RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Bioinform.

• Publication date

  2006-10-15

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btl476PMID 16982708
• 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.

• Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses.

  2006cited by this paper
• Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue.

  2006cited by this paper
• Multiple-laboratory comparison of microarray platforms

  2005cited by this paper
• Molecular mechanisms of steroid hormone signaling in plants.

  2005cited by this paper
• Association of valproate‐induced teratogenesis with histone deacetylase inhibition in vivo

  2005cited by this paper
• Rank-based Methods as a Non-parametric Alternative of the T-statistic for the Analysis of Biological Microarray Data

  2005cited by this paper
• ArrayExpress—a public repository for microarray gene expression data at the EBI

  2004cited by this paper
• Bioconductor: open software development for computational biology and bioinformatics

  2004cited by this paper
• Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments

  2004cited by this paper
• Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

  2004cited by this paper
• Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression.

  2004cited by this paper
• GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w]

  2004cited by this paper
• Combining multiple microarray studies and modeling interstudy variation

  2003cited by this paper

• Targeting Colorectal Cancer Stem Cells Through Inhibition of the Fibroblast Growth Factor Receptor 4 Pathway with a Novel Antibody

  2026influential citation
• Transforming evidence synthesis: A systematic review of the evolution of automated meta-analysis in the age of AI

  2026cites this paper
• Development and application of meta-analysis in environmental health research

  2025influential citation
• Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle

  2025cites this paper
• Integration of a 4-gene risk score model enhances prognostic accuracy in acute myeloid leukemia

  2025cites this paper
• Differential producibility analysis reveals drug-associated carbon and nitrogen metabolite expressions in Mycobacterium tuberculosis

  2025influential citation
• Two distinct phenotypes in Snijders Blok-Campeau syndrome and characterization of the behavioral phenotype in a zebrafish model

  2025cites this paper
• Model systems for comprehensive assessment of the nutraceuticals expected efficiency in relation to metabolic syndrome

  2025cites this paper
• Transforming Evidence Synthesis: A Systematic Review of the Evolution of Automated Meta-Analysis in the Age of AI

  2025cites this paper
• Integrated multi-sample transcriptomic analysis of COVID-19 patients against controls using a bioinformatics pipeline

  2025cites this paper
• Privacy-preserving multicenter differential protein abundance analysis with FedProt

  2025cites this paper
• Polysaccharides and atherosclerosis: Focus on the role of key genes of cholesterol metabolism in macrophages

  2024cites this paper
• Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots.

  2024cites this paper
• Nucleotide metabolism in cancer cells fuels a UDP-driven macrophage cross-talk, promoting immunosuppression and immunotherapy resistance

  2024cites this paper
• Integrated transcriptomic data reveal a regulatory network for the lignin biosynthesis in Nicotiana tabacum upon drought stress

  2024cites this paper
• Network Analysis Performed on Transcriptomes of Parkinson’s Disease Patients Reveals Dysfunction in Protein Translation

  2024cites this paper
• Rank Aggregation Methods and Tools in Genomic Data Analysis

  2024cites this paper
• Meta-analysis of RNA interaction profiles of RNA-binding protein using the RBPInper tool

  2024cites this paper
• Overcoming Therapy Resistance in Colorectal Cancer: Targeting the Rac1 Signaling Pathway as a Potential Therapeutic Approach

  2024cites this paper
• Perivascular localized cells commit erythropoiesis in PDGF‐B‐expressing solid tumors

  2023cites this paper
• Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions

  2023influential citation
• Susceptibility identification for seasonal influenza A/H3N2 based on baseline blood transcriptome

  2023cites this paper
• Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle

  2023cites this paper
• Time space and single-cell resolved tissue lineage trajectories and laterality of body plan at gastrulation

  2023cites this paper
• Commercially Available Glucans of Various Raw Materials – Use Optimization from the Nutrigenomics Standpoint

  2023cites this paper
• Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis

  2023cites this paper
• Mechanism for Utilization of the Populus-Derived Metabolite Salicin by a Pseudomonas—Rahnella Co-Culture

  2023cites this paper
• Transcriptional landscape of oncogene-induced senescence: a machine learning based meta analytic approach.

