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DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG - Nucleic Acids Res. (2014)

Bottom Line: The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments.More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database.DIANA-TarBase v7.0 is freely available.

View Article: PubMed Central - PubMed

Affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, 11527 Athens, Greece arhatzig@uth.gr dalamag@imis.athena-innovation.gr ivlachos@lessr.eu.

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Entries per methodology for TarBase v7.0 and TarBase v6.0. The y-axis (number of entries) is in log2 scale and each mark signifies doubling of available entries.
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Figure 1: Entries per methodology for TarBase v7.0 and TarBase v6.0. The y-axis (number of entries) is in log2 scale and each mark signifies doubling of available entries.

Mentions: The database comprises more than half a million interactions spanning 24 species, a 9- to 250-fold increase compared to TarBase 6.0 and other manually curated databases, including miRTarBase and miRecords. The database encompasses interactions derived from the widest variety of experiments to date, which are performed utilizing 28 different experimental techniques, 356 cell types and 59 different tissues. Results from all methodologies presented in Table 1 and their variations are included to the database. The number of targets derived from major method classes is depicted in Figure 1. Importantly, we have paid significant attention to curate articles utilizing highly specific low-yield techniques, such as reporter genes, as well as state-of-the-art methodologies, such as CLIP-Seq and CLASH experiments. The updated database contains more than 7500 interactions derived from specific techniques (4-fold increase versus TarBase v6.0) and more than 500 000 interactions derived from high-throughput experiments (9-fold increase versus TarBase v6.0). Specifically, DIANA-TarBase v7.0 incorporates data derived from 154 CLIP-Seq/CLASH data sets, as well as more than a hundred other high-throughput data sets including Degradome-Seq (22), AGO-IP (7), biotin pull-down (7), miTRAP (23), 3′Life (24) and IMPACT-Seq (25).


DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG - Nucleic Acids Res. (2014)

Entries per methodology for TarBase v7.0 and TarBase v6.0. The y-axis (number of entries) is in log2 scale and each mark signifies doubling of available entries.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383989&req=5

Figure 1: Entries per methodology for TarBase v7.0 and TarBase v6.0. The y-axis (number of entries) is in log2 scale and each mark signifies doubling of available entries.
Mentions: The database comprises more than half a million interactions spanning 24 species, a 9- to 250-fold increase compared to TarBase 6.0 and other manually curated databases, including miRTarBase and miRecords. The database encompasses interactions derived from the widest variety of experiments to date, which are performed utilizing 28 different experimental techniques, 356 cell types and 59 different tissues. Results from all methodologies presented in Table 1 and their variations are included to the database. The number of targets derived from major method classes is depicted in Figure 1. Importantly, we have paid significant attention to curate articles utilizing highly specific low-yield techniques, such as reporter genes, as well as state-of-the-art methodologies, such as CLIP-Seq and CLASH experiments. The updated database contains more than 7500 interactions derived from specific techniques (4-fold increase versus TarBase v6.0) and more than 500 000 interactions derived from high-throughput experiments (9-fold increase versus TarBase v6.0). Specifically, DIANA-TarBase v7.0 incorporates data derived from 154 CLIP-Seq/CLASH data sets, as well as more than a hundred other high-throughput data sets including Degradome-Seq (22), AGO-IP (7), biotin pull-down (7), miTRAP (23), 3′Life (24) and IMPACT-Seq (25).

Bottom Line: The new interface provides also advanced information ranging from the binding site location, as identified experimentally as well as in silico, to the primer sequences used for cloning experiments.More than half a million miRNA:gene interactions have been curated from published experiments on 356 different cell types from 24 species, corresponding to 9- to 250-fold more entries than any other relevant database.DIANA-TarBase v7.0 is freely available.

View Article: PubMed Central - PubMed

Affiliation: DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, 382 21 Volos, Greece Laboratory for Experimental Surgery and Surgical Research 'N.S. Christeas', Medical School of Athens, University of Athens, 11527 Athens, Greece arhatzig@uth.gr dalamag@imis.athena-innovation.gr ivlachos@lessr.eu.

Show MeSH
Related in: MedlinePlus