AIMC Topic: Gene Expression Profiling

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g:Profiler-a web server for functional interpretation of gene lists (2016 update).

Nucleic acids research Apr 20, 2016
Functional enrichment analysis is a key step in interpreting gene lists discovered in diverse high-throughput experiments. g:Profiler studies flat and ranked gene lists and finds statistically significant Gene Ontology terms, pathways and other gene ...
Molecular Sequence Annotation Gene Ontology Binding Sites Computer Graphics Vertebrates Plants Fungi Insecta Gene Expression Regulation Humans Animals Protein Binding Transcription Factors Internet Gene Expression Profiling User-Computer Interface
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Exploring information from the topology beneath the Gene Ontology terms to improve semantic similarity measures.

Gene Apr 12, 2016
Measuring the similarity between pairs of biological entities is important in molecular biology. The introduction of Gene Ontology (GO) provides us with a promising approach to quantifying the semantic similarity between two genes or gene products. T...
Databases, Protein Semantics Yeasts Terminology as Topic Humans Algorithms Gene Expression Profiling Proteins Gene Ontology
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Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci.

Arteriosclerosis, thrombosis, and vascular biology Mar 10, 2016
OBJECTIVE: Recent genome-wide association studies of coronary artery disease (CAD) have revealed 58 genome-wide significant and 148 suggestive genetic loci. However, the molecular mechanisms through which they contribute to CAD and the clinical impli...
Humans Neural Networks, Computer Phenotype Genome-Wide Association Study Protein Interaction Maps Gene Regulatory Networks Mice Genomics Computer Simulation Animals Gene Expression Profiling Case-Control Studies Gene Expression Regulation Lumican Bayes Theorem Coronary Artery Disease STAT3 Transcription Factor Genetic Loci Genetic Predisposition to Disease Computational Biology Signal Transduction Databases, Genetic
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MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis.

Bioinformatics (Oxford, England) Mar 2, 2016
MOTIVATION: Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational pot...
Supervised Machine Learning Genomics DNA Methylation Idiopathic Pulmonary Fibrosis Meta-Analysis as Topic Humans Prognosis Breast Neoplasms Gene Expression Profiling Algorithms Research Design
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Network stratification analysis for identifying function-specific network layers.

Molecular bioSystems Feb 16, 2016
A major challenge of systems biology is to capture the rewiring of biological functions (e.g. signaling pathways) in a molecular network. To address this problem, we proposed a novel computational framework, namely network stratification analysis (Ne...
Gene Expression Regulation, Fungal Transcription, Genetic Gene Expression Regulation, Neoplastic Signal Transduction Carcinoma, Hepatocellular Neural Networks, Computer Protein Interaction Maps Algorithms Cluster Analysis Gene Regulatory Networks Humans Disease Progression Models, Biological Computational Biology Gene Expression Profiling Liver Neoplasms
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Machine learning-based classification of diffuse large B-cell lymphoma patients by eight gene expression profiles.

Cancer medicine Feb 11, 2016
Gene expression profiling (GEP) had divided the diffuse large B-cell lymphoma (DLBCL) into molecular subgroups: germinal center B-cell like (GCB), activated B-cell like (ABC), and unclassified (UC) subtype. However, this classification with prognosti...
Humans Prognosis Sensitivity and Specificity Lymphoma, Large B-Cell, Diffuse Male Female Aged Cyclophosphamide Treatment Outcome Databases, Genetic Middle Aged Germinal Center Genes, Neoplasm Support Vector Machine Doxorubicin Gene Expression Profiling Antibodies, Monoclonal, Murine-Derived Survival Analysis ROC Curve Antineoplastic Combined Chemotherapy Protocols Prednisone Rituximab Vincristine
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Integrative modeling of multi-omics data to identify cancer drivers and infer patient-specific gene activity.

BMC systems biology Feb 11, 2016
BACKGROUND: High throughput technologies have been used to profile genes in multiple different dimensions, such as genetic variation, copy number, gene and protein expression, epigenetics, metabolomics. Computational analyses often treat these differ...
Tumor Suppressor Proteins Gene Dosage Oncogenes Computational Biology Fuzzy Logic Mutation Models, Biological Neoplasms Antineoplastic Agents Gene Expression Profiling Cell Line, Tumor Humans Colorectal Neoplasms
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ZeitZeiger: supervised learning for high-dimensional data from an oscillatory system.

Nucleic acids research Jan 26, 2016
Numerous biological systems oscillate over time or space. Despite these oscillators' importance, data from an oscillatory system is problematic for existing methods of regularized supervised learning. We present ZeitZeiger, a method to predict a peri...
Mice Algorithms Time Computational Biology Animals Periodicity Supervised Machine Learning Gene Expression Profiling Circadian Clocks Gene Regulatory Networks
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Missing value imputation for microRNA expression data by using a GO-based similarity measure.

BMC bioinformatics Jan 11, 2016
BACKGROUND: Missing values are commonly present in microarray data profiles. Instead of discarding genes or samples with incomplete expression level, missing values need to be properly imputed for accurate data analysis. The imputation methods can be...
Oligonucleotide Array Sequence Analysis Humans Algorithms MicroRNAs Models, Statistical Gene Ontology Gene Expression Profiling Computational Biology
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Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.

BMC bioinformatics Jan 11, 2016
BACKGROUND: A living cell has a complex, hierarchically organized signaling system that encodes and assimilates diverse environmental and intracellular signals, and it further transmits signals that control cellular responses, including a tightly con...
Systems Biology Signal Transduction Saccharomyces cerevisiae Neural Networks, Computer Models, Theoretical Gene Expression Regulation, Fungal Computer Simulation Transcription Factors Saccharomyces cerevisiae Proteins Gene Expression Profiling
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