Cluster analysis and display of genome-wide expression patterns

Abstract

following correction should be noted. In Fig. 1b, the designed sequence of amino acids S 36 contains a typographical error in that only 35 of its 36 monomers appear. The missing amino acid is of type R and should be located between amino acids E (sixth) and G (seventh). The correct sequence is:Although this typographical error does not change the results presented in the paper because they were obtained with the correct number and sequence of amino acids, it constitutes a nuisance for anybody interested in reproducing our results, and we apologize for the inconvenience. We want to thank Prof. H. S. Chan, of the University of Toronto, for calling our attention to this error.Cell Biology. In the article "Quantitative analysis of biological membrane lipids at the low picomole level by nanoelectrospray ionization tandem mass spectrometry" by B. Brügger, G. Erben, R. Sandhoff, F. T. Wieland, and W. D.Lehmann, which appeared in number 6, March 18, 1997, of Proc. Natl. Acad. Sci. USA (94,(2339)(2340)(2341)(2342)(2343)(2344), Table 1

Tumor mutational burden is a determinant of immune-mediated survival in breast cancer

“…Hierarchical clustering of gene and tumor expression profiles, followed by heatmap-based visualization of data was performed using Eisen’s Cluster (v2.11) and TreeView (v1.60) software. 59 Data were mean centered on genes and clustered using average linkage clustering and uncentered Pearson correlation. The Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resource version 6.7 60 was used to study enrichment of Gene Ontologies associated with genes amplified in immune subclasses.…”

Pharmacogenomics of infliximab treatment using peripheral blood cells of patients with rheumatoid arthritis

“…33 A gene was considered as significantly differential expressed if the false discovery rate was equal to or o5%. Cluster analysis 34 was used to define clusters of co-coordinately changed genes after which the data were visualized using Treeview (http://rana.lbl.gov/ EisenSoftware.htm). To interpret our data after significance analysis of microarray analysis, we applied PANTHER Classification System (Applied Biosystems, Foster City, CA, USA) at http://PANTHER.appliedbiosystem.com.…”

Akt-dependent nuclear localization of Y-box-binding protein 1 in acquisition of malignant characteristics by human ovarian cancer cells

“…Hierarchical clustering can be used to group cell lines and genes in term of their patterns of gene expression. To obtain cluster trees for genes that showed distinct expression patterns across the 60 cell lines, we used the program 'Cluster' and 'Tree View' (http://rana.lbl.gov/) with average linkage clustering and a correlation metric (Eisen et al, 1998).…”