ABA ncRNA Database Information

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The ABA ncRNA Database provides a means to search the data from our analysis of the probes and targets in the Allen Brain Atlas. Results can be filtered on probe/target features and/or normalized ABA expression values (Level, Density, Rank). All search fields are optional (entering no selective criteria will output the complete probe database).

Detailed information, raw data, and methodology is available in the associated manuscript (open access):

Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008). Specific expression of long noncoding RNAs in the adult mouse brain. Proc Natl Acad Sci USA, 105(2): 716-721.

Contents

Finding an ncRNA associated with a particular gene

The database search interface does not presently allow the identification of ncRNAs thay may be associated with known genes. There are two approaches that can be used to search for potential ncRNAs associated with a specified gene:

1. Download Supplementary Table 5, which contains all ncRNAs that we identified in the ABA that could be associated with a protein-coding gene and search it using Excel.

2. Download the chromosomal mapping coordinates of all ncRNAs (mm8; bed format) we identified in the ABA and upload it to the UCSC Genome Browser as a custom track. Once this is done, use the genome browser to locate your gene of interest and see if there are any ABA probes nearby that target ncRNAs. A bed file containing the mappings of all ABA probes is also available.

Data export

To export results from the database, select either the Output to Bed or Output To Tab-Delimited options. These options create text files that can be downloaded for further analyses. Please note that currently expression-filtered data cannot be exported to a bed file, so if Output To Bed is selected, any expression filters are ignored. Scores in bed files indicate the probe match score.

Citation

If you use any of the analyses performed to create this database in your own work (such as the noncoding definitions), please cite:

Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008). Specific expression of long noncoding RNAs in the adult mouse brain. Proc Natl Acad Sci USA, 105(2): 716-721.

If you use any of the raw expression data or ABA images, please cite:

Lein et al. (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124): 168-176.

Contact

The database was developed and is administered by Marcel Dinger. For comments, suggestions, and bug reports, please contact him.

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