Display per-tissue or per-cell type gene expression data from the Human Protein Atlas.

tissue_expression_level.py

from typing import Callable
import pandas as pd
from dl_and_rezip import dl_and_rezip # see https://gist.github.com/dmyersturnbull/a6591676fc98da355c5250d48e26844e


def _load(filter_fn: Callable[[pd.DataFrame], pd.DataFrame]=pd.DataFrame.dropna) -> pd.DataFrame:
    """Get a DataFrame of Human Protein Atlas tissue expression data, indexed by Gene name and with the 'Gene' and 'Reliability' columns dropped.
    The expression level ('Level') is replaced using this map: {'Not detected': 0, 'Low': 1, 'Medium': 2, 'High': 3}.
    Downloads the file from http://www.proteinatlas.org/download/normal_tissue.csv.zip and reloads from normal_tissue.csv.gz thereafter.
    """
    dl_and_rezip('http://www.proteinatlas.org/download/normal_tissue.csv.zip', 'normal_tissue.csv')
    tissue = pd.read_csv('normal_tissue.csv.gz').drop('Gene', axis=1).drop('Reliability', axis=1)
    tissue = filter_fn(tissue)
    tissue['Level'] = tissue['Level'].map({'Not detected': 0, 'Low': 1, 'Medium': 2, 'High': 3}.get).astype(float)
    return tissue.set_index('Gene name')


class TissueTable(object):
    """Contains a Pandas DataFrame of tissue- and cell type-level expression for genes from the Human Protein Atlas.
    Example usage:
        tt = TissueTable()
        tt.tissue('MKNK2') # returns a DataFrame with mean expression of MKNK2 per tissue type. MKN2 is the HGNC symbol.
    """

    def __init__(self):
        self.df = _load()
    
    def level(self, gene_name: str, group_by: str='Cell type') -> pd.DataFrame:
        """Returns a DataFrame of the mean expression levels by tissue or cell type."""
        if gene_name not in self.df.index.get_level_values('Gene name'):
            raise ValueError("Gene with HGNC symbol {} not found.".format(gene_name))
        gene = self.df[self.df.index.get_level_values('Gene name') == gene_name]
        assert gene is not None
        return gene.groupby(group_by).mean().sort_values('Level', ascending=False)

    def tissue(self, name: str):
        return self.level(name, group_by='Tissue')
    
    def cell_type(self, name: str):
        return self.level(name, group_by='Cell type')

Per-tissue expression of HTR3E

tt = TissueExpression()
tt.tissue('HTR3E')