Schemas › Biology & Biotechnology › RNA-Seq Differential Gene Expression Analysis Workflow

RNA-Seq Differential Gene Expression Analysis Workflow

A SciSchema.org Process Schema

Domain: Biology & Biotechnology
Schema: RNA-Seq Differential Gene Expression Analysis Workflow
Current version: 1.0.0

RNA-Seq differential gene expression analysis is a computational workflow used to quantify and compare gene activity across biological conditions.

Properties from RNA-Seq Differential Gene Expression Analysis Workflow

The table below lists the top-level properties of this master schema. Each property may contain more detailed nested fields in the JSON Schema representation.

Property Expected Type Description Required
biological_source_material Object Biological source, experimental conditions, and replicate structure. Yes
rna_extraction_and_quality_metrics Object RNA isolation protocol and quality control measurements. Yes
library_preparation_protocol Object cDNA library construction parameters. Yes
sequencing_platform_and_configuration Object Sequencing instrument and run configuration. Yes
raw_data_quality_control Object Preprocessing and quality control steps applied to raw sequencing reads. No
read_alignment Object Read alignment or pseudoalignment to the reference genome or transcriptome. Yes
expression_quantification Object Strategy for estimating gene or transcript expression levels from aligned reads. Yes
normalization_method Object Between-sample normalization to correct for library size and composition biases. RPKM/FPKM are within-sample metrics and not appropriate for DGE. Yes
statistical_analysis Object Statistical framework for differential expression testing, including model specification, batch correction, and significance criteria. Yes
output_artifacts Array Files and visualizations generated by the workflow. No
reproducibility_metadata Object Metadata required to reproduce the workflow and ensure FAIR compliance. Yes

Machine-readable schema representations

This schema is available in two machine-readable representations: as an ORKG template, which can be exported as SHACL, and as a JSON Schema document for download and reuse.