To search for your long non-coding RNA, simply type its name or alias in the top
text box titled "ncRNA name". Alternatively you can search for any text
in the annotations or by sequence. When you have completed your search, a list of long non-coding RNAs will be shown
in the grid below the search functions. Only the first 200 results are shown by
default, although this can be changed by changing the "Max Records" parameter
in the bottom of the left panel.
The search results grid shows records in pages of 15 entries at a time. You can
advance through pages using the page selector at the bottom of the control.
lncRNAdb entries for each curated lncRNA will include one or more annotations (refer
to following section on viewing results). These can be searched by entering a search
term into the Annotation/Sequence search box. When searching annotations basic logic
functions are accepted i.e. promoter AND cancer will search for lncRNA with annotations
including both search terms.
If the search string in the Annotation/Sequence search box is at least 7 characters
and consists entirely of GAT(U)C, lncRNAdb will instead search entries for matches
to their sequence. All other search criteria are ignored when searching by sequence.
Entering a species in the "Select Species" search box will restrict the
search to those species selected. It is important to note that the list of species
in which an lncRNA is found may not be comprehensive due to limited information
regarding orthologs in some instances. Please note that NRED expression information
is only available for human and mouse. The genomic location of some lncRNAs is not
available in the literature and so a link to the UCSC Browser is not always possible.
Each entry in lncRNAdb has a number of tags which mark specific traits of each lncRNA.
These include imprinted, developmentally regulated, disease associated, pathogen
induced/derived, bifunctional, functionally tested and unknown function. To search
by one of these tags, select it from the "Select Tags" search box in the
left hand search panel.
Annotations and Literature
Once you have the results of your search, you can see the detail of your selected
ncRNA by clicking on its name in the results grid. A list of annotations, literature
species, sequence and aliases for the lncRNA are known to be associated with and associated genetic features
will be listed on a new page. Both the literature and annotation entries can contain
links to pubmed, clicking on these links opens the relevant abstract in Pubmed.
Where a list of species in which the lncRNA is known has been curated, these species
are listed below the literature section. Each entry may also include a direct link
to the UCSC Browser http://genome.ucsc.edu/
and the Non-Coding RNA Expression Database NRED
http://jsm-research.imb.uq.edu.au/nred/cgi-bin/ncrnadb.pl. Clicking on these
links will open the relevant entry in each database.
Any genetic components known or anticipated to be associated with each lncRNA are
listed at the bottom of the right hand results panel.
To export your results in a tab delimited file, click on the Export Results button.
Results will be exported for all ncRNAs shown in the search results grids. Use the
search functions to define your lncRNA(s) of interest before trying to export.
To peruse the entire database, enter an empty search prior to exporting.
Similarly, the Export Sequence option will create a file containing the name, aliases
and sequence including sequence notes. The format is a fasta file where the first
line of each entry contains the name of the transcript and any notes regarding the
sequence such as species specificity and isoform..
If you find this resource useful please cite lncRNAdb;
Amaral PP, Clark MB, Gascoigne DK, Dinger ME, Mattick JS (2011). lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-151.
This project is from the Mattick Lab