• What is this for?
    1. For a list of up- and downregulated (1) mRNAs and (2) mRNAs 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 general and disease-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 p-value treshold for the overrepresentation analysis, the associated disease, and the confidence level (experimentally validated and/or predicted interactions)
  • 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 TFmiR?
    These databases are used:
    Interaction Databases (P/E) * Genes miRNAs Regulatory links Version /frozen date
    TF → gene TRANSFAC  (E) [1] 1279 -- 2943 V11.4
    OregAnno (E) [2] 1132 -- 1083 Nov 2010
    TRED (P) [3] 3038 -- 6462 2007
    TF → miRNA TransmiR (E) [4] 158 175 567 V1.2, Jan 2013
    PMID20584335 (E) [5] 58 56 102 Apr 2009
    ChipBase (P) [6] 119 1380 33087 V1.1, Nov 2012
    miRNA → gene miRTarBase (E) [7] 2244 551 5640 V4.5, Nov 2013
    TarBase (E) [8] 422 79 492 V7.0
    miRecords (E) [9] 543 157 780 Mar 2009
    starBase (P) [10] 5720 249 56051 V2.0, Sept 2013
    miRNA → miRNA PmmR(P) [11] -- 312 3846 Mar 2011
    (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