Gene expression ≈ Gene expression
View article: The GTEx Consortium atlas of genetic regulatory effects across human tissues
The GTEx Consortium atlas of genetic regulatory effects across human tissues Open
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
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GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis Open
Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. He…
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Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation Open
MicroRNAs (miRNAs) are a class of non-coding RNAs that play important roles in regulating gene expression. The majority of miRNAs are transcribed from DNA sequences into primary miRNAs and processed into precursor miRNAs, and finally matur…
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KEGG: integrating viruses and cellular organisms Open
KEGG (https://www.kegg.jp/) is a manually curated resource integrating eighteen databases categorized into systems, genomic, chemical and health information. It also provides KEGG mapping tools, which enable understanding of cellular and o…
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Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression Open
We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic…
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Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics Open
Slingshot is a uniquely robust and flexible tool which combines the highly stable techniques necessary for noisy single-cell data with the ability to identify multiple trajectories. Accurate lineage inference is a critical step in the iden…
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High expression of ACE2 receptor of 2019-nCoV on the epithelial cells of oral mucosa Open
It has been reported that ACE2 is the main host cell receptor of 2019-nCoV and plays a crucial role in the entry of virus into the cell to cause the final infection. To investigate the potential route of 2019-nCov infection on the mucosa o…
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Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma Open
Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC c…
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The role of MicroRNAs in human cancer Open
MicroRNAs (miRNAs) are endogenous, small non-coding RNAs that function in regulation of gene expression. Compelling evidences have demonstrated that miRNA expression is dysregulated in human cancer through various mechanisms, including amp…
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Endogenous microRNA sponges: evidence and controversy Open
The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for lo…
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Adjuvant Chemotherapy Guided by a 21-Gene Expression Assay in Breast Cancer Open
Adjuvant endocrine therapy and chemoendocrine therapy had similar efficacy in women with hormone-receptor-positive, HER2-negative, axillary node-negative breast cancer who had a midrange 21-gene recurrence score, although some benefit of c…
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Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma Open
BACKGROUND: Diffuse large B-cell lymphomas (DLBCLs) are phenotypically and genetically heterogeneous. Gene-expression profiling has identified subgroups of DLBCL (activated B-cell-like [ABC], germinal-center B-cell-like [GCB], and unclassi…
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New approach for understanding genome variations in KEGG Open
KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated databas…
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JASPAR 2020: update of the open-access database of transcription factor binding profiles Open
JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In thi…
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Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences Open
High-throughput sequencing of cDNA (RNA-seq) is used extensively to characterize the transcriptome of cells. Many transcriptomic studies aim at comparing either abundance levels or the transcriptome composition between given conditions, an…
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NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis Open
The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting ge…
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Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism Open
N 6 -methyladenosine (m 6 A) is a chemical modification present in multiple RNA species, being most abundant in mRNAs. Studies on enzymes or factors that catalyze, recognize, and remove m 6 A have revealed its comprehensive roles in almost…
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iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data Open
Combining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
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The biochemical basis of microRNA targeting efficacy Open
Biochemical prediction of miRNA targeting MicroRNAs (miRNAs) regulate most human messenger RNAs and play essential roles in diverse developmental and physiological processes. Correctly predicting the function of each miRNA requires a bette…
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SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data Open
Background Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-fr…
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Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding Open
Identifying single-cell types in the mouse brain The recent development of single-cell genomic techniques allows us to profile gene expression at the single-cell level easily, although many of these methods have limited throughput. Rosenbe…
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Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays Open
Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies p…
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Mediator and RNA polymerase II clusters associate in transcription-dependent condensates Open
Phase separation and gene control Many components of eukaryotic transcription machinery—such as transcription factors and cofactors including BRD4, subunits of the Mediator complex, and RNA polymerase II—contain intrinsically disordered lo…
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Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data Open
Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene express…
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g:Profiler—a web server for functional interpretation of gene lists (2016 update) Open
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 …
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From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline Open
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed…
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RNA modifications modulate gene expression during development Open
RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition of many of these modifications is required for …
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Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder Open
INTRODUCTION Our understanding of the pathophysiology of psychiatric disorders, including autism spectrum disorder (ASD), schizophrenia (SCZ), and bipolar disorder (BD), lags behind other fields of medicine. The diagnosis and study of thes…
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An environment-dependent transcriptional network specifies human microglia identity Open
Of mice and men's microglia Microglia are immune system cells that function in protecting and maintaining the brain. Gosselin et al. examined the epigenetics and RNA transcripts from single microglial cells and observed consistent profiles…
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Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis Open
Rationale: The contributions of diverse cell populations in the human lung to pulmonary fibrosis pathogenesis are poorly understood. Single-cell RNA sequencing can reveal changes within individual cell populations during pulmonary fibrosis…