  2023cites this paper
• Ischemic stroke-related gene expression profiles across species: a meta-analysis

  2023cites this paper
• An ancestral molecular response to nanomaterial particulates

  2023cites this paper
• Transcriptomic profile comparison of monocytes from rheumatoid arthritis patients in treatment with methotrexate, anti-TNFa, abatacept or tocilizumab

  2023cites this paper
• NOTCH1-mutated chronic lymphocytic leukemia displays high endoplasmic reticulum stress response with druggable potential

  2023cites this paper
• The impact of violating the independence assumption in meta-analysis on biomarker discovery

  2023cites this paper
• Microarray meta-analysis reveals comprehensive effects of 3,4,5-tricaffeolyquinic acid in cell differentiation and signaling.

  2023cites this paper
• Transcriptomic data of bevacizumab-adapted colorectal adenocarcinoma cells HCT-116.

  2023cites this paper
• Prioritization and functional validation of target genes from single-cell transcriptomics studies

  2023cites this paper
• Macrophages promote anti-androgen resistance in prostate cancer bone disease

  2023cites this paper
• Application of 4 × 44 Oligo Microarray to Transcriptomic Analysis of Immune Response in Rainbow Trout Infected with Aeromonas salmonicida

  2023cites this paper
• A novel IRE1 kinase inhibitor for adjuvant glioblastoma treatment

  2023cites this paper
• Deciphering the molecular basis of abiotic stress response in cucumber (Cucumis sativus L.) using RNA-Seq meta-analysis, systems biology, and machine learning approaches

  2023cites this paper
• Time, Space and Single-Cell Resolved Molecular Trajectory of Cell Populations and the Laterality of the Body Plan at Gastrulation

  2023cites this paper
• 553. H3K27me3 predicted regulation of gene expression linked to calcium quantification in Nelore muscle

  2022cites this paper
• Prediction of Track of Super Cyclone Amphan using WRF-ARW Model

  2022cites this paper
• Integrating transcriptomic datasets across neurological disease identifies unique myeloid subpopulations driving disease‐specific signatures

  2022influential citation
• Selective decrease of donor-reactive Tregs after liver transplantation limits Treg therapy for promoting allograft tolerance in humans

  2022cites this paper
• Machine Learning Using Gene-Sets to Infer miRNA Function.

  2022cites this paper
• Comprehensive meta-analysis and machine learning approaches identified the role of novel drought specific genes in Oryza sativa

  2022cites this paper
• Cell-type specific transcriptional networks in root xylem adjacent cell layers

  2022cites this paper
• A review of bioinformatics tools and web servers in different microarray platforms used in cancer research.

  2022cites this paper
• Comprehensive characterization of the prostate tumor microenvironment identifies CXCR4/CXCL12 crosstalk as a novel antiangiogenic therapeutic target in prostate cancer

  2022cites this paper
• BioTEA: Containerized Methods of Analysis for Microarray-Based Transcriptomics Data

  2022influential citation
• Apoptotic effects of human amniotic fluid mesenchymal stem cells conditioned medium on human MCF-7 breast cancer cell line

  2022cites this paper
• Neurodegeneration and neuroinflammation are linked, but independent of alpha‐synuclein inclusions, in a seeding/spreading mouse model of Parkinson's disease

  2022cites this paper
• Schlafen2 is a regulator of quiescence in adult murine hematopoietic stem cells

  2022cites this paper
• Unraveling the Molecular Basis of the Dystrophic Process in Limb-Girdle Muscular Dystrophy LGMD-R12 by Differential Gene Expression Profiles in Diseased and Healthy Muscles

  2022cites this paper
• Hierarchical identification of a transcriptional panel for the histological diagnosis of lung neuroendocrine tumors

  2022cites this paper
• Assessment of Sex Bias in Housekeeping Gene Expression in Adipose Tissue Through the Massive Analysis of Transcriptomics Data

  2022cites this paper
• Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains

  2022cites this paper
• Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations

  2022cites this paper
• A novel blood brain barrier-permeable IRE1 kinase inhibitor sensitizes glioblastoma to chemotherapy in mice

  2022cites this paper
• The Transcriptional Landscape of BRAF Wild Type Metastatic Melanoma: A Pilot Study

  2022cites this paper
• Gill and Liver Transcript Expression Changes Associated With Gill Damage in Atlantic Salmon (Salmo salar)

  2022cites this paper
• MSPJ: Discovering potential biomarkers in small gene expression datasets via ensemble learning

  2022cites this paper
• Meta-analysis highlights the key drought responsive genes in genes: PEPC and TaSAG7 are hubs response networks

  2022cites this paper
• Transcriptional landscape in BRAF wild type metastatic melanoma

  2022cites this paper
• OMiCC: An expanded and enhanced platform for meta-analysis of public gene expression data

  2022influential citation
• How can artificial intelligence be used for peptidomics?

