Making sense out of massive data by going beyond differential expression

No abstract is available for this paper.

• Publication year

  2012

• Venue

  Proceedings of the National Academy of Sciences of the United States of America

• Publication date

  2012-03-01

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1073/pnas.1118792109PMID 22447773PMCID PMC3326474
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Activation of peroxisome proliferator-activated receptor-α enhances fatty acid oxidation in human adipocytes.

  2011cited by this paper
• Polymorphisms of ADIPOQ and ADIPOR1 and prostate cancer risk.

  2011cited by this paper
• Common Polymorphisms in the Adiponectin and Its Receptor Genes, Adiponectin Levels and the Risk of Prostate Cancer

  2011cited by this paper
• Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

  2011cited by this paper
• Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2

  2011cited by this paper
• NCBI GEO: archive for functional genomics data sets—10 years on

  2010influential reference
• Network medicine: a network-based approach to human disease

  2010cited by this paper
• Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression

  2010cited by this paper
• Biomarker and drug discovery for gastroenterology through translational bioinformatics.

  2010cited by this paper
• A global map of human gene expression

  2010cited by this paper
• The twin questions of personalized medicine: who are you and whom do you most resemble?

  2009cited by this paper
• Identification of a Putative Protein Profile Associated with Tamoxifen Therapy Resistance in Breast Cancer*S⃞

  2009cited by this paper
• Next generation software for functional trend analysis

  2009cited by this paper
• RNA-Seq: a revolutionary tool for transcriptomics

  2009cited by this paper
• Disease signatures are robust across tissues and experiments

  2009cited by this paper
• A Practical Platform for Blood Biomarker Study by Using Global Gene Expression Profiling of Peripheral Whole Blood

  2009cited by this paper
• TiGER: A database for tissue-specific gene expression and regulation

  2008cited by this paper
• Gene expression profiling may improve diagnosis in patients with carcinoma of unknown primary

  2008cited by this paper
• Peroxisome proliferator-activated receptor-alpha (PPARA) genetic polymorphisms and breast cancer risk: a Long Island ancillary study.

  2008cited by this paper
• Statistical Challenges in Preprocessing in Microarray Experiments in Cancer

  2008cited by this paper
• MiMiR – an integrated platform for microarray data sharing, mining and analysis

  2008cited by this paper
• Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles.

  2007cited by this paper
• Human disease classification in the postgenomic era: A complex systems approach to human pathobiology

  2007cited by this paper
• The Connectivity Map: a new tool for biomedical research

  2007cited by this paper
• The incidentalome: a threat to genomic medicine.

  2006cited by this paper
• Creation and implications of a phenome-genome network

  2006cited by this paper
• Bias as a threat to the validity of cancer molecular-marker research

  2005cited by this paper
• Gene Expression Profiling Predicts Survival in Conventional Renal Cell Carcinoma

  2005cited by this paper
• BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression

  2005cited by this paper
• Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.

  2004cited by this paper
• The Unified Medical Language System (UMLS): integrating biomedical terminology

  2004cited by this paper
• Type 2 diabetes and subsequent incidence of breast cancer in the Nurses' Health Study.

  2003cited by this paper
• Gene expression patterns in ovarian carcinomas.

  2003cited by this paper
• Development of anti-TNF therapy for rheumatoid arthritis

  2002cited by this paper
• Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program

  2001cited by this paper
• Over-expression of ERT(ESX/ESE-1/ELF3), an ets-related transcription factor, induces endogenous TGF-β type II receptor expression and restores the TGF-β signaling pathway in Hs578t human breast cancer cells

  2000cited by this paper
• Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.

  1999cited by this paper
• Dsp First: A Multimedia Approach

  1997influential reference

• Improved prediction of smoking status via isoform-aware RNA-seq deep learning models

  2020cites this paper
• Identification of gene expression logical invariants in Arabidopsis

  2019cites this paper
• Machine learning techniques combined with dose profiles indicate radiation response biomarkers

  2019cites this paper
• A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.

  2019cites this paper
• Exploratory Gene Ontology Analysis with Interactive Visualization

  2018cites this paper
• Computational Curation of Open Science Data

  2018cites this paper
• Transcriptional Networks in Single Perivascular Cells Sorted from Human Adipose Tissue Reveal a Hierarchy of Mesenchymal Stem Cells

  2017cites this paper
• Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis

  2017cites this paper
• HEROD: a human ethnic and regional specific omics database

  2017cites this paper
• HCSGD: An integrated database of human cellular senescence genes.

  2017cites this paper
• Bioinformatics and Precision Medicine

  2017cites this paper
• Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

  2016cites this paper
• Data sources for in vivo molecular profiling of human phenotypes

  2016cites this paper
• Integration of flow studies for robust selection of mechanoresponsive genes

  2016cites this paper
• Principal components analysis and the reported low intrinsic dimensionality of gene expression microarray data

  2016cites this paper
• Transcriptomics analysis of iPSC-derived neurons and modeling of neuropsychiatric disorders.

  2016cites this paper
• Detecting gene similarities using large-scale content-based search systems

  2016cites this paper
• Targeted analyses of very large genome-wide data collections

  2016cites this paper
• Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression

  2016cites this paper
• Computational epigenomics: gene regulation, comparative methodologies, and epigenetic patterns

  2016cites this paper
• Understanding multicellular function and disease with human tissue-specific networks

  2015cites this paper
• Novel methods for integrative analysis of heterogeneous large scale biomedical data

  2015cites this paper
• Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures

  2015cites this paper
• An interactive web application for the dissemination of human systems immunology data

  2015cites this paper
• Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets

  2015cites this paper
• Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data

  2015cites this paper
• Integrative analysis of heterogeneous genomic datasets to discover genetic etiology of autism spectrum disorders

  2014cites this paper
• Toward Computational Cumulative Biology by Combining Models of Biological Datasets

  2014cites this paper
• iPSC-derived neurons as a higher-throughput readout for autism: promises and pitfalls.

  2014cites this paper
• Bayesian Multi-Way Models for Data Translation in Computational Biology

  2014cites this paper
• Tools, methods, and applications for optophysiology in neuroscience

  2013cites this paper
• Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

  2013cites this paper
• Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis.

  2013cites this paper
• Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

  2013cites this paper
• Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability

  2013cites this paper
• Tools, methods, and applications for optophysiology in

  2013cites this paper
• miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients

  2013cites this paper
• Computational solutions for omics data

  2013cites this paper
• Using pathway correlation profiles for understanding pathway perturbation

  2012cites this paper
• InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor

  2012cites this paper
• A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases

  2012influential citation
• A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers

  2012cites this paper
• Reuse of public genome-wide gene expression data

  2012cites this paper
• RESPONSE PROFILES FOR HIGH AND THERAPEUTIC RADIATION DOSES IN BREAST CANCER PATIENTS

  year unknowncites this paper