Feature Description Download
aa_class_change Twenty six amino class change categories (e.g. Positive => Aromatic) Included by orchid_db
cadd; cadd_raw Combined Annotation Dependent Depletion scores (c-scores and raw values) annotation / index
consequence_type snpEff consequences (e.g. nsSNP, 5’UTR, etc…) Included by orchid_db
context The trinucleotide context as per Alexandrov et. al. Included by orchid_db
copy_number segment mean log2 copy number values, averaged over ICGC donors Dataset specific, please obtain your own
dann Deep Artificial Neural Network (deleteriousness) annotation / index
dbsuper Super enhancers (all cell types) annotation
dnase Encode DNASE I Hypersensitivity distal and proximal (all cell type) annotation
encode Encode enhancer, promoter histone marks (distal and proximal; any cell type) annotation
frequency Number of donors sharing this mutation Included by orchid_db
funseq2 Somatic mutation variant prioritization (deleteriousness) annotation / index
gwas Boolean presence of GWAS Annotated SNPs annotation
impact Four SNPEff predicted functional impact categories (Modifier, Low, Moderate, High) Included by orchid_db
kegg_cancer_gene Boolean presence/absence within a cancer pathway Generated by orchid_db (ask us)
kegg_pathways Biological cancer pathway membership (22 pathways) Generated by orchid_db (ask us)
phyloP Primate evolutionary conservation score (deleteriousness) original / orchid annotation / orchid index
remap ChIP-seq analysis of regulatory elements annotation
rfecs Random Forest Enhancer / Chromatin States (11 cell types) annotation
segmentation ChromHMM and Segway genomic state predictors annotation
targetscans miRNAs sites annotation
transcript_biotype Transcript biotype as reported by SNPEff (35 categories) Included by orchid_db
wgrna Whole Genome RNA predicted binding site (any) annotation