AppleMDO

AppleMDO integrates genomic, transcriptomic, and epigenomic datasets for apple to enable analysis of gene co-expression, functional modules, and chromatin states.

Key Features:

• Co-expression Networks: Co-expression networks are constructed from 112 RNA-seq datasets and include both global and tissue-preferential networks with queries by locus ID.
• Functional Modules Identification: A total of 1,076 functional modules of closely related genes have been identified and subjected to functional enrichment analyses linked to development, secondary metabolism, hormone response, and transcriptional regulation.
• Chromatin State Prediction: Incorporates 20 epigenomic datasets, including ChIP-seq, DNase-seq, and DNA methylation data, and uses the ChromHMM algorithm to classify the genome into 620,122 fragments across 24 chromatin states.
• Gene Annotation and Functional Support: Provides structural and functional annotations including gene families, KEGG pathways, Gene Ontology (GO) terms, Pfam domains, orthologues in thirteen species, and computational resources such as GO analysis, BLAST, motif analysis, ID conversion, sequence extraction, and integration with the UCSC Genome Browser.

Scientific Applications:

• Gene Function Prediction: Supports genome-wide prediction of gene function through co-expression networks and functional module analyses.
• Regulatory Mechanism Analysis: Enables investigation of gene regulatory relationships and chromatin-state–associated regulatory elements using co-expression and chromatin-state data.
• Agronomic Trait Studies: Facilitates exploration of gene roles in agronomic traits in apple and aids hypothesis generation for experimental design.
• Comparative and Cross-species Analysis: Supports comparative studies via orthologue mappings to thirteen species and integrated pathway and domain annotations.

Methodology:

Co-expression networks were constructed from 112 RNA-seq datasets to produce global and tissue-preferential networks; ChromHMM was applied to 20 epigenomic datasets (ChIP-seq, DNase-seq, DNA methylation) to segment the genome into 620,122 fragments across 24 chromatin states; 1,076 functional modules were identified and subjected to functional enrichment analyses; gene annotations were integrated from KEGG, GO, Pfam and orthologue mappings to thirteen species.