Guide to CellMontage
What is CellMontage?
CellMontage is a system for searching gene expression databases for cells or tissues similar to the query gene expression profile. The similarity of two profiles is computed by comparing the order of genes ranked by expression. Although this is a simple measure we have observed that it is sufficient to characterize cell types across different microarray platforms.
What characterizes cells?
Gene sets and expression value ranges differ between platforms, making direct comparison impossible. Given this situation, we use "gene expression ranks" as a way to compare expression data across platforms.
Spearman's rank correlation coefficient
Spearman's method uses the correlation coefficient &rho between two rank numbers.
How many genes are needed to detect cell types?
We investigated the top hits obtained by searches using queries from seven normal cell types. The precentage of top hits from each cell type increased rapidly as the number of genes used in the query increased. The number of randomly chosen genes required to retrieve seven normal cell types is only 64-128 (on the same platform).
Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P. "CellMontage: similar expression profile search server." Bioinformatics. 2007 Nov 15;23(22):3103-4.
Natalia Polouliakh, Tohru Natsume, Hajime Harada, Wataru Fujibuchi, & Paul Horton, "Comparative Genomic Analysis of Transcription Regulation Elements Involved In Human Map Kinase G-Protein Coupling Pathway", Journal of Bioinformatics and Computational Biology, 2006 Apr;4(2):469-82.
Wataru Fujibuchi, Larisa Kiseleva, Takeaki Taniguchi & Paul Horton, "Development of Cell Knowledge Base and Prediction of Cell Types and Characteristics by Gene Expression Profiles" (in Japanese), IPSJ SIG Technical Report 2005-BIO-2, pp. 33-37. 2005.
"GENE EXPRESSION PROFILE RETRIEVING APPARATUS, GENE EXPRESSION PROFILE RETRIEV\ ING METHOD, AND PROGRAM" US patent [US_11/235150] 2005/09/27
Reality for finding homologous gene expression profiles, Fujibuchi, W. and Horton, P., poster presentation at BITS 2004 Oct. 30 in Kazusa DNA research institute, Chiba.http://www.kap.co.jp/bits2004/
CellMontage - Cell type retrieval system by gene expression profiles, Fujibuchi, W., oral presentation at AIST bioinformatics educational course symposium, 2004 Oct. 1.
Microarray analysis on many genes determine a cell type., Fujibuchi, W., poster presentation at ISMB 2004 Aug. in Glasgow.http://www.iscb.org/ismb2004/cgi-bin/posterabstracts.cgi
Development of similar cell search system, "Cell Montage" from gene expression profiles., Fujibuchi, W. and Horton, P., poster presentation at life science field research workshop, 2004 Feb. 3(Japanese).
NCBI GEO: mining millions of expression profiles--database and tools.: Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R., Nucleic Acids Res. 2005 Jan. 1;33 Database Issue:D562-6.