Cluster analysis of an extensive human breast cancer cell line protein expression map database.

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Harris RA, Yang A, Stein RC, Lucy K, Brusten L, Herath A, Parekh R, Waterfield MD, O'Hare MJ, Neville MA, Page MJ, Zvelebil MJ

Cluster analysis of an extensive human breast cancer cell line protein expression map database.

Proteomics. 2002 Feb;2(2):212-23.

PubMed ID
11840567 [ View in PubMed
]
Abstract

In the current study, the protein expression maps (PEMs) of 26 breast cancer cell lines and three cell lines derived from normal breast or benign disease tissue were visualised by high resolution two-dimensional gel electrophoresis. Analysis of this data was performed with ChiClust and ChiMap, two analytical bioinformatics tools that are described here. These tools are designed to facilitate recognition of specific patterns shared by two or more (a series) PEMs. Both tools use PEMs that were matched by an image analysis program and locally written programs to create a match table that is saved in an object relational database. The ChiClust tool uses clustering and subclustering methods to extract statistically significant protein expression patterns from a large series of PEMs. The ChiMap tool calculates a differential value (either as percentage change or a fold change) and represents these graphically. All such differentials or just those identified using ChiClust can be submitted to ChiMap. These methods are not dependent on any particular commercial image analysis program, and the whole software package gives an integrated procedure for the comparison and analysis of a series of PEMs. The ChiClust tool was used here to order the breast cell lines into groups according to biological characteristics including morphology in vitro and tumour forming ability in vivo. ChiMap was then used to highlight eight major protein feature-changes detected between breast cancer cell lines that either do or do not proliferate in nude mice. Mass spectrometry was used to identify the proteins. The possible role of these proteins in cancer is discussed.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Tyrosine-protein kinase LckP06239Details
Protein ERGIC-53P49257Details
Neuronal acetylcholine receptor subunit alpha-7P36544Details
Keratin, type II cytoskeletal 7P08729Details
Tubulin gamma-1 chainP23258Details
Solute carrier family 2, facilitated glucose transporter member 5P22732Details
Protein disulfide-isomerase A3P30101Details
Heterogeneous nuclear ribonucleoprotein KP61978Details
Tropomyosin alpha-1 chainP09493Details
Keratin, type I cytoskeletal 16P08779Details