GENE-Counter

GENE-Counter analyzes RNA-Sequencing (RNA-Seq) data to identify differentially expressed genes across eukaryotic and prokaryotic organisms, including non-model organisms without a reference genome, using a Perl-based pipeline.

Key Features:

• Alignment Flexibility: Supports CASHX, Bowtie, and BWA and can integrate any Sequence Alignment/Map (SAM)-compliant aligner.
• Differential Gene Expression Analysis: Provides three statistical packages based on variations of the negative binomial distribution, with a default over-parameterized negative binomial test tailored for small sample sizes and high variability.
• Gene Ontology Enrichment: Includes three methods for assessing enriched Gene Ontology (GO) terms.
• Data Management: Stores results in a MySQL relational database.

Scientific Applications:

• Arabidopsis thaliana defense response: Applied to next-generation RNA-Seq data from Arabidopsis thaliana to analyze defense-related differential expression.
• Method validation: Demonstrated substantial overlap in results across the three statistical packages, supporting method concordance.

Methodology:

Alignment is performed with CASHX, Bowtie, BWA or any SAM-compliant program; differential expression is tested using three negative-binomial-based statistical packages with a default over-parameterized negative binomial test; Gene Ontology enrichment is assessed by three methods; and results are stored in a MySQL relational database.