How to Use LocusLink
1) What is LocusLink?
2) How does LocusLink relate to PubMed, RefSeq, and other NCBI databases?
3) How do I use LocusLink?
4) What do the search results mean?
5) Quick Quiz
1) What is LocusLink?
LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink) is a National Center for
Biotechnology Information (NCBI) online resource. It is principally intended for use by
graduate students and professional researchers in the biomedical sciences. It is designed
to bring together related information on genetic loci and gene products from several
sources. LocusLink provides a central point of access for basic biomedical information
and molecular data for genes, transcripts, and proteins from model organisms, currently
including human, rat, mouse, fruit fly, and zebrafish.
2) How does LocusLink relate to PubMed, RefSeq, and other NCBI databases?
NCBI has a large and growing number of search tools for biologists to obtain
information. A few of these include:
PubMed: a searchable biomedical literature citation index. For a given genetic
locus, LocusLink leads directly to a short list of PubMed citations for that gene.
(This list usually includes reports pertaining to central genetic or molecular
biological discoveries, and to reports on disease-causing alleles, for the gene in
question.)
RefSeq: Another new NCBI database, RefSeq (Reference Sequence) entries are
intended to serve as "authority files" for genetic sequence information. For a
given genetic open reading frame, RefSeq provides a curated file on the gene
sequence and its transcriptional and translational processing (where available).
An professional review process helps to ensure the biological accuracy of these
authority files. RefSeq files are accessible directly from the LocusLink entry for
the genetic locus in question.
OMIM (Online Mendelian Inheritance in Man): a database of human genes and
genetic diseases, including knowledge of their molecular and physiological roles
and causes. The writeups for genetic loci and their roles in physiology are often
extensive and are frequently updated. OMIM files are accessible directly from
the LocusLink entry for the genetic locus in question.
GenBank, Protein Database, Homologene, UniGene, genetic variations
database (single nucleotide polymorphisms): links to gene-specific information
from each of these databases are directly available from the LocusLink entry for
the genetic locus in question.
3) How do I use LocusLink?
Go to the LocusLink home page: http://www.ncbi.nlm.nih.gov/LocusLink. Although an
alphabetical list of entries is available, LocusLink can be most easily searched using the
query box at the top of the page. Users can enter a wide variety of terms, for example:
gene name or gene symbol (e.g., SDHA), protein name (succinate dehydrogenase
flavoprotein), protein symbol (SDH), EC (Enzyme Commission) number (1.3.5.1), and
disease states (Leigh syndrome). Type in your search query into the "Query:" box, then
press "go".
What data is LocusLink searching?
LocusLink searches the full text of the files within its database for the individual
terms queried.
Can I do truncation searches?
Yes. You can use the asterisk as a truncation symbol (e.g., search term: succin*)
to obtain, in this example, information on a variety of genetic loci involved in
metabolism of succinate or succinyl-derivatives.
Can I do Boolean (AND, OR, NOT) searches?
If multiple terms are entered (e.g., succinate dehydrogenase) the search engine
automatically searched for files containing both words (succinate and
dehydrogenase) in the file. Searches can also be constructed using the terms
AND, OR (to find files containing both or either search terms), and NOT (to find
files containing the first but not the second term). Presently, however, proximity
searches (succinate within “x” words of dehydrogenase), searches on phrases
("succinate dehydrogenase" where the two words must be immediately adjacent),
and synonyms are not fully supported.
4) What do the search results mean?
On the results page, first note that the number of entries returned is given. If you get no
results, refer to the "help" section, linked in the left-hand bar on the page. If you do get
hits, you can explore the NCBI site databases in a number of ways, depending on the data
available for a given locus. These will be listed in a table with the headings "LocusID",
"Org", "Symbol", "Description", "Position", and "Links." Each of these is described
below:
Click on the blue "LocusID" number to get an overview description of the gene
locus and its function,. (This is the unique database number for the entry.)
The "Org" column lists abbreviations for the organism that the gene was isolated
from (Hs = Homo sapiens, Mm = Mus musculus, Dm = Drosophila melanogaster,
etc.)
The "Symbol" column lists the common gene abbreviation for the locus.
"Description" is a brief explanation of the function of the locus.
The "Position" column gives the chromosomal map location of the genetic locus.
Clicking the blue entry links to a visual chromosomal map with the gene marked
on it.
The rainbow-colored "Links" column gives links to several other NCBI
databases:
“P” PubMed
“O” Online Mendelian Inheritance in Man (OMIM)
“R” RefSeq database
“G” GenBank database
“P” Protein database
“H” Homologene database
“U” Unigene database
“V” Variation data: single nucelotide polymorphism (SNP) database
If you can't find the genetic information you're looking for using LocusLink (or don’t
understand why you found what you did!), please feel free to contact University of
Illinois Library graduate assistant Kevin Messner (krmessne@uiuc.edu), or visit the
reference desk of your biomedical library.
5) Quick Quiz:
a) How can I find a picture of the human chromosome map location of the SOD1 gene
via LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink)?
Answer: Search LocusLink for SOD1, then click on the "Position" link for the Homo
sapiens (Hs) entry in the results table to bring up a chromosomal map with the gene
marked.
b) Where can I find a basic description of function of the SOD1 gene and protein, and
perhaps a description of genetic diseases it is related to?
Answer: Use LocusLink, then on the results page click on the OMIM button (orange
button with an "O") for the SOD1 entry.
c) Using LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink), can I find any known
single nucleotide polymorphisms for the SOD1 gene? How about GenBank entries for
the gene?
Answer: On the results page for SOD1, click on the V ("variations") to reach the SNP
database entries for the SOD1 gene. Click on the G to access GenBank records.
d) When I search for SOD1, I also get a hit on a "CCS" gene. Why do I get this?
Answer: As the description states, CCS stands for copper chaperone for superoxide
dismutase. The "SOD1" appears in the record for this gene, so it comes up as a hit as
well. (Look at this not as a "bad" hit, but realize that such a result can come in handy
when you're learning about a gene: if you didn't know that there was a copper chaperone
for SOD1, now you do!)