ROCK: a breast cancer functional genomics resource (original) (raw)
Harris JR, Morrow M, Lippman ME, Osborne CK (2009) Diseases of the breast, 4th edn. Lippincott Williams & Wilkins, London, p 1408
Hicks J et al (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16(12):1465–1479 ArticleCASPubMed Google Scholar
Hu Z et al (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 7:96 ArticlePubMed Google Scholar
Natrajan R et al (2009) Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin Cancer Res 15(8):2711–2722 ArticleCASPubMed Google Scholar
Parker JS et al (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27(8):1160–1167 ArticlePubMed Google Scholar
Iorns E et al (2009) Integrated functional, gene expression and genomic analysis for the identification of cancer targets. PLoS One 4(4):e5120 ArticlePubMed Google Scholar
Barrett T et al (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucl Acids Res 35(Database issue):D760–D765 ArticleCASPubMed Google Scholar
Parkinson H et al (2007) ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucl Acids Res 35(Database issue):D747–D750 ArticleCASPubMed Google Scholar
Bamford S et al (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 91(2):355–358 CASPubMed Google Scholar
Gollub J et al (2003) The Stanford microarray database: data access and quality assessment tools. Nucl Acids Res 31(1):94–96 ArticleCASPubMed Google Scholar
Tavassoli AF, Devilee P (2003) Tumours of the breast and female genital organs, WHO classification of tumours
NHS Breast Screening Programme (2005) Pathology reporting of breast disease, vol 58. NHS
Elston CW, Ellis IO (1991) Pathological prognostic factors in breast cancer. I. The value of histological grade in breast cancer: experience from a large study with long-term follow-up. Histopathology 19(5):403–410 ArticleCASPubMed Google Scholar
Singletary SE et al (2002) Revision of the American Joint Committee on Cancer staging system for breast cancer. J Clin Oncol 20(17):3628–3636 ArticlePubMed Google Scholar
Tibshirani R et al (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99(10):6567–6572 ArticleCASPubMed Google Scholar
Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98(9):5116–5121 ArticleCASPubMed Google Scholar
Venkatraman ES, Olshen AB (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6):657–663 ArticleCASPubMed Google Scholar
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B 57(1):289–300 Google Scholar
Boutros M, Bras LP, Huber W (2006) Analysis of cell-based RNAi screens. Genome Biol 7(7):R66 ArticlePubMed Google Scholar
Alfarano C et al (2005) The biomolecular interaction network database and related tools 2005 update. Nucl Acids Res 33(Database issue):D418–D424 ArticleCASPubMed Google Scholar
Chatr-aryamontri A et al (2007) MINT: the molecular interaction database. Nucl Acids Res 35(Database issue):D572–D574 ArticleCASPubMed Google Scholar
Kerrien S et al (2007) IntAct—open source resource for molecular interaction data. Nucl Acids Res 35(Database issue):D561–D565 ArticleCASPubMed Google Scholar
Matthews L et al (2009) Reactome knowledgebase of human biological pathways and processes. Nucl Acids Res 37(Database issue):D619–D622 ArticleCASPubMed Google Scholar
Pagel P et al (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21(6):832–834 ArticleCASPubMed Google Scholar
Peri S et al (2004) Human protein reference database as a discovery resource for proteomics. Nucl Acids Res 32(Database issue):D497–D501 ArticleCASPubMed Google Scholar
Stark C et al (2006) BioGRID: a general repository for interaction datasets. Nucl Acids Res 34(Database issue):D535–D539 ArticleCASPubMed Google Scholar
Tweedie S et al (2009) FlyBase: enhancing drosophila gene ontology annotations. Nucl Acids Res 37(Database issue):D555–D559 ArticleCASPubMed Google Scholar
Okuda S et al (2008) KEGG Atlas mapping for global analysis of metabolic pathways. Nucl Acids Res 36(Web Server issue):W423–W426 ArticleCASPubMed Google Scholar
Schaefer CF et al (2009) PID: the pathway interaction database. Nucl Acids Res 37(Database issue):D674–D679 ArticleCASPubMed Google Scholar
Zhao F et al (2005) TRED: a transcriptional regulatory element database and a platform for in silico gene regulation studies. Nucl Acids Res 33(Database issue):D103–D107 ArticleCASPubMed Google Scholar
Overington JP, Al-Lazikani B, Hopkins AL (2006) How many drug targets are there? Nat Rev Drug Discov 5(12):993–996 ArticleCASPubMed Google Scholar
Maglott D et al (2005) Entrez Gene: gene-centered information at NCBI. Nucl Acids Res 33(Database issue):D54–D58 ArticleCASPubMed Google Scholar
Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl Acids Res 33(Database issue):D501–D504 ArticleCASPubMed Google Scholar
Bruford EA et al (2008) The HGNC database in 2008: a resource for the human genome. Nucl Acids Res 36(Database issue):D445–D448 CASPubMed Google Scholar
Wheeler DL et al (2003) Database resources of the National Center for Biotechnology. Nucl Acids Res 31(1):28–33 ArticleCASPubMed Google Scholar
Pruitt KD et al (2009) The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes. Genome Res 19(7):1316–1323 ArticleCASPubMed Google Scholar
Consortium TU (2009) The Universal Protein Resource (UniProt) 2009. Nucl Acids Res 37(Database issue):D169–D174 Article Google Scholar
Bult CJ et al (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucl Acids Res 36(Database issue):D724–D728 CASPubMed Google Scholar
Chen N et al (2005) WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucl Acids Res 33(Database issue):D383–D389 ArticleCASPubMed Google Scholar
O’Brien KP, Remm M, Sonnhammer EL (2005) Inparanoid: a comprehensive database of eukaryotic orthologs. Nucl Acids Res 33(Database issue):D476–D480 ArticlePubMed Google Scholar
Barrell D et al (2009) The GOA database in 2009–an integrated gene ontology annotation resource. Nucl Acids Res 37(Database issue):D396–D403 ArticleCASPubMed Google Scholar
Hunter S et al (2009) InterPro: the integrative protein signature database. Nucl Acids Res 37(Database issue):D211–D215 ArticleCASPubMed Google Scholar
Rhodes DR et al (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles. Neoplasia 9(2):166–180 ArticleCASPubMed Google Scholar
Chin K et al (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10(6):529–541 ArticleCASPubMed Google Scholar
Miller LD et al (2005) An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 102(38):13550–13555 ArticleCASPubMed Google Scholar
Mackay A et al (2009) A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines. Breast Cancer Res Treat 118:481–498 Google Scholar
Sotiriou C et al (2006) Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98(4):262–272 ArticleCASPubMed Google Scholar
Neve RM et al (2006) A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 10(6):515–527 ArticleCASPubMed Google Scholar