2

Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments.

Inference of gene regulatory networks from gene perturbation experiments is the most reliable approach for investigating interdependence between genes. Here, we describe the initial gene perturbations, expression measurements, and preparation steps, …

A curated human cellular microRNAome based on 196 primary cell types

Background: An incomplete picture of the expression distribution of microRNAs (miRNAs) across human cell types has long hindered our understanding of this important regulatory class of RNA. With the continued increase in available public small RNA …

A systems genomics approach uncovers molecular associates of RSV severity.

Respiratory syncytial virus (RSV) infection results in millions of hospitalizations and thousands of deaths each year. Variations in the adaptive and innate immune response appear to be associated with RSV severity. To investigate the host response …

Gene network modeling via TopNet reveals functional dependencies between diverse tumorcritical mediator genes.

Malignant cell transformation requires the cooperation of multiple oncogenic mutations. Here, we demonstrate that non-mutated genes function within a network of strong genetic interdependencies that are critical to the malignant state. Our network modeling methodology, TopNet, reveals a sparse topological gene network architecture, effectively pinpointing functionally relevant gene interactions.

The effect of tissue composition on gene co-expression

Variable cellular composition of tissue samples represents a significant challenge for the interpretation of genomic profiling studies. Substantial effort has been devoted to modeling and adjusting for compositional differences when estimating …

Multiple imputation and direct estimation for qPCR data with non-detects

Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. An important aspect of qPCR data that has been largely ignored is the presence of non-detects: reactions failing to exceed the quantification …

Auto-regressive modeling and diagnostics for qPCR amplification

Current methods used to analyze real-time quantitative polymerase chain reaction (qPCR) data exhibit systematic deviations from the assumed model over the progression of the reaction. Slight variations in the amount of the initial target molecule or …

Systematic exploration of cell morphological phenotypes associated with a transcriptomic query

Cell morphological phenotypes, including shape, size, intensity, and texture of cellular compartments have been shown to change in response to perturbation with small molecule compounds. Image-based cell profiling or cell morphological profiling has …

Big Strides in Cellular MicroRNA Expression

A lack of knowledge of the cellular origin of miRNAs has greatly confounded functional and biomarkers studies. Recently, three studies characterized miRNA expression patterns across 78 human cell types. These combined data expand our knowledge of …

Toward the human cellular microRNAome

MicroRNAs are short RNAs that serve as regulators of gene expression and are essential components of normal development as well as modulators of disease. MicroRNAs generally act cell-autonomously, and thus their localization to specific cell types is …