The screening and treatment of laryngeal squamous cell carcinoma (LSCC) still perplexes clinicians, making it necessary to explore new markers. To this end, this research examined the underlying molecular mechanism of LSCC based on high-throughput datasets (
n
= 249) from multiple databases. It also identified transcription factors (TFs) independently associated with LSCC prognosis. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, differential expression genes of LSCC were deemed relevant to the extracellular matrix and its related structures or pathways, suggesting that the extracellular matrix plays an important role in LSCC. At the same time, several hub genes that may also have important roles in LSCC were identified via protein–protein interaction analysis, including
CDC45, TPX2, AURKA, KIF2C, NUF, MUC1, MUC7, MUC4, MUC15,
and
MUC21
. Eight unreported LSCC prognostic TFs –
BCAT1, CHD4, FOXA2, GATA6, HNF1A, HOXB13, MAFF,
and
TCF4
– were screened via Kaplan–Meier curves. Cox analysis determined for the first time that
HOXB13
expression and gender were independently associated with LSCC prognosis. Compared to control tissues, elevated expression of
HOXB13
was found in LSCC tissues (standardized mean difference = 0.44, 95% confidence interval [0.13–0.76]).
HOXB13
expression also makes it feasible to screen LSCC from non-LSCC (area under the curve = 0.77), and
HOXB13
may play an essential role in LSCC by regulating
HOXB7
. In conclusion,
HOXB13
may be a novel marker for LSCC clinical screening and treatment.