title: DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data.
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.
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, Athens 11527, Greece ivlachos@lessr.eu.
authors.forename: Ioannis S
authors.initials: IS
authors.lastname: Vlachos
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece.
authors.forename: Thanasis
authors.initials: T
authors.lastname: Vergoulis
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Paraskevopoulou
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece.
authors.forename: Filopoimin
authors.initials: F
authors.lastname: Lykokanellos
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Georgakilas
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece.
authors.forename: Penny
authors.initials: P
authors.lastname: Georgiou
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece.
authors.forename: Serafeim
authors.initials: S
authors.lastname: Chatzopoulos
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece.
authors.forename: Dimitra
authors.initials: D
authors.lastname: Karagkouni
authors.affiliation: Miroculus, San Francisco, CA 94107, USA.
authors.forename: Foteini
authors.initials: F
authors.lastname: Christodoulou
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece.
authors.forename: Theodore
authors.initials: T
authors.lastname: Dalamagas
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 38221 Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece arhatzig@uth.gr.
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D020407:Internet; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D012984:Software; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors