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...rformed a major update on target prediction data by employing the up-to-date miRNAand target gene annotations. AllmiRNAsequences and annotations were downloaded from miRBase (version 21) in June 2014 =-=(7)-=-. We have adopted the NCBI RefSeq database for identification of 3′-UTR sequences. In brief, RefSeq sequences were downloaded fromNCBI’s ftp site (8) and further parsed with the BioPerl program to obt...

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... (25). INTERFACE Querying the database The database query can be performed by entering any combination of miRNA and/or gene names or supported identifiers (ENSEMBL (26) gene IDs for genes and miRBase =-=(27)-=- MIMAT accessions for miRNAs). If genes and miRNAs are concurrently provided, TarBase will return all indexed interactions of the selected miRNAs with any of the provided genes. The interface (Figure ...

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...on, the user can enter one or more miRNA IDs, e.g. hsa-let-7a-3p, mmu-mir-128-1, cel-mir-90. For this option, the sequences are retrieved from an internal database built from release 20 of themiRBase =-=(17)-=-. Alternatively, one ormoremiRNA sequences can be pasted into the input box in FASTA format, or uploaded from aFASTAfile (Figure 1). There is no limit on the number of miRNA sequences that can be ente...

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...s and miRNA combinations using all datasets, or their subsets (GO cellular component, biological processes or molecular function). Gene and miRNA annotations are derived from Ensembl (19) and miRBase =-=(20)-=-, respectively. Single nucleotide polymorphism locations and pathogenicity are derived from dbSNP (21). miRNA:gene interactions are derived from the in silico miRNA target prediction algorithms: DIANA...

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...With that purpose, we used four different databases of experimentally verified interactions between miRNAs and mRNAs (16–19) and a dictionary to translate everymiRNA nomenclatures into miRBase format =-=(20)-=-. Since almost every miRNA–mRNA interaction found to date is an inhibiting one, from a list of up-regulated miRNAs we could infer a list of down-regulated genes. Likewise, from a list of downregulated...

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...ment, cellular differentiation, proliferation, apoptosis and the pathogenesis of human diseases such as cancer and metabolic disorders (8). In human, more than 1800 miRNAs have been identified so far =-=(9)-=-. In canonical human miRNA biogenesis, primary miRNA transcripts (pri-miRNAs) are initially transcribed forming stem-loop structures. Maturation of miRNAs occurs in two steps. First, pri-miRNAs are pr...

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...companied by the need for a central registry and repository database and an interface for their systematic annotation. Such an environment, ‘microRNA Registry’ (miRBase) was first established in 2002 =-=[6, 7]-=-. miRBase aimed to give standardized names to miRNAs by providing a web interface for the submission of the miRNA sequence during the pre-publication process. To prevent misannotations and overlapping...

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... (25). INTERFACE Querying the database The database query can be performed by entering any combination of miRNA and/or gene names or supported identifiers (ENSEMBL (26) gene IDs for genes and miRBase =-=(27)-=- MIMAT accessions for miRNAs). If genes and miRNAs are concurrently provided, TarBase will return all indexed interactions of the selected miRNAs with any of the provided genes. The interface (Figure ...

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...With that purpose, we used four different databases of experimentally verified interactions between miRNAs and mRNAs (16–19) and a dictionary to translate everymiRNA nomenclatures into miRBase format =-=(20)-=-. Since almost every miRNA–mRNA interaction found to date is an inhibiting one, from a list of up-regulated miRNAs we could infer a list of down-regulated genes. Likewise, from a list of downregulated...

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...RNAand its target is not required, although base pairing of nucleotides at 2–8 positions of the miRNA, the so-called seed region, is generally essential (2). The human genome encodes over 2000 miRNAs =-=(9)-=-, which are estimated to regulate the expression of most protein-coding genes (10), thereby exhibiting a tremendous impact on normal developmental and physiological processes and disease states. Recen...