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An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P - Nucleic Acids Res. (2014)

Bottom Line: To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation.Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data.As a result, a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download.

View Article: PubMed Central - PubMed

Affiliation: Center for Medical Genetics, Ghent University, Ghent 9000, Belgium.

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Many lncRNA loci are conserved in mouse or zebrafish. Locus conservation is a novel tool to determine the orthologous locus of a human lncRNA in another species. When the order of the flanking protein-coding genes is conserved in another species, the lncRNA locus is considered conserved. The majority of the conserved loci in zebrafish are also conserved in mouse, this fraction is depicted in gray.
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Figure 2: Many lncRNA loci are conserved in mouse or zebrafish. Locus conservation is a novel tool to determine the orthologous locus of a human lncRNA in another species. When the order of the flanking protein-coding genes is conserved in another species, the lncRNA locus is considered conserved. The majority of the conserved loci in zebrafish are also conserved in mouse, this fraction is depicted in gray.

Mentions: The identification of orthologous lncRNAs is an important step for animal modeling and functional research across species. Conservation of gene order is a straightforward metric often used in comparative genomics. We applied the concept of gene order conservation to determine the orthologous locus of a lncRNA in another species. Using the Ensembl Compara API, we have assessed the conservation in the order of the flanking protein-coding genes. Currently, orthologs for non-coding genes are not as well annotated as for protein-coding genes, flanking non-coding genes were therefore not taken into account. When the order is conserved in mouse or zebrafish we report the locus as conserved. In this way, we find locus conservation for 55% of the human lncRNA genes in mouse, and for 27% in zebrafish (Figure 2). The majority of the conserved loci in zebrafish are also conserved in mouse, as one would expect. While locus conservation is no proof for the functional conservation of the lncRNA itself, it may serve a first step in finding the orthologous lncRNA.


An update on LNCipedia: a database for annotated human lncRNA sequences.

Volders PJ, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P - Nucleic Acids Res. (2014)

Many lncRNA loci are conserved in mouse or zebrafish. Locus conservation is a novel tool to determine the orthologous locus of a human lncRNA in another species. When the order of the flanking protein-coding genes is conserved in another species, the lncRNA locus is considered conserved. The majority of the conserved loci in zebrafish are also conserved in mouse, this fraction is depicted in gray.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383901&req=5

Figure 2: Many lncRNA loci are conserved in mouse or zebrafish. Locus conservation is a novel tool to determine the orthologous locus of a human lncRNA in another species. When the order of the flanking protein-coding genes is conserved in another species, the lncRNA locus is considered conserved. The majority of the conserved loci in zebrafish are also conserved in mouse, this fraction is depicted in gray.
Mentions: The identification of orthologous lncRNAs is an important step for animal modeling and functional research across species. Conservation of gene order is a straightforward metric often used in comparative genomics. We applied the concept of gene order conservation to determine the orthologous locus of a lncRNA in another species. Using the Ensembl Compara API, we have assessed the conservation in the order of the flanking protein-coding genes. Currently, orthologs for non-coding genes are not as well annotated as for protein-coding genes, flanking non-coding genes were therefore not taken into account. When the order is conserved in mouse or zebrafish we report the locus as conserved. In this way, we find locus conservation for 55% of the human lncRNA genes in mouse, and for 27% in zebrafish (Figure 2). The majority of the conserved loci in zebrafish are also conserved in mouse, as one would expect. While locus conservation is no proof for the functional conservation of the lncRNA itself, it may serve a first step in finding the orthologous lncRNA.

Bottom Line: To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation.Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data.As a result, a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download.

View Article: PubMed Central - PubMed

Affiliation: Center for Medical Genetics, Ghent University, Ghent 9000, Belgium.

Show MeSH