Genomics has the potential to revolutionize the diagnosis and management of cancer by offering an unprecedented comprehensive view of the molecular underpinnings of pathology. Computational analysis is essential to transform the masses of generated data into a mechanistic understanding of disease. Here we review current research aimed at uncovering the modular organization and function of transcriptional networks and responses in cancer. We first describe how methods that analyze biological processes in terms of higher-level modules can identify robust signatures of disease mechanisms. We then discuss methods that aim to identify the regulatory mechanisms underlying these modules and processes. Finally, we show how comparative analysis, combining human data with model organisms, can lead to more robust findings. We conclude by discussing the challenges of generalizing these methods from cells to tissues and the opportunities they offer to improve cancer diagnosis and management.
Loss of JunB activity enhances stromelysin 1 expression in a model of the epithelial-to-mesenchymal transition of mouse skin tumors
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
Identification of genes periodically expressed in the human cell cycle and their expression in tumors
Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes
Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics
NFATC2 transcription factor regulates cell cycle progression during lymphocyte activation: evidence of its involvement in the control of cyclin gene expression
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations
Comparing genomic expression patterns across species identifies shared transcriptional profile in aging
Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds
Identification of genes whose expression is upregulated in lung adenocarcinoma cells in comparison with type II alveolar cells and bronchiolar epithelial cells in vivo
Calculating the statistical significance of physical clusters of co-regulated genes in the genome: the role of chromatin in domain-wide gene regulation
Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
Introducing coordinated care (2): evaluation of design features and implementation processes implications for a preferred health system reform model
Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival
Current concepts in the molecular genetics of pediatric brain tumors: implications for emerging therapies
Inferring the skeleton cell cycle regulatory network of malaria parasite using comparative genomic and variational Bayesian approaches
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors
Regulation of conformer-specific activation of the integrin LFA-1 by a chemokine-triggered Rho signaling module
Identifying grade/stage-related active modules in human co-regulatory networks: a case study for breast cancer
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling
Expression signature developed from a complex series of mouse models accurately predicts human breast cancer survival
Met-regulated expression signature defines a subset of human hepatocellular carcinomas with poor prognosis and aggressive phenotype
A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients
Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks
Dissecting systems-wide data using mixture models: application to identify affected cellular processes
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns
Gene selection and classification for cancer microarray data based on machine learning and similarity measures
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks
Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements
A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation
A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana
Patterns of human gene expression variance show strong associations with signaling network hierarchy
Genome-wide matching of genes to cellular roles using guilt-by-association models derived from single sample analysis
Integrating expression profiling and whole-genome association for dissection of fat traits in a porcine model.
Epidermal growth factor-containing fibulin-like extracellular matrix protein 1, EFEMP1, a novel tumor-suppressor gene detected in hepatocellular carcinoma using double combination array analysis
Feature selection and classification of MAQC-II breast cancer and multiple myeloma microarray gene expression data
Assessing the biological significance of gene expression signatures and co-expression modules by studying their network properties
A novel five gene signature derived from stem-like side population cells predicts overall and recurrence-free survival in NSCLC
Cancer-risk module identification and module-based disease risk evaluation: a case study on lung cancer
Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes?
Peeling off the hidden genetic heterogeneities of cancers based on disease-relevant functional modules
An Integrated Statistical Approach to Compare Transcriptomics Data Across Experiments: A Case Study on the Identification of Candidate Target Genes of the Transcription Factor PPARα
Human cancer classification: a systems biology- based model integrating morphology, cancer stem cells, proteomics, and genomics
Genome-block expression-assisted association studies discover malaria resistance genes in Anopheles gambiae
An omics strategy for discovering pulmonary biomarkers potentially relevant to the evaluation of tobacco products
Integrated genomic and prospective clinical studies show the importance of modular pleiotropy for disease susceptibility, diagnosis and treatment
Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers
A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas
miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients
Molecular screening for breast cancer prevention, early detection, and treatment planning: combining biomarkers from DNA, RNA, and protein
Tissue inhibitor of metalloproteinase-3 is up-regulated by transforming growth factor-beta1 in vitro and expressed in fibroblastic foci in vivo in idiopathic pulmonary fibrosis
Integrative transcriptional analysis between human and mouse cancer cells provides a common set of transformation associated genes
From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases
Laquinimod suppress antigen presentation in relapsing-remitting multiple sclerosis: in-vitro high-throughput gene expression study
Joint high-dimensional Bayesian variable and covariance selection with an application to eQTL analysis
Bayesian Network Inference Enables Unbiased Phenotypic Anchoring of Transcriptomic Responses to Cigarette Smoke in Humans
Customising an antibody leukocyte capture microarray for systemic lupus erythematosus: beyond biomarker discovery
Microarray analysis identifies altered regulation of nuclear receptor family members in the pre-disease state of multiple sclerosis
Gene expression profiling of ovarian tissues for determination of molecular pathways reflective of tumorigenesis
Decoding NMDA receptor signaling: identification of genomic programs specifying neuronal survival and death
European Organisation for Research and Treatment of Cancer (EORTC) Pathobiology Group standard operating procedure for the preparation of human tumour tissue extracts suited for the quantitative analysis of tissue-associated biomarkers
Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach
A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus
A neural network-based biomarker association information extraction approach for cancer classification
Deciphering molecular determinants of chemotherapy in gastrointestinal malignancy using systems biology approaches
Cytokine-like factor 1 gene expression is enriched in idiopathic pulmonary fibrosis and drives the accumulation of CD4+ T cells in murine lungs: evidence for an antifibrotic role in bleomycin injury
Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Multi-organ whole-genome measurements and reverse engineering to uncover gene networks underlying complex traits.
Advanced Hepatocellular Carcinoma: Pretreatment Contrast-enhanced CT Texture Parameters as Predictive Biomarkers of Survival in Patients Treated with Sorafenib
Stomatin-like protein 2 inhibits cisplatin-induced apoptosis through MEK/ERK signaling and the mitochondrial apoptosis pathway in cervical cancer cells
Technology insight: pharmacoproteomics for cancer--promises of patient-tailored medicine using protein microarrays
Genome-wide expression studies of atherosclerosis: critical issues in methodology, analysis, interpretation of transcriptomics data
Automated brain tumor biopsy prediction using single-labeling cDNA microarrays-based gene expression profiling
Use of a rainbow trout oligonucleotide microarray to determine transcriptional patterns in aflatoxin B1-induced hepatocellular carcinoma compared to adjacent liver
Innovative genomic-based model for personalized treatment of gastric cancer: integrating current standards and new technologies
A framework to identify physiological responses in microarray-based gene expression studies: selection and interpretation of biologically relevant genes
Construction of gene causal regulatory networks using microarray data with the coefficient of intrinsic dependence
A new insight into underlying disease mechanism through semi-parametric latent differential network model
A statistical normalization method and differential expression analysis for RNA-seq data between different species
A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks
Multidisciplinary insight into clonal expansion of HTLV-1-infected cells in adult T-cell leukemia via modeling by deterministic finite automata coupled with high-throughput sequencing
Identifying dysregulated pathways in postmenopausal osteoporosis through investigation of crosstalk between pathways
Exploration of gene functions for esophageal squamous cell carcinoma using network-based guilt by association principle
A modular analysis of breast cancer reveals a novel low-grade molecular signature in estrogen receptor-positive tumors
Integrative genomic analysis of phosphatidylinositol 3'-kinase family identifies PIK3R3 as a potential therapeutic target in epithelial ovarian cancer
Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.
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