Chickspress

Chickspress provides integrated access to chicken RNA and peptide expression data from high-throughput sequencing and proteomics to enable comparative evaluation of NCBI and Ensembl gene models against experimental mRNA, miRNA, protein, and peptide evidence across tissues and developmental stages.

Key Features:

• Integration of Gene Models: Integrates NCBI and Ensembl gene models to enable direct comparison of annotation pipelines against experimental expression data.
• Linkage with Experimental Data and QTL: Links gene sets to experimental gene expression datasets and quantitative trait loci (QTL) information to associate gene products with tissues and developmental stages.
• Comprehensive Data Sets: Aggregates 161 gene expression datasets encompassing mRNAs, miRNAs, proteins, and peptides derived from high-throughput sequencing and proteomics.

Scientific Applications:

• Functional Genomics: Provides experimental expression evidence for mRNAs, miRNAs, proteins, and peptides to support gene function studies.
• Comparative Genomics: Enables direct comparison between NCBI and Ensembl annotations to assess annotation differences.
• Evolutionary Biology: Facilitates comparison of expression patterns across tissues and developmental stages for evolutionary analyses.
• QTL and Trait Genetics: Integrates QTL information to aid investigation of the genetic basis of phenotypic traits.

Methodology:

Aggregates publicly available RNA and peptide datasets from the NCBI Sequence Read Archive and proteome archives and incorporates NCBI and Ensembl gene models for comparative analyses.