Pathway analysis is a key analytical stage in the interpretation of omics data, providing a
powerful method for detecting alterations in cellular processes. We recently developed a …

Motivation At present, a fundamental challenge in single-cell RNA-sequencing data analysis
is functional interpretation and annotation of cell clusters. Biological pathways in distinct cell …

To demonstrate the benefits of RNA-Seq over microarray in transcriptome profiling, both
RNA-Seq and microarray analyses were performed on RNA samples from a human T cell …

Human T cells coordinate adaptive immunity in diverse anatomic compartments through
production of cytokines and effector molecules, but it is unclear how tissue site influences T …

Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in
response to cytokines. However, the cytokine responses in memory T cells remain largely …

Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating
data from different 'omics technologies and different species still requires considerable …

Background A proper balance between different T helper (Th) cell subsets is necessary for
normal functioning of the adaptive immune system. Revealing key genes and pathways …

Transcriptomic profiling by RNA sequencing (RNA-Seq) represents the preferred approach
to measure genome-wide gene expression for understanding cellular function, tissue …

High-throughput experiments are routinely performed in modern biological studies.
However, extracting meaningful results from massive experimental data sets is a …

Cells require coordinated control over gene expression when responding to environmental
stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting …