@article{3170646,
    title = "DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with
crucial roles in NGS expression data",
    author = "Vlachos, Ioannis S. and Vergoulis, Thanasis and Paraskevopoulou, Maria and D. and Lykokanellos, Filopoimin and Georgakilas, Georgios and Georgiou, and Penny and Chatzopoulos, Serafeim and Karagkouni, Dimitra and and Christodoulou, Foteini and Dalamagas, Theodore and Hatzigeorgiou, and Artemis G.",
    journal = "Nucleic Acids Research",
    year = "2016",
    volume = "44",
    number = "W1",
    pages = "W128-W134",
    publisher = "Oxford University Press",
    issn = "0305-1048, 1362-4962",
    doi = "10.1093/nar/gkw455",
    abstract = "Differential expression analysis (DEA) is one of the main instruments
utilized for revealing molecular mechanisms in pathological and
physiological conditions. DIANA-mirExTra v2.0
(http://www.microrna.gr/mirextrav2) performs a combined DEA of mRNAs and
microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs)
playing important regulatory roles between two investigated states. The
web server uses as input miRNA/RNA-Seq read count data sets that can be
uploaded for analysis. Users can combine their data with 350
small-RNA-Seq and 65 RNA-Seq in-house analyzed libraries which are
provided by DIANA-mirExTra v2.0.
The web server utilizes miRNA:mRNA, TF:mRNA and TF:miRNA interactions
derived from extensive experimental data sets. More than 450 000 miRNA
interactions and 2 000 000 TF binding sites from specific or
high-throughput techniques have been incorporated, while accurate miRNA
TSS annotation is obtained from microTSS experimental/in silico
framework. These comprehensive data sets enable users to perform
analyses based solely on experimentally supported information and to
uncover central regulators within sequencing data: miRNAs controlling
mRNAs and TFs regulating mRNA or miRNA expression. The server also
supports predicted miRNA:gene interactions from DIANA-microT-CDS for 4
species (human, mouse, nematode and fruit fly). DIANA-mirExTra v2.0 has
an intuitive user interface and is freely available to all users without
any login requirement."
}