How to subset specific genes from microarray dataset using Python?

Question

[melissachua90]

I want to isolate VEGF-related and HSP-related genes for microarray time-series analysis. I'm not sure if my code is correct or whether I'm missing some genes.

coding_gene_df = df[~df.index.str.contains("---")] # Assume that genes must have Gene Symbols; remove rows without gene symbols

hsp_df = coding_gene_df[coding_gene_df["mrna_assignment"].str.contains("Hsp")]



vegf_df = coding_gene_df[coding_gene_df["mrna_assignment"].str.contains("VEGF")]

Original df:

df.head().to_dict()

{'0_P1_T1_TimeC1_PIDC4_Non-Survivor': {'---': '4.43'},
 '0_P2_T1_TimeC2_PIDC2_Survivor': {'---': '4.17'},
 '0_P3_T1_TimeC1_PIDC1_Survivor': {'---': '3.88'},
 '0_P4_T1_TimeC1_PIDC1_Survivor': {'---': '4.4'},
 '0_P5_T1_TimeC4_PIDC3_Survivor': {'---': '3.94'},
 '12_P1_T4_TimeC2_PIDC4_Non-Survivor': {'---': '4.56'},
 '12_P2_T4_TimeC3_PIDC2_Survivor': {'---': '3.98'},
 '12_P3_T4_TimeC2_PIDC1_Survivor': {'---': '4.17'},
 '12_P4_T4_TimeC2_PIDC2_Survivor': {'---': '4.63'},
 '12_P5_T4_TimeC2_PIDC3_Survivor': {'---': '4.03'},
 '24_P1_T5_TimeC4_PIDC4_Non-Survivor': {'---': '4.78'},
 '24_P2_T5_TimeC3_PIDC2_Survivor': {'---': '3.26'},
 '24_P3_T5_TimeC3_PIDC1_Survivor': {'---': '3.53'},
 '24_P4_T5_TimeC3_PIDC2_Survivor': {'---': '4.54'},
 '24_P5_T5_TimeC3_PIDC3_Survivor': {'---': '4.31'},
 '48_P1_T6_TimeC3_PIDC1_Non-Survivor': {'---': '3.69'},
 '48_P2_T6_TimeC3_PIDC3_Survivor': {'---': '3.78'},
 '48_P3_T6_TimeC3_PIDC1_Survivor': {'---': '5.14'},
 '48_P4_T6_TimeC3_PIDC2_Survivor': {'---': '4.35'},
 '48_P5_T6_TimeC3_PIDC3_Survivor': {'---': '4.33'},
 '4_P1_T2_TimeC1_PIDC4_Non-Survivor': {'---': '3.47'},
 '4_P2_T2_TimeC2_PIDC1_Survivor': {'---': '4.1'},
 '4_P3_T2_TimeC2_PIDC1_Survivor': {'---': '4.8'},
 '4_P5_T2_TimeC2_PIDC3_Survivor': {'---': '3.63'},
 '8_P1_T3_TimeC4_PIDC4_Non-Survivor': {'---': '3.69'},
 '8_P2_T3_TimeC2_PIDC2_Survivor': {'---': '3.78'},
 '8_P3_T3_TimeC4_PIDC1_Survivor': {'---': '3.99'},
 '8_P4_T3_TimeC4_PIDC1_Survivor': {'---': '3.38'},
 '8_P5_T3_TimeC4_PIDC3_Survivor': {'---': '4.53'},
 'Cytoband': {'---': '---'},
 'Entrez Gene': {'---': '---'},
 'GO Biological Process': {'---': nan},
 'GO Cellular Component': {'---': nan},
 'GO Molecular Function': {'---': nan},
 'GO_biological_process': {'---': '---'},
 'GO_cellular_component': {'---': '---'},
 'GO_molecular_function': {'---': '---'},
 'Gene Title': {'---': '---'},
 'Pathway': {'---': nan},
 'Probe ID': {'---': '7892505'},
 'Protein Domains': {'---': nan},
 'Swiss-Prot': {'---': '---'},
 'UniGene': {'---': nan},
 'category': {'---': 'normgene->intron'},
 'crosshyb_type': {'---': '---'},
 'gene_assignment': {'---': '---'},
 'mrna_assignment': {'---': '--- // --- // neg_control // --- // --- // --- // --- // --- // ---'},
 nan: {'---': nan},
 'pathway': {'---': '---'},
 'protein_domains': {'---': '---'},
 'seqname': {'---': '---'},
 'start': {'---': '---'},
 'stop': {'---': '---'},
 'strand': {'---': '---'},
 'swissprot': {'---': '---'},
 'total_probes': {'---': '4'},
 'unigene': {'---': '---'}}