Pedican

Pedican curates a comprehensive literature-based gene resource for pediatric cancers, compiling 735 human genes, 88 gene fusion events, and 24 chromosomal abnormalities derived from 2,245 PubMed abstracts to support genetic and molecular analysis.

Key Features:

• Curated gene catalog: A curated list of 735 human genes implicated in pediatric cancers.
• Gene fusion events: A curated list of 88 gene fusion events associated with pediatric cancers.
• Chromosomal abnormalities: A curated list of 24 chromosomal abnormality occurrences reported in pediatric cancers.
• Literature curation: Manual extraction and curation of data from 2,245 PubMed abstracts.
• Entrez Gene information: Entrez Gene identifiers and basic gene metadata for each entry.
• Pathway annotations: Annotations of involved pathways implicated in pediatric cancers.
• Protein-Protein Interactions (PPI): Protein-protein interaction networks linking genes to cancer-relevant partners.
• Gene expression data: Quantitative gene expression measurements across tissues and conditions.
• Epigenetic modifications: Annotations of DNA methylation, histone modifications, and chromatin accessibility.
• Functional annotations: Gene Ontology terms and pathway memberships derived from experimental and computational analyses.
• Variant annotations: Information on single nucleotide polymorphisms (SNPs), copy number variations (CNVs), and structural variants.
• Phenotype associations: Links between genes/variants and clinical phenotypes, disease associations, and functional consequences.
• Drug response data: Drug sensitivity, resistance, and pharmacogenomic associations for genes and variants.
• Evolutionary conservation: Comparative genomics data highlighting conserved and divergent regions across species.

Scientific Applications:

• Genetic etiology mapping: Elucidation of genetic abnormalities and cellular mechanisms underlying pediatric cancers.
• Candidate gene and biomarker identification: Identification and prioritization of candidate driver genes, fusion events, and biomarkers for research and translational studies.
• Therapeutic target and pharmacogenomics research: Analysis of drug response and pharmacogenomic associations to support therapy development.
• Integrative molecular analysis: Integration of expression, epigenetic, PPI, and variant data to study tumor biology and pathways.
• Comparative and evolutionary studies: Use of evolutionary conservation data to assess functional relevance of genes and variants.

Methodology:

Data were collected by literature curation and data integration from 2,245 PubMed abstracts, and annotations were compiled from experimental and computational analyses.