Gene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity

Keywords

Immune system, Biology, Cancer research, Carcinogenesis, Downregulation and upregulation

References

• A multigene predictor of metastatic outcome in early stage hormone receptor-negative and triple-negative breast cancerSteven D. Dolvin — 2010
• MCLUST Version 3: An R Package for Normal Mixture Modeling and Model-Based ClusteringChris Fraley, Adrian E. Raftery — 2006
• The Bimodality Index: A Criterion for Discovering and Ranking Bimodal Signatures from Cancer Gene Expression Profiling DataJing Wang, Sijin Wen, W. Fraser Symmans — 2009
• From molecular to modular cell biologyLeland H. Hartwell, J. J. Hopfield, Stanislas Leibler — 1999
• Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumorWieslawa I. Mentzen, Matteo Floris, Alberto de la Fuente — 2009
• The hallmarks of cancerTony Gutschner, Sven Diederichs — 2012
• Statistical Significance of Clustering for High-Dimension, Low–Sample Size DataYufeng Liu, D. Neil Hayes, Andrew B. Nobel — 2008
• Motifs, modules and games in bacteria.Denise M. Wolf, Adam P. Arkin — 2003
• The application of gene co-expression network reconstruction based on CNVs and gene expression microarray data in breast cancerYan Xu, Huizi DuanMu, Zhiqiang Chang — 2012
• The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroupsMETABRIC Group, Christina Curtis, Sohrab P. Shah — 2012
• Bimodal gene expression patterns in breast cancerMarina Bessarabova, Eugene Kirillov, Weiwei Shi — 2010
• Tissue architecture and function: dynamic reciprocity via extra- and intra-cellular matricesRen Xu, Aaron Boudreau, Mina J. Bissell — 2009
• A robust classifier of high predictive value to identify good prognosis patients in ER-negative breast cancerAndrew E. Teschendorff, Carlos Caldas — 2008
• Endocrine resistance in breast cancer: new roles for ErbB3 and ErbB4Robert L. Sutherland — 2011
• Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancerAvrum Spira, Jennifer Beane, Vishal Shah — 2007
• Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome StabilityJie Zhang, Kewei Lü, Yang Xiang — 2012
• Genes that mediate breast cancer metastasis to the brainPaula D. Bos, Xiang H.-F. Zhang, Cristina Nadal — 2009
• g:Profiler—a web server for functional interpretation of gene lists (2011 update)Jüri Reimand, T. V. Arak, Jaak Vilo — 2011
• Gene expression profiling of response to mTOR inhibitor everolimus in pre-operatively treated post-menopausal women with oestrogen receptor-positive breast cancerVicky S. Sabine, Andrew H. Sims, E. Jane Macaskill — 2010
• Statistical Significance of Clustering using Soft ThresholdingHanwen Huang, Yufeng Liu, Ming Yuan — 2013

Cited by

• Transcriptional Profiling of Breast Cancer Metastases Identifies Liver Metastasis–Selective Genes Associated with Adverse Outcome in Luminal A Primary Breast CancerSiker Kimbung, Ida Johansson, Anna Danielsson — 2015
• Clinical and molecular complexity of breast cancer metastases.Siker Kimbung, Niklas Loman, Ingrid Hedenfalk — 2015
• Metastatic Breast Cancer: Biomolecular Characterization and Targeted TherapySiker Kimbung — 2014
• Dissecting the Tumor Myeloid Compartment Reveals Rare Activating Antigen Presenting Cells, Critical for T cell ImmunityMiranda L. Broz, Mikhail Binnewies, Bijan Boldajipour — 2014
• Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and responseMark Jesus M. Magbanua, Denise M. Wolf, Christina Yau — 2015
• GeneFriends: a human RNA-seq-based gene and transcript co-expression databaseSipko van Dam, Thomas Craig, João Pedro de Magalhães — 2014
• Interferons and the Immunogenic Effects of Cancer TherapyAndy J. Minn — 2015
• Covariance-based analyses of biological pathwaysPatrick Danaher, Debashis Paul, Pei Wang — 2015
• The dual role of asporin in breast cancer progressionDana Šimková, Gvantsa Kharaishvili, Gabriela Kořínková — 2016
• The Role of Proliferation in Determining Response to Neoadjuvant Chemotherapy in Breast Cancer: A Gene Expression-Based Meta-AnalysisDaniel G. Stover, Jonathan L. Coloff, William T. Barry — 2016
• The Critical Role of CD103+ Dendritic Cells in Anti-Tumor T Cell ImmunityMiranda L. Broz — 2015
• Co-expression modules identified from published immune signatures reveal five distinct immune subtypes in breast cancerDominic Amara, Denise M. Wolf, Laura van ‘t Veer — 2016
• CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalkVenkata Manem, George Alexandru Adam, Tina Gruosso — 2017
• Gene co-expression network reconstruction: a review on computational methods for inferring functional information from plant-based expression dataAbbasali Emamjomeh, Elham Saboori Robat, Javad Zahiri — 2017
• Coexpressed modular gene expression reveals inverse correlation between immune responsive transcription and aggressiveness in gastric tumoursKalaivani Kalamohan, Dhanasekaran Rathinam, Ponmathi Panneerpandian — 2017
• Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancerEsra Göv, Kazım Yalçın Arğa — 2017
• Implementation and Application of Method for Differential Correlation Network Analysis.Magnus Olav Helland — 2017
• A moment-distance hybrid method for estimating a mixture of two symmetric densitiesDavid Källberg, Yuri K. Belyaev, Patrik Rydén — 2018
• Perspective on Oncogenic Processes at the End of the Beginning of Cancer GenomicsLi Ding, Matthew H. Bailey, Eduard Porta‐Pardo — 2018
• Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of CancerKatherine A. Hoadley, Christina Yau, Toshinori Hinoue — 2018

Related papers

• Analysis of host responses to microbial infection using gene expression profiling.Martin F. Kagnoff, Lars Eckmann — 2001
• Aging-associated changes in cardiac gene expression: large scale transcriptome analysis.S V Anisimov, Kenneth R. Boheler — 2003
• Discrimination of toxic impacts of various chemicals using chemical-gene expression profiling of Escherichia coli DNA microarrayByoung Chan Kim, Man Bock Gu — 2007
• Microarray-based Gene Expression Fingerprint in Leukocytes of Half-marathon Runners: 900Elvira Fehrenbach, Derek Zieker, Janko Dietzsch — 2006
• Serial gene expression profiling in the intact human heart.Brian D. Lowes, R. Zolty, Wayne Minobe — 2006
• Gene expression profiling of cerebellar development with high-throughput functional analysis.Sakae Saito, Kimi Honma, Hiroko Kita‐Matsuo — 2005
• Differential gene expression profiling in whole blood during acute systemic inflammation in lipopolysaccharide-treated rats.Rick D. Fannin, J. Todd Auman, Maribel Bruno — 2005
• Gene expression profiling of mouse host response to Listeria monocytogenes infection.Hanna H. Ng, Christopher E. Frantz, Linda Rausch — 2005
• Comparison of different isolation techniques prior gene expression profiling of blood derived cells: impact on physiological responses, on overall expression and the role of different cell typesSvenja Debey, U. Schoenbeck, Martin Hellmich — 2004