This review focuses on tools for studying a cell's transcriptome, the collection of all RNA transcripts produced at a specific time, and the tools available for determining how these changes in gene expression relate to the functional changes in an organism. While the microarray-based (analog) gene-expression profiling technology has dominated the 'omics' era, Next-Generation Sequencing based gene-expression profiling (RNA-Seq) is likely to replace this analog technology in the future. RNA-Seq shows much promise for transcriptomic studies as the genes of interest do not have to be known a priori, new classes of RNA, SNPs and alternative splice variants can be detected, and it is also theoretically possible to detect transcripts from all biologically relevant abundance classes. However, the technology also brings with it new issues to resolve: the specific technical properties of RNA-Seq data differ to those of analog data, leading to novel systematic biases which must be accounted for when analysing this type of data. Additionally, multireads and splice junctions can cause problems when mapping the sequences back to a genome, and concepts such as cloud computing may be required because of the massive amounts of data generated.
Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome
Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays
Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays
The expression of P-glycoprotein in AML cells with FLT3 internal tandem duplications is associated with reduced apoptosis in response to FLT3 inhibitors
Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep
Gene expression levels assessed by oligonucleotide microarray analysis and quantitative real-time RT-PCR -- how well do they correlate?
Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
Gene expression profiling of naïve sheep genetically resistant and susceptible to gastrointestinal nematodes
Molecular profiling of a rat model of colitis: validation of known inflammatory genes and identification of novel disease-associated targets
FUNC: a package for detecting significant associations between gene sets and ontological annotations
Interpretation of microarray data: trudging out of the abyss towards elucidation of biological significance
Nutrigenomics applied to an animal model of Inflammatory Bowel Diseases: transcriptomic analysis of the effects of eicosapentaenoic acid- and arachidonic acid-enriched diets
EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species
Comprehensive analysis of PPARalpha-dependent regulation of hepatic lipid metabolism by expression profiling
Assessment of the immune capacity of mammary epithelial cells: comparison with mammary tissue after challenge with Escherichia coli
Genome-wide analysis of dietary eicosapentaenoic acid- and oleic acid-induced modulation of colon inflammation in interleukin-10 gene-deficient mice
Terminal differentiation of goat mammary tissue during pregnancy requires the expression of genes involved in immune functions
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer
Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain
Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro
RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions
Seasonal variation of urinary microRNA expression in male goats (Capra hircus) as assessed by next generation sequencing
Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies
Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms
RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications
Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis
Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD)
A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models
MicroRNA profile comparison of testicular tissues derived from successful and unsuccessful microdissection testicular sperm extraction retrieval in non-obstructive azoospermia patients
Comparative transcriptome analysis reveals K+ transporter gene contributing to salt tolerance in eggplant
De novo transcriptomic analysis of light-induced flavonoid pathway, transcription factors in the flower buds of Lonicera japonica
Identification and Validation of Gene Expression Patterns in Cystitis Glandularis Patients and Controls
A Leveraged Signal-to-Noise Ratio (LSTNR) Method to Extract Differentially Expressed Genes and Multivariate Patterns of Expression From Noisy and Low-Replication RNAseq Data
Patterns, Profiles, and Parsimony: Dissecting Transcriptional Signatures From Minimal Single-Cell RNA-Seq Output With SALSA
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.
Synthetic Genetic Array Analysis
Synthetic genetic arrays allow the systematic examination of genetic interactions. Here is the latest research focusing on synthetic genetic arrays and their analyses.
Congenital hyperinsulinism is caused by genetic mutations resulting in excess insulin secretion from beta cells of the pancreas. Here is the latest research.
Neural Activity: Imaging
Imaging of neural activity in vivo has developed rapidly recently with the advancement of fluorescence microscopy, including new applications using miniaturized microscopes (miniscopes). This feed follows the progress in this growing field.
Chronic Fatigue Syndrome
Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.
Epigenetic memory refers to the heritable genetic changes that are not explained by the DNA sequence. Find the latest research on epigenetic memory here.
Cell Atlas of the Human Eye
Constructing a cell atlas of the human eye will require transcriptomic and histologic analysis over the lifespan. This understanding will aid in the study of development and disease. Find the latest research pertaining to the Cell Atlas of the Human Eye here.
Femoral Neoplasms are bone tumors that arise in the femur. Discover the latest research on femoral neoplasms here.
STING Receptor Agonists
Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.