Table 1 PyCellBase resource-specific clients and available data. The different clients that are currently implemented for each biological data type are shown along with the main data that can be obtained from each one of them
Client | Data |
|---|---|
Gene | Clinical data, protein-protein interactions, biotype, TFBSs, expression, transcripts, protein, variants |
Transcript | Sequence, function prediction, XREFs, biotype, genes, proteins, exons |
Protein | Amino acid sequence, substitution scores, organism, genes, protein features, evidence, bibliography |
Variation | Variants, biological impact, consequence types |
Xref | Associated IDs from multiple databases (ENSEMBL, UCSC, UniProt, RefSeq, GO, Reactome, PDB, OMIM, RNAcentral, miRBase...) |
Genomic region | Sequence, clinical variants, conservation scores, regulatory elements, repeat sequences, genes, transcripts, variants |
Variant | Consequence types, genes, transcripts, proteins, population frequencies, HGVS, clinical significance, functional score |
Genome sequence | Cytobands |
Clinical | ClinVar, COSMIC, inheritance, evidence, pathogenicity, diseases |
TFBS | Histones, open chromatin, polymerases, transcription factors |