MIMAT0005939 GAPDH 1110.29 5'UTR 916.29 hsa-miR-1281 701.271 0.108 126 1.356
NM_002046.5 40 MIMAT0000750 GAPDH 1110.29 5'UTR 916.29 hsa-miR-340-3p 483.409 0.019 22 0.042
NM_002046.5 44 MIMAT0002875 GAPDH 1110.29 5'UTR 916.29 hsa-miR-504-5p 504.002 0.021 23 0.048
NM_002046.5 46 MIMAT0000446 GAPDH 1110.29 5'UTR 916.29 hsa-miR-127-3p 1646.59 0.018 25 0.046
NM_002046.5 61 MIMAT0004983 GAPDH 1110.29 5'UTR 984.29 hsa-miR-940 852.508 0.038 45 0.169
NM_002046.5 62 MIMAT0006767 GAPDH 1110.29 5'UTR 984.29 hsa-miR-1827 480.95 0.021 23 0.049
NM_002046.5 63 MIMAT0003320 GAPDH 1110.29 5'UTR 984.29 hsa-miR-650 686.415 0.02 23 0.046
NM_002046.5 65 MIMAT0003336 GAPDH 1110.29 5'UTR 984.29 hsa-miR-658 729.215 0.024 29 0.07
NM_002046.5 68 MIMAT0004284 GAPDH 1110.29 5'UTR 1032.29 hsa-miR-675-5p 681.192 0.035 40 0.139
NM_002046.5 69 MIMAT0018925 GAPDH 1110.29 5'UTR 1032.29 hsa-miR-1268b 3090.61 0.034 49 0.168
NM_002046.5 70 MIMAT0004694 GAPDH 1110.29 5'UTR 1032.29 hsa-miR-342-5p 652.246 0.039 44 0.171
NM_002046.5 70 MIMAT0004982 GAPDH 1110.29 5'UTR 1032.29 hsa-miR-939-5p 950.908 0.027 34 0.092
NM_002046.5 73 MIMAT0003307 GAPDH 1110.29 5'UTR 1032.29 hsa-miR-637 592.854 0.038 44 0.167
NM_002046.5 90 MIMAT0000080 GAPDH 1110.29 5'UTR 974.29 hsa-miR-24-3p 26827.5 0.025 45 0.111
NM_002046.5 91 MIMAT0004501 GAPDH 1110.29 5'UTR 974.29 hsa-miR-27a-5p 1610.78 0.024 33 0.08
NM_002046.5 94 MIMAT0005576 GAPDH 1110.29 5'UTR 974.29 hsa-miR-1226-5p 633.0 0.019 22 0.042
NM_002046.5 97 MIMAT0003272 GAPDH 1110.29 5'UTR 974.29 hsa-miR-604 567.114 0.105 119 1.247
NM_002046.5 98 MIMAT0003317 GAPDH 1110.29 5'UTR 974.29 hsa-miR-647 877.197 0.027 33 0.089
NM_002046.5 99 MIMAT0004689 GAPDH 1110.29 5'UTR 974.29 hsa-miR-377-5p 528.158 0.027 31 0.084
NM_002046.5 99 MIMAT0002175 GAPDH 1110.29 5'UTR 974.29 hsa-miR-485-5p 668.361 0.091 105 0.952
NM_002046.5 100 MIMAT0003320 GAPDH 1110.29 5'UTR 974.29 hsa-miR-650 686.415 0.028 32 0.089
NM_002046.5 102 MIMAT0004589 GAPDH 1110.29 5'UTR 974.29 hsa-miR-30b-3p 510.115 0.035 39 0.135
NM_002046.5 102 MIMAT0005952 GAPDH 1110.29 5'UTR 974.29 hsa-miR-1321 633.0 0.033 38 0.125
NM_002046.5 118 MIMAT0004762 GAPDH 1110.29 5'UTR 974.29 hsa-miR-486-3p 706.471 0.019 22 0.042
NM_002046.5 119 MIMAT0004926 GAPDH 1110.29 5'UTR 974.29 hsa-miR-708-5p 615.765 0.02 24 0.049
NM_002046.5 119 MIMAT0000085 GAPDH 1110.29 5'UTR 974.29 hsa-miR-28-5p 2306.84 0.02 28 0.057
NM_002046.5 120 MIMAT0004982 GAPDH 1110.29 5'UTR 974.29 hsa-miR-939-5p 950.908 0.022 27 0.059
NM_002046.5 121 MIMAT0003945 GAPDH 1110.29 5'UTR 974.29 hsa-miR-765 867.25 0.095 115 1.09
NM_002046.5 134 MIMAT0004986 GAPDH 1110.29 5'UTR 995.29 hsa-miR-943 785.359 0.063 76 0.481
NM_002046.5 137 MIMAT0000734 GAPDH 1110.29 5'UTR 995.29 hsa-miR-380-5p 511.94 0.023 26 0.059
NM_002046.5 137 MIMAT0003227 GAPDH 1110.29 5'UTR 995.29 hsa-miR-563 735.085 0.023 27 0.061
NM_002046.5 139 MIMAT0002175 GAPDH 1110.29 5'UTR 995.29 hsa-miR-485-5p 668.361 0.02 22 0.043
NM_002046.5 143 MIMAT0004796 GAPDH 1110.29 5'UTR 995.29 hsa-miR-576-3p 557.612 0.02 22 0.043
NM_002046.5 157 MIMAT0004552 GAPDH 1110.29 5'UTR 1034.29 hsa-miR-139-3p 557.612 0.02 23 0.045
NM_002046.5 160 MIMAT0000430 GAPDH 1110.29 5'UTR 1034.29 hsa-miR-138-5p 4750.03 0.028 43 0.122
NM_002046.5 164 MIMAT0005951 GAPDH 1110.29 5'UTR 1045.29 hsa-miR-1307-3p 1476.27 0.032 42 0.135
NM_002046.5 165 MIMAT0001340 GAPDH 1110.29 5'UTR 1045.29 hsa-miR-423-3p 3927.43 0.044 65 0.285
NM_002046.5 170 MIMAT0003314 GAPDH 1110.29 5'UTR 1045.29 hsa-miR-644a 569.378 0.019 21 0.039
NM_002046.5 172 MIMAT0004796 GAPDH 1110.29 5'UTR 1045.29 hsa-miR-576-3p 557.612 0.02 23 0.046
NM_002046.5 191 MIMAT0000762 GAPDH 1110.29 CDS 1030.29 hsa-miR-324-3p 934.824 0.02 25 0.05
NM_002046.5 197 MIMAT0002170 GAPDH 1110.29 CDS 1030.29 hsa-miR-412-3p 755.048 0.067 80 0.54
NM_002046.5 231 MIMAT0003230 GAPDH 1110.29 CDS 897.29 hsa-miR-566 736.352 0.045 54 0.245
NM_002046.5 233 MIMAT0002839 GAPDH 1110.29 CDS 897.29 hsa-miR-525-3p 476.325 0.026 29 0.076

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.