  2021cites this paper
• The pathogenesis of mesothelioma is driven by a dysregulated translatome

  2021cites this paper
• Reviewing and assessing existing meta-analysis models and tools

  2021cites this paper
• Endogenous retroviruses drive lineage-specific regulatory evolution across primate and rodent placentae.

  2021cites this paper
• Biomarker Categorization in Transcriptomic Meta-Analysis by Concordant Patterns With Application to Pan-Cancer Studies

  2021cites this paper
• Influence of Varying Dietary ω6 to ω3 Fatty Acid Ratios on the Hepatic Transcriptome, and Association with Phenotypic Traits (Growth, Somatic Indices, and Tissue Lipid Composition), in Atlantic Salmon (Salmo salar)

  2021cites this paper
• Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies

  2021cites this paper
• POMAShiny: A user-friendly web-based workflow for metabolomics and proteomics data analysis

  2021cites this paper
• Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings

  2021cites this paper
• In vivo and in vitro transcriptomics meta-analyses reveal that BPA may affect TGF-beta signaling regardless of the toxicology system employed.

  2021cites this paper
• A Transcriptomic Approach Reveals Selective Ribosomal Remodelling in the Tumour Versus the Stromal Compartment of Metastatic Colorectal Cancer

  2021cites this paper
• Multi-omics analyses reveal the roles of the ASR1 transcription factor in tomato fruits.

  2021cites this paper
• Meta-Analysis of Microdissected Breast Tumors Reveals Genes Regulated in the Stroma but Hidden in Bulk Analysis

  2021cites this paper
• Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study

  2021cites this paper
• Molecular Mechanisms Underlying Ascl1-Mediated Astrocyte-to-Neuron Conversion

  2021influential citation
• Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

  2021cites this paper
• Powerful p-value combination methods to detect incomplete association

  2021cites this paper
• Enhanced influenza A H1N1 T cell epitope recognition and cross-reactivity to protein-O-mannosyltransferase 1 in Pandemrix-associated narcolepsy type 1

  2021cites this paper
• The prognostic and clinical significance of IFI44L aberrant downregulation in patients with oral squamous cell carcinoma

  2021cites this paper
• Flimma: a federated and privacy-aware tool for differential gene expression analysis

  2021cites this paper
• A Qualitative Transcriptional Signature for the Histological Reclassi cation of Lung Squamous Cell carcinomas and Adenocarcinomas

  2021cites this paper
• mslp: a comprehensive pipeline in predicting cancer mutations specific synthetic lethal partners

  2021cites this paper
• Mitochondrial inhibitors circumvent adaptive resistance to venetoclax and cytarabine combination therapy in acute myeloid leukemia

  2021cites this paper
• Sequence Mutations of Genes Pertaining to Malignancy in Cancer

  2021cites this paper
• Meta-Analysis of Immune Induced Gene Expression Changes in Diverse Drosophila melanogaster Innate Immune Responses

  2021cites this paper
• The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination.

  2021cites this paper
• Synergistische Wirkung des BRD4-Inhibitors MK-8628 und PLK1-Inhibitors Volasertib in vorklinischen Modellen des Medulloblastoms

  2021cites this paper
• Integrated analysis of mRNA and miRNA profiles revealed the role of miR-193 and miR-210 as potential regulatory biomarkers in different molecular subtypes of breast cancer

  2021cites this paper
• Calorie intake rather than food quantity consumed is the key factor for the anti-aging effect of calorie restriction

  2021cites this paper
• Bioinformatic Analysis and Integration of Transcriptome and Proteome Results Identify Key Coding and Noncoding Genes Predicting Malignancy in Intraductal Papillary Mucinous Neoplasms of the Pancreas

  2021cites this paper
• Extracellular miRNA biomarkers in neurologic disease: is cerebrospinal fluid helpful?

  2021cites this paper
• Polymerase IV Plays a Crucial Role in Pollen Development in Capsella[OPEN]

  2020influential citation
• Liver Transcriptome Profiling Reveals That Dietary DHA and EPA Levels Influence Suites of Genes Involved in Metabolism, Redox Homeostasis, and Immune Function in Atlantic Salmon (Salmo salar)

  2020cites this paper
• Etiology of atherosclerosis informs choice of animal models and tissues for initial functional genomic studies of resveratrol.

  2020cites this paper