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Human Protein Atlas (HPA)

Access protein expression data via the HPA API.

Overview

The Human Protein Atlas provides data on:

  • Tissue Expression - Protein levels across tissues
  • Blood Expression - Protein levels in blood
  • Brain Expression - Brain region-specific expression
  • Subcellular Location - Where proteins are located in cells
  • Pathology - Cancer expression data

Quick Start

from biodbs.fetch import (
    hpa_get_gene,
    hpa_get_tissue_expression,
    hpa_get_subcellular_location,
)

# Get gene data
gene = hpa_get_gene("TP53")

Gene Data

Get Gene

from biodbs.fetch import hpa_get_gene, hpa_get_genes

gene = hpa_get_gene("TP53")
genes = hpa_get_genes(["TP53", "BRCA1", "EGFR"])

from biodbs.fetch import hpa_search

results = hpa_search("kinase")

Expression Data

Tissue Expression

from biodbs.fetch import hpa_get_tissue_expression

expression = hpa_get_tissue_expression("TP53")
df = expression.as_dataframe()

Blood Expression

from biodbs.fetch import hpa_get_blood_expression

expression = hpa_get_blood_expression("TP53")

Brain Expression

from biodbs.fetch import hpa_get_brain_expression

expression = hpa_get_brain_expression("TP53")

Subcellular Location

from biodbs.fetch import hpa_get_subcellular_location

location = hpa_get_subcellular_location("TP53")

Pathology Data

from biodbs.fetch import hpa_get_pathology

pathology = hpa_get_pathology("TP53")

Protein Classes

from biodbs.fetch import hpa_get_protein_class

classes = hpa_get_protein_class("TP53")

Using the Fetcher Class

from biodbs.fetch.HPA import HPA_Fetcher

fetcher = HPA_Fetcher()
gene = fetcher.get_gene("TP53")
  • UniProt - Get detailed protein information, including subcellular localization annotations.
  • Ensembl - Get genomic context and transcript information for genes.
  • ID Translation - Translate between gene symbols and other identifiers for use with HPA.