Gene Annotations

Loading GENCODE Annotations

from gcell.rna.gencode import Gencode

# Load annotations for specific genome
gencode = Gencode(assembly="hg38")  # Human GRCh38
gencode = Gencode(assembly="hg19")  # Human GRCh37
gencode = Gencode(assembly="mm10")  # Mouse mm10

Accessing Gene Information

# Get gene by symbol
gene = gencode.get_gene("TP53")
gene = gencode.get_gene("BRCA1")
gene = gencode.get_gene("MYC")

# Gene attributes
print(gene.id)         # Ensembl ID: "ENSG00000141510"
print(gene.name)       # Symbol: "TP53"
print(gene.chrom)      # Chromosome: "chr17"
print(gene.strand)     # Strand: "-"

# Gene coordinates
print(gene.tss_coordinate)  # Primary TSS coordinate
print(gene.tes)             # Primary TES coordinate

# Full gene body
chrom, start, end, strand = gene.genomic_range

Transcription Start Sites (TSS)

# Get list of TSS objects (one per transcript)
for tss in gene.tss:
    print(tss.chrom, tss.start, tss.strand)

# Get primary TSS coordinate
tss_coord = gene.tss_coordinate

# Access TSS DataFrame for detailed info
print(gene.tss_list)  # DataFrame with Chromosome, Start, End, Strand, gene_name, gene_id

Query Genes by Region

# Find genes in a genomic region
result = gencode.query_region("chr17", 41196312, 41277500)

# Returns DataFrame with matching genes
print(result[['gene_name', 'Chromosome', 'Start', 'End', 'Strand']])

Gencode Lookup Properties

# Quick lookups without creating Gene objects
strand = gencode.gene_to_strand["TP53"]  # "-"
chrom = gencode.gene_to_chrom["TP53"]    # "chr17"
tss = gencode.gene_to_tss["TP53"]        # 7687538
tes = gencode.gene_to_tes["TP53"]        # 7668421
gene_type = gencode.gene_to_type["TP53"] # "protein_coding"
gene_id = gencode.gene_to_id["TP53"]     # "ENSG00000141510"

Key Classes

Data Location

• Annotations: ~/.gcell_data/annotations/
• Override: GCELLANNOTATIONDIR environment variable