• What is this for?
    1. For a list of up- and downregulated (1) mRNAs and (2) miRNAs from a differential analysis, TFmiR builds a co-regulatory network based on parameters set (3).
    2. Database retrieval of predicted and experimentally validated interactions, based on confidence level
    3. Generate complete, disease-, tissue-, process-, disease & process-, tissue & process- and disease & tissue-specific co-regulatory networks
  • What does the input look like?
    The input consists of
    1. a list of mRNA identifiers with an indicator for their up- or downregulation (-1/1)
    2. (optional) a list of miRNA identifiers with an indicator for their up- or downregulation (-1/1)
    3. parameters that determine the enrichment p-value (mRNA/miRNA), p-value treshold for the overrepresentation analysis, the associated disease, the associated process, the associated tissue, the confidence level (experimentally validated and/or predicted interactions), PPI/GGI threshold and randomization method for detection of motifs.
  • How exactly has a file to look like?
    An input file (for mRNA, miRNA analogous) looks like: 
    AATK	-1
ABCB8	1
ABCG4	1
ABHD10	1
ABLIM1	-1
ABT1	1
etc...
    However, you can try the dataset we used for breast neoplasm:
    mirna.bc.txt
     
    mrna.bc.txt

    Alternatively, you can just click the "Load example data" at the start screen to load the dataset automatically.
    • Which databases are incorporated into TFmiR2 for human?
    These databases are used:
    Interaction Databases (P/E) * Genes miRNAs Regulatory links Version /frozen date
    TF → gene TRANSFAC  (E) [1] 1279 -- 2943 V11.4
    TRRUST  (E) [2] 2862 -- 8427 V2
    OregAnno (E) [3] 23506 -- 215832 Nov 2016
    TRED (P) [4] 3038 -- 6462 2007
    TF → miRNA TransmiR (E) [5] 369 402 2678 V2.0, Oct 2018
    PMID20584335 (E) [6] 58 56 102 Apr 2009
    ChipBase (P) [7] 119 1380 33087 V1.1, Nov 2012
    TransmiR (E) [5] 600 1861 1203375 V2.0, Oct 2018
    miRNA → gene miRTarBase (E) [8] 2849 740 8489 V7.0, Sep 2013
    TarBase (E) [9] 422 79 492 V7.0
    miRecords (E) [10] 1106 280 1716 April 2013
    starBase (P) [11] 1 190 190 V3.0, 2018
    miRNA → miRNA PmmR(P) [12] -- 312 3846 Mar 2011
    gene → gene mentha(E) [13] 18861 -- 339559 June 2019
    STRING(P) [14] 19344 -- 11754228 v11.0
  • Which databases are incorporated into TFmiR2 for mouse?
    These databases are used:
    Interaction Databases (P/E) * Genes miRNAs Regulatory links Version /frozen date
    TF → gene TRRUST  (E) [2] 2456 -- 6490 V2
    OregAnno (E) [3] 22209 -- 54376 Nov 2016
    ITFB (P) [15] 5118 -- 34679 --
    TF → miRNA TransmiR (E) [5] 147 230 748 V2.0, Oct 2018
    ChipBase (P) [6] 63 623 5764 --
    TransmiR (E) [5] 534 1186 449894 V2.0, Oct 2018
    miRNA → gene miRTarBase (E) [8] 846 292 1526 --
    TarBase (E) [8] 83 44 122 --
    miRecords (E) [9] 274 146 384 April 2013
    starBase (P) [10] 1 84 98 --
    gene → gene mentha(E) [13] 14328 -- 7325 June 2019
    STRING(P) [14] 21291 -- 11944806 v11.0
    (P) means predicted interactions and (E) means experimentally validated interactions.
  • I am still stuck!
    Contact us for help:
    m.hamed@bioinformatik.uni-saarland.de
    christian.spaniol@bioinformatik.uni-saarland.de
    maryam.nazarieh@bioinformatik.uni-saarland.de
    thorsten.will@bioinformatik.uni-saarland.de