SQUAT: A web tool to mine human, murine and avian SAGE data.
BACKGROUND
There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns.


METHODS
We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: http://bsmc.insa-lyon.fr/squat/. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: <<what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?>>. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated.


CONCLUSIONS
SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.
Leyritz
Johan
J
Equipe Bases Moléculaires de l'Autorenouvellement et de ses Altérations, Université de Lyon, F-69622, Université Lyon 1, Villeurbanne, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellualire, Lyon, France. jleyritz@gmail.com
Schicklin
Stéphane
S
Blachon
Sylvain
S
Keime
Céline
C
Robardet
Céline
C
Boulicaut
Jean-François
JF
Besson
Jérémy
J
Pensa
Ruggero G
RG
Gandrillon
Olivier
O
D000465:Algorithms; D000818:Animals; D001717:Birds; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D051379:Mice; D012984:Software; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
D014157:Transcription Factors
Genome Res. 2002 Apr;12(4):656-64
11932250
Cell Prolif. 2008 Oct;41(5):726-38
18823497
Bioinformatics. 2003 Jan;19(1):79-86
12499296
Genome Biol. 2002;3(12):RESEARCH0067
12537556
Genome Biol. 2003;4(5):P3
12734009
Oncogene. 2004 Oct 7;23(46):7628-43
15378009
J Immunol. 1994 Sep 1;153(5):1955-62
8051400
Science. 1995 Oct 20;270(5235):484-7
7570003
BMC Bioinformatics. 2004 Oct 6;5:143
15469608
BMC Genomics. 2004 Dec 21;5:98
15610564
IUBMB Life. 2004 Nov-Dec;56(11-12):671-9
15804831
Nat Rev Genet. 2005 Jun;6(6):451-64
15883588
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W693-5
15980565
Genome Biol. 2005;6(9):R81
16168088
Bioinformatics. 2005 Sep 1;21 Suppl 2:ii123-9
16204090
Invest Ophthalmol Vis Sci. 2006 Mar;47(3):1016-23
16505036
Bioinformatics. 2006 May 1;22(9):1122-9
16500941
Anal Biochem. 2006 Jun 1;353(1):43-56
16624241
IEEE/ACM Trans Comput Biol Bioinform. 2004 Jan-Mar;1(1):24-45
17048406
Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5
17130148
BMC Genomics. 2007;8:390
17961265
In Silico Biol. 2007;7(4-5):467-83
18391238
Bioinformatics. 2003 Jan;19(1):71-8
12499295