QServer: QUalitative BIClustering server
Release 2.0.0, on December 20, 2011
1. What is the QServer ?
QServer is a web server based on the biclustering algorithm QUBIC (1). The detailed information of the technique biclustering can be found in the main page of this server or the Wikipedia:Biclustering.
2. How to use QServer ?
By clicking "BiCluster"
in the left navigation bar, a user can go to the interface of the
QServer . A user needs to choose which organism he/she is working on, and a data
matrix generated from multiple expression array data sets. A subset of
gene names may also be provided, so that only biclusters containing these
genes will be displayed in the Results
3. How to generate the data matrix as the input of QServer ?
The data matrix file is a TAB-delimited text file with the following format:
The expression levels should be normalized before being included in the matrix. Each row consists of the expression levels of one gene, and each column lists the expression levels of all the genes under one condition/microarray.
4. How to directly generate the data matrix from the raw microarray data sets?
For the user's convenience, we provide a Perl script to generate the data matrix normalized from multiple raw microarray data sets. The Perl script, MatrixMaker 1.0, can be downloaded from here: http://csbl1.bmb.uga.edu/~ffzhou/QServer/MatrixMaker.1.0.tar.gz. This program is for Linux only. You may also need to download the Linux version of Affymetrix Power Tools (the program apt-probeset-summarize) from the Affymetrix web site.
4.1. decompress the file MatrixMaker.1.0.tar.gz after downloading:
The reason, why we didn't incorporate this matrix-making functionality directly into our server, is that the raw microarray data set is too big to be uploaded. For example, the raw files (.CEL) for the study GSE2125 occupy 389 Mb, even after be compressed by GZip. The decompressed raw files of GSE2125 need 1.5 Gb. After making the matrix locally, the RMA matrix just needs 21 Mb, and the GZip compressed one is 11 Mb, a reduction of 97.17% in file size.
5. Explanation of the parameters in the "BiCluster" page.
QUBIC has a number of parameters, namely, the flag d to parse discrete data, the range r of possible ranks, the percentage q of the regulating conditions for each gene, the required consistency level c for a bicluster, the desired number o of the output biclusters, and the control parameter f for overlaps among to-be-identified biclusters. For each of these parameters, we allow the user to adjust the default value to provide some flexibility.
Number of blocks to report : number of biclusters to report. default: 100
Data type : the flag of discrete input data, which format is used in the data. default: continuous data
Quantile discretization for continuous data : quantile discretization for continuous data (0,0.5). default: 0.06
The number of ranks : the number of ranks
as which we treat the up(down)-regulated value when discretization.
Filtering overlapping blocks : filtering
overlapping blocks (0 - 1.0]
Minimum condition (column) numbers : minimum number of conditions in a bicluster. default: 5% of the total columns.
Conservative of the block : consistency
level of the bicluster (0.5-1.0]. default: 0.95
Promoter motif finding program : bobro or meme. default: bobro.
 G Li, Q Ma, H Tang, AH Paterson and Y Xu, "QUBIC: a qualitative biclustering algorithm for analyses of gene expression data", Nucleic Acids Research 2009 37:e101. PubMed.
For scientific or technical questions about this database, please contact Dr Fengfeng Zhou.