title: DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators.
abstract: microRNAs (miRNAs) are small non-coding RNAs that actively fine-tune gene expression. The accurate characterization of the mechanisms underlying miRNA transcription regulation will further expand our knowledge regarding their implication in homeostatic and pathobiological networks. Aim of DIANA-miRGen v3.0 (http://www.microrna.gr/mirgen) is to provide for the first time accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. To this end, more than 7.3 billion RNA-, ChIP- and DNase-Seq next generation sequencing reads were analyzed/assembled and combined with state-of-the-art miRNA TSS prediction and TF binding site identification algorithms. The new database schema and web interface facilitates user interaction, provides advanced queries and innate connection with other DIANA resources for miRNA target identification and pathway analysis. The database currently supports 276 miRNA TSSs that correspond to 428 precursors and >19M binding sites of 202 TFs on a genome-wide scale in nine cell-lines and six tissues of Homo sapiens and Mus musculus.
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece Hellenic Pasteur Institute, 115 21 Athens, Greece georgakilas@inf.uth.gr.
authors.forename: Georgios
authors.initials: G
authors.lastname: Georgakilas
authors.affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece Hellenic Pasteur Institute, 115 21 Athens, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, 11527 Athens, Greece.
authors.forename: Ioannis S
authors.initials: IS
authors.lastname: Vlachos
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece University of Peloponnese, Department of Informatics and Telecommunications, 22100 Tripoli, Greece.
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Zagganas
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, 382 21 Volos, Greece Hellenic Pasteur Institute, 115 21 Athens, Greece.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Paraskevopoulou
authors.affiliation: 'Athena' Research and Innovation Center, 11524 Athens, Greece School of Electrical and Computer Engineering, NTUA, 15773 Zografou, Greece.
authors.forename: Ilias
authors.initials: I
authors.lastname: Kanellos
authors.affiliation: School of Electrical and Computer Engineering, NTUA, 15773 Zografou, Greece Greek Research and Technology Network (GRNET), Athens 11527, Greece.
authors.forename: Panayiotis
authors.initials: P
authors.lastname: Tsanakas
authors.affiliation: Greek Research and Technology Network (GRNET), Athens 11527, Greece.
authors.forename: Dimitris
authors.initials: D
authors.lastname: Dellis
authors.affiliation: Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Fevgas
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, 382 21 Volos, Greece Hellenic Pasteur Institute, 115 21 Athens, Greece 'Athena' Research and Innovation Center, 11524 Athens, Greece arhatzig@inf.uth.gr.
authors.forename: Artemis G
authors.initials: AG
authors.lastname: Hatzigeorgiou
mesh_terms: D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D011401:Promoter Regions, Genetic; D014157:Transcription Factors / Q000378:metabolism; D024363:Transcription Initiation Site
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors