Portraits of breast cancer progression.

PubWeight™: 1.17‹?› | Rank: Top 10%

🔗 View Article (PMC 1978212)

Published in BMC Bioinformatics on August 06, 2007

Authors

Gul S Dalgin1, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles DeLisi, Gyan Bhanot

Author Affiliations

1: Boston University, Boston, MA 02215, USA. sdalgin@bu.edu

Articles citing this

Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns. Genes Cancer (2010) 3.78

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med (2010) 3.43

Evidence that molecular changes in cells occur before morphological alterations during the progression of breast ductal carcinoma. Breast Cancer Res (2008) 1.38

HER2/ErbB2-induced breast cancer cell migration and invasion require p120 catenin activation of Rac1 and Cdc42. J Biol Chem (2010) 1.24

Ductal carcinoma in situ: terminology, classification, and natural history. J Natl Cancer Inst Monogr (2010) 1.16

Amplified loci on chromosomes 8 and 17 predict early relapse in ER-positive breast cancers. PLoS One (2012) 1.10

Genomic and proteomic biomarkers for cancer: a multitude of opportunities. Biochim Biophys Acta (2009) 1.03

A highly efficient multi-core algorithm for clustering extremely large datasets. BMC Bioinformatics (2010) 0.89

Simultaneous class discovery and classification of microarray data using spectral analysis. J Comput Biol (2009) 0.86

Identification of the YES1 Kinase as a Therapeutic Target in Basal-Like Breast Cancers. Genes Cancer (2010) 0.83

A Bayesian approach for inducing sparsity in generalized linear models with multi-category response. BMC Bioinformatics (2015) 0.79

Modelling gene expression profiles related to prostate tumor progression using binary states. Theor Biol Med Model (2013) 0.78

Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. BMC Med Genomics (2015) 0.76

Articles cited by this

The hallmarks of cancer. Cell (2000) 113.05

Molecular portraits of human breast tumours. Nature (2000) 94.14

DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79

Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science (1999) 83.27

Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet (2005) 29.45

Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis. Cell (1996) 23.99

MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol (2003) 8.66

Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res (2001) 8.34

A gene network for navigating the literature. Nat Genet (2004) 6.43

Gene expression profiles of human breast cancer progression. Proc Natl Acad Sci U S A (2003) 6.35

Microarray analysis and tumor classification. N Engl J Med (2006) 3.35

Distinct molecular mechanisms underlying clinically relevant subtypes of breast cancer: gene expression analyses across three different platforms. BMC Genomics (2006) 2.86

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48

Basal phenotype identifies a poor prognostic subgroup of breast cancer of clinical importance. Eur J Cancer (2006) 1.76

Gene expression profiles do not consistently predict the clinical treatment response in locally advanced breast cancer. Mol Cancer Ther (2006) 1.64

Survivin, Survivin-2B, and Survivin-deItaEx3 expression in medulloblastoma: biologic markers of tumour morphology and clinical outcome. Br J Cancer (2005) 1.11

Molecular profiling in breast cancer. Rev Endocr Metab Disord (2007) 1.10

Survivin, a novel anti-apoptosis inhibitor, expression in uterine cervical cancer and relationship with prognostic factors. Int J Gynecol Cancer (2005) 1.01

Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns. Cancer Inform (2007) 1.00

Articles by these authors

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59

Integrative genomics viewer. Nat Biotechnol (2011) 42.83

Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature (2012) 31.78

GenePattern 2.0. Nat Genet (2006) 29.07

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58

ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72

Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27

Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36

Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01

Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30

Dicer-deficient mouse embryonic stem cells are defective in differentiation and centromeric silencing. Genes Dev (2005) 12.15

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46

Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A (2004) 10.47

Autophagy suppresses tumorigenesis through elimination of p62. Cell (2009) 9.95

Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature (2008) 8.38

Molecular signatures database (MSigDB) 3.0. Bioinformatics (2011) 8.08

Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res (2003) 8.06

SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet (2009) 7.48

X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell (2006) 7.17

GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics (2007) 6.63

Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells. Cell (2009) 6.55

CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature (2008) 6.24

Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet (2007) 5.99

Comment on "The consensus coding sequences of human breast and colorectal cancers". Science (2007) 5.88

53BP1 loss rescues BRCA1 deficiency and is associated with triple-negative and BRCA-mutated breast cancers. Nat Struct Mol Biol (2010) 5.59

Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol (2010) 5.50

Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature (2012) 5.23

Automated high-dimensional flow cytometric data analysis. Proc Natl Acad Sci U S A (2009) 4.91

Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J Clin Oncol (2010) 4.48

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc Natl Acad Sci U S A (2011) 4.15

Carcinoma-associated fibroblast-like differentiation of human mesenchymal stem cells. Cancer Res (2008) 3.97

Molecular Stratification of Clear Cell Renal Cell Carcinoma by Consensus Clustering Reveals Distinct Subtypes and Survival Patterns. Genes Cancer (2010) 3.78

Single cell profiling of circulating tumor cells: transcriptional heterogeneity and diversity from breast cancer cell lines. PLoS One (2012) 3.74

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest (2012) 3.64

β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. Cell (2012) 3.33

Predictome: a database of putative functional links between proteins. Nucleic Acids Res (2002) 3.32

Tight regulation of memory CD8(+) T cells limits their effectiveness during sustained high viral load. Immunity (2011) 3.19

Criteria for the use of omics-based predictors in clinical trials. Nature (2013) 3.15

Targeting MYCN in neuroblastoma by BET bromodomain inhibition. Cancer Discov (2013) 3.11

VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics (2004) 2.88

VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85

Loss of 53BP1 causes PARP inhibitor resistance in Brca1-mutated mouse mammary tumors. Cancer Discov (2012) 2.74

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res (2009) 2.71

Comparative gene marker selection suite. Bioinformatics (2006) 2.71

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi. Genome Res (2005) 2.69

Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc Natl Acad Sci U S A (2007) 2.60

GeneCruiser: a web service for the annotation of microarray data. Bioinformatics (2005) 2.59

Computerized image-based detection and grading of lymphocytic infiltration in HER2+ breast cancer histopathology. IEEE Trans Biomed Eng (2009) 2.56

Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology. IEEE Trans Biomed Eng (2010) 2.52

Combo: a whole genome comparative browser. Bioinformatics (2006) 2.52

Identifying mRNA targets of microRNA dysregulated in cancer: with application to clear cell Renal Cell Carcinoma. BMC Syst Biol (2010) 2.49

High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates. Cancer Res (2007) 2.48

Gene expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol (2003) 2.45

Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33

Identification of a microRNA panel for clear-cell kidney cancer. Urology (2009) 2.32

Subclass mapping: identifying common subtypes in independent disease data sets. PLoS One (2007) 2.32

Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol (2009) 2.27

Estimating dataset size requirements for classifying DNA microarray data. J Comput Biol (2003) 2.23

MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A (2010) 2.21

Towards zoomable multidimensional maps of the cell. Nat Biotechnol (2007) 2.20

VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17

Akt-mediated phosphorylation of Bmi1 modulates its oncogenic potential, E3 ligase activity, and DNA damage repair activity in mouse prostate cancer. J Clin Invest (2012) 2.03

The telomerase reverse transcriptase regulates chromatin state and DNA damage responses. Proc Natl Acad Sci U S A (2005) 2.01

Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. Mol Cancer Res (2008) 1.99

An erythroid differentiation signature predicts response to lenalidomide in myelodysplastic syndrome. PLoS Med (2008) 1.97

Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog (2008) 1.96

Inactivation of the Snf5 tumor suppressor stimulates cell cycle progression and cooperates with p53 loss in oncogenic transformation. Proc Natl Acad Sci U S A (2005) 1.96