SomaLogic Mapping

SomaLogic Mapping Dataset

This dataset provides a mapping of SomaLogic aptamers to their corresponding genomic coordinates and gene identifiers. The data is derived from the SomaLogic v5.0 Plasma ADAT file.

Data Generation Summary

The mapping was generated using the following steps:

1. Input Data: Raw data was retrieved from the SomaLogic GitHub repository (Example Data v5.0 Plasma ADAT).
2. Formatting:
   • Split multiple entries for UniProt, Entrez Gene ID, and Entrez Gene Symbol.
   • Filtered for Human organism only.
   • Filtered for Protein type (removing controls).
   • Excluded all entries flagged as “internal use only”.
3. Mapping: UniProt IDs, Entrez IDs, and HGNC symbols were mapped to Ensembl Gene IDs using biomaRt (Ensembl dataset hsapiens_gene_ensembl).
4. Filtering:
   • Only protein_coding genes were retained.
   • Only standard chromosomes (1-22, X, Y) were retained.
   • Mappings were cross-referenced to ensure symbol consistency.
5. Genomic Positions: Start and End positions were retrieved for both hg19 and hg38 builds using TxDb.Hsapiens.UCSC.hg19.knownGene and TxDb.Hsapiens.UCSC.hg38.knownGene.

Column Descriptions

Column	Description
SeqId	SomaLogic Sequence ID
SomaId	SomaLogic Aptamer ID
UNIPROT	UniProt ID provided by SomaLogic
Target	Target gene symbol (HGNC)
TargetFullName	Full protein name
EntrezGeneID	Entrez Gene ID provided by SomaLogic
EntrezGeneSymbol	Entrez Gene Symbol provided by SomaLogic
uniprot_gn_id	Mapped UniProt gene ID
uniprot_gn_symbol	Mapped UniProt gene symbol
entrezgene_id	Mapped Entrez gene ID
entrezgene_accession	Mapped Entrez accession
hgnc_id	Mapped HGNC ID
hgnc_symbol	Mapped HGNC symbol
ensembl_gene_id	Mapped Ensembl Gene ID
external_gene_name	External gene name
gene_biotype	Gene biotype (e.g. protein_coding)
CHR	Chromosome name
START_hg19	Start position (hg19)
END_hg19	End position (hg19)
strand_hg19	Strand (hg19)
START_hg38	Start position (hg38)
END_hg38	End position (hg38)
strand_hg38	Strand (hg38)

Interactive Table