QServer: QUalitative BIClustering server

Release 2.0.0, on December 20, 2011

Biclustering is a data mining technique that simultaneously clustering along the rows and columns of a data matrix. Such a data matrix usually consists of the expression data of genes (in each row) under different conditions (in each column). A basic idea of biclustering problem and algorithms could be found at Wikipedia.

Some of the available biclustering programs are listed here for the convenience of the users of this server.
Algorithm Link Reference Comment
QUBIC http://csbl.bmb.uga.edu/publications/materials/ffzhou/QServer/ This server server and software
GEMS http://genomics10.bu.edu/terrence/gems/ Wu CJ, et. al. server
BiGGEsTS http://kdbio.inesc-id.pt/software/e-ccc-biclustering/ Madeira SC, et. al software
FABIA http://www.bioinf.jku.at/software/fabia/fabia.html McCarroll SA, et. al R package
bioNMF http://bionmf.dacya.ucm.es/webservices.html Mejia-Roa E, et. al server
BicAT http://www.tik.ee.ethz.ch/sop/bicat/?page=download.php Prelic A, et al software
ISA This is included in BicAT Ihmels J, et al  
Samba http://acgt.cs.tau.ac.il/expander/ Tanay A, et al software
RMSBE http://www.cs.cityu.edu.hk/~lwang/software/msbe/help.html Liu X, et al  

Other useful tools and data resources
Name Resource Reference Comment
BOLBOA Extending bicluster analysis to annotate unclassified ORFs and predict novel functional modules using expression data Bryan K, et al contact the authors
NNN Nearest Neighbor Networks: clustering expression data based on gene neighborhoods Huttenhower C, et al contact the authors
Bubble Application of simulated annealing to the biclustering of gene expression data. Bryan K, et al contact the authors
M3D http://m3d.bu.edu/cgi-bin/web/array/index.pl?section=home   microarray data
Leukemia http://www.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=63   Leukemia expression data
PED http://bioinfo.ucr.edu/projects/Unknowns/external/express.html   Plant Gene Expression Database
ArrayExpress http://www.ebi.ac.uk/microarray-as/ae/browse.html   EBI Expression data
GEO http://www.ncbi.nlm.nih.gov/geo/   Gene Expression Omnibus
KEGG http://www.genome.jp/kegg/   Functional analysis
GO http://www.geneontology.org/   Functional analysis
COG http://www.ncbi.nlm.nih.gov/COG/   Functional analysis
RegulonDB http://regulondb.ccg.unam.mx/index.jsp#   Functional analysis
Cluster http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/ Hoon MJL et al Clustering program

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