Centre for Cancer Research - Research Publications

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Start date: 2000 × End date: 2009 × Author: Grimmond, Sean × Author: Pang, Ken Chung-Ren ×

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    NRED: a database of long noncoding RNA expression
    Dinger, ME ; Pang, KC ; Mercer, TR ; Crowe, ML ; Grimmond, SM ; Mattick, JS (OXFORD UNIV PRESS, 2009-01)
    In mammals, thousands of long non-protein-coding RNAs (ncRNAs) (>200 nt) have recently been described. However, the biological significance and function of the vast majority of these transcripts remain unclear. We have constructed a public repository, the Noncoding RNA Expression Database (NRED), which provides gene expression information for thousands of long ncRNAs in human and mouse. The database contains both microarray and in situ hybridization data, much of which is described here for the first time. NRED also supplies a rich tapestry of ancillary information for featured ncRNAs, including evolutionary conservation, secondary structure evidence, genomic context links and antisense relationships. The database is available at http://jsm-research.imb.uq.edu.au/NRED, and the web interface enables both advanced searches and data downloads. Taken together, NRED should significantly advance the study and understanding of long ncRNAs, and provides a timely and valuable resource to the scientific community.
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    The abundance of short proteins in the mammalian proteome
    Frith, MC ; Forrest, AR ; Nourbakhsh, E ; Pang, KC ; Kai, C ; Kawai, J ; Carninci, P ; Hayashizaki, Y ; Bailey, TL ; Grimmond, SM ; Blake, J ; Hancock, J ; Pavan, B ; Stubbs, L (PUBLIC LIBRARY SCIENCE, 2006-04)
    Short proteins play key roles in cell signalling and other processes, but their abundance in the mammalian proteome is unknown. Current catalogues of mammalian proteins exhibit an artefactual discontinuity at a length of 100 aa, so that protein abundance peaks just above this length and falls off sharply below it. To clarify the abundance of short proteins, we identify proteins in the FANTOM collection of mouse cDNAs by analysing synonymous and non-synonymous substitutions with the computer program CRITICA. This analysis confirms that there is no real discontinuity at length 100. Roughly 10% of mouse proteins are shorter than 100 aa, although the majority of these are variants of proteins longer than 100 aa. We identify many novel short proteins, including a "dark matter" subset containing ones that lack detectable homology to other known proteins. Translation assays confirm that some of these novel proteins can be translated and localised to the secretory pathway.