Multi Target Scan
Bioinformatics, IRCCS AOU San Martino IST, Genova
paolo.romano@hsanmartino.it


Welcome to Multi Target Scan (MTS), the new tool for automating search of gene targets for many miRNA in a single run through Target Scan.

The use of MTS should be straightforward. Results are displayed in a simple format. Nevertheless, should you have any problem, see below some information.

This document is under active development. Please forgive us for any issues... and email us your comments!

You may find it useful to perform a first analysis by using the example input data file miRNAlist1.txt that is provided for testing purposes.
In the following, you will find links to output files that were generated by MTS from this input data.

Data file formats

Here, the formats that are used by MTS are shortly introduced.


Input data file
The input data file is a simple text file including a list of miRNA names, one per line. The required input consists in a list of miRNA names, written according to the miRBase naming format (e.g. hsa-miR-121), which are included in text file, one per line. See the complete list of accepted names.

Example

hsa-mir-1226
hsa-mir-3180-3p
hsa-mir-3185
hsa-mir-3188
hsa-mir-3648
hsa-mir-3656
hsa-mir-425
hsa-mir-4466
hsa-mir-4497
hsa-mir-4508
hsa-mir-4523
hsa-mir-4649-3p


Output data file
Results are reported in the output page as a simple table. The format of this table is essentially the same used by Target Scan. For each interaction, the table includes the representative miRNA in the miRNA family of the queries miRNA, i.e. the miRNA with the lowest total context+ score for the given interaction in the family or, in case of equality, the miRNA with the lowest number / letter. Additionally, the name of the queried miRNA (the miRNA used for the query) is also reported.
The table may be ordered by queried miRNA, by gene symbol, and by representative miRNA. This effect can be obtained by clicking on the column header of the desired information. By default, the table is ordered by queried miRNA.
For each record, the following external links are provided:

See an example output page in figure 1 below (click to enlarge).

Results are also reported in a text file, formatted as a CSV (comma separated values) file, with fields' contents enclosed by double quote characters ("). In this case, no links are provided and the jobnumber is added.
Example file
The following file was generated by MTS from the example input data file. This file can easily be read by any word processor or spreadsheet manager, e.g. Excel.

Here is an excerpt (10 results out of more than 14,000).
"jobnumber","target_gene_number","target_gene_symbol","transcript_accession","target_gene_name","cs_total","cs_8mer","cs_7mer_m8","cs_7mer_1A","pcs_total","pcs_8mer","pcs_7mer_m8","pcs_7mer_1A","rep_mirna","context_score","agg_pct","taxid","mirna_member","query_mirna"
"20150204_test","4144","MAT2A","NM_005911","methionine adenosyltransferase II, alpha",2,0,2,0,2,0,2,0,"hsa-miR-1226",-0.76,"N/A",9606,"miR-1226/1656/1838","hsa-mir-1226"
"20150204_test","6497","SKI","NM_003036","v-ski sarcoma viral oncogene homolog (avian)",1,0,1,0,1,1,0,0,"hsa-miR-3648",-0.54,"N/A",9606,"miR-3648","hsa-mir-3648"
"20150204_test","84630","TTBK1","NM_032538","tau tubulin kinase 1",1,1,0,0,2,0,2,0,"hsa-miR-3656",-0.78,"N/A",9606,"miR-3656","hsa-mir-3656"
"20150204_test","26512","INTS6","NM_001039937","integrator complex subunit 6",1,0,0,1,1,1,0,0,"hsa-miR-3185",-0.42,"N/A",9606,"miR-3185","hsa-mir-3185"
"20150204_test","253260","RICTOR","NM_152756","RPTOR independent companion of MTOR, complex 2",2,1,1,0,2,0,0,2,"hsa-miR-3188",-0.88,"N/A",9606,"miR-879/3188","hsa-mir-3188"
"20150204_test","5799","PTPRN2","NM_002847","protein tyrosine phosphatase, receptor type, N polypeptide 2",1,1,0,0,0,0,0,0,"hsa-miR-425",-0.46,"< 0.1",0,"","hsa-mir-425"
"20150204_test","255057","C19orf26","NM_152769","chromosome 19 open reading frame 26",1,1,0,0,1,0,0,1,"hsa-miR-4508",-0.63,"N/A",9606,"miR-4508","hsa-mir-4508"
"20150204_test","79763","ISOC2","NM_001136201","isochorismatase domain containing 2",1,1,0,0,0,0,0,0,"hsa-miR-4497",-0.52,"N/A",9606,"miR-4497","hsa-mir-4497"
"20150204_test","2677","GGCX","NM_000821","gamma-glutamyl carboxylase",1,1,0,0,0,0,0,0,"hsa-miR-675",-0.49,"N/A",9606,"miR-675-5p/4466","hsa-mir-4466"
"20150204_test","91","ACVR1B","NM_004302","activin A receptor, type IB",1,1,0,0,0,0,0,0,"hsa-miR-4523",-0.54,"N/A",9606,"miR-4523","hsa-mir-4523"

The information included in the output is shortly described in the following table:
posdatadescriptionexample values (see first result above)
1jobnumberjobnumber, a free text that uniquely define a job, as inserted by the user in the initial pageexample
2target_gene_numbera number, the Gene ID in NCBI Gene database4144
3target_gene_symbolthe official symbol of the gene in NCBI Gene database as provided by HGNCMAT2A
4transcript_accessionthe accession number of the reference sequence for the gene in NCBI GenBankNM_005911
5target_gene_namethe official full name of the gene in NCBI Gene database, as provided by HGNCmethionine adenosyltransferase II, alpha
6cs_totalthe total number of conserved sites2
7cs_8merthe number of conserved 8mer sites0
8cs_7mer_m8the number of conserved 7mer_m8 sites2
9cs_7mer_1Athe number of conserved 7mer_1A sites0
10pcs_totalthe total number of poorly conserved sites2
11pcs_8merthe number of poorly conserved 8mer sites0
12pcs_7mer_m8the number of poorly conserved 7mer_m8 sites2
13pcs_7mer_1Athe number of poorly conserved 7mer_1A sites0
14rep_mirnarepresentative miRNAi in the familyhsa-miR-1226
15context_scorethe sum of context+ scores for all sites for the miRNA.
The single context+ score for a site is the sum of the contribution of the following features:
site-type contribution, 3' pairing contribution, local AU contribution, position contribution, TA (target site abundance) contribution, SPS (seed-pairing stability) contribution
(see context+ score definition and Garcia et al., 2011)
-0.76
16agg_pctthe probability of conserved targeting
(see PCT definition and Friedman et al., 2009)
N/A
17taxidTaxon ID9606
18mirna_membermiRNA family of the queried miRNAmiR-1226/1656/1838
19query_mirnathe miRNA used for the queryhsa-mir-1226

Definitions (from Target Scan)

8mer
An exact match to positions 2-8 of the mature miRNA (the seed + position 8) followed by an 'A'.
7mer-m8
An exact match to positions 2-8 of the mature miRNA (the seed + position 8).
7mer-1A
An exact match to positions 2-7 of the mature miRNA (the seed) followed by an 'A'.
broadly conserved
conserved across most vertebrates, usually to zebrafish
conserved
conserved across most mammals, but usually not beyond placental mammals
seed region
positions 2-7 of a mature miRNA.
miRNA family
miRNAs with the same seed+m8 sequence (positions 2-8 of the mature miRNA).
representative miRNA
The miRNA in his family with the lowest total context+ score for the target gene or, in case of equality, the miRNA with the lowest number / letter.