SGID

SGID provides integrated genomic, transcriptomic, epigenomic, and population-genetic data and analysis for Bombyx mori to support genetic, functional genomics, and evolutionary studies.

Key Features:

• Comprehensive Data Integration: Integrates gene annotations for Bombyx mori including function description, gene ontology, KEGG pathways, cellular localization, transmembrane topology, secondary and tertiary protein structure, homologous groups, and transcription factors, with function annotation for 98% of genes.
• Sequence-based Gene Inquiry: Supports sequence alignment searches against genomes and specific genes for gene-level queries and analyses.
• Genome-scale Visualization: Presents genome-scale visualization of population genetics test results derived from high-depth resequencing data of 158 silkworm samples.
• Transcriptomic and Epigenomic Data Analysis: Includes analytical resources for transcriptomic and epigenomic datasets sourced from 79 NCBI BioProjects.

Scientific Applications:

• Genetics: Provides annotated gene information and sequence resources to support genetic studies in Bombyx mori.
• Functional Genomics: Enables functional genomics analyses using integrated annotations, KEGG pathways, protein structure, and transcription factor data.
• Transcriptomics: Supports analysis of transcriptomic datasets from the included NCBI BioProjects to study gene expression patterns.
• Epigenetics: Facilitates investigation of epigenomic datasets to study regulatory modifications in Bombyx mori.
• Population Genetics and Evolutionary Biology: Supports population-genetic and evolutionary analyses using population genetics test results from 158 high-depth resequenced samples.

Methodology:

SGID integrates annotations and datasets compiled from Silkbase, SilkDB, and Ensembl Insects and incorporates high-depth resequencing data and transcriptomic and epigenomic datasets from 79 NCBI BioProjects, leveraging existing data-analysis methods and the growth of sequencing datasets.