We found that RSPO3, ADAMTS8, DMBT1, DOCK8, STMN2, SPINK6 and TUSC3 were the co-genes of HOXA11-AS in lung adenocarcinoma whereas RSPO3, ADAMTS8, DMBT1, DOCK8, STMN2, SPINK6, TUSC3 and C8orf22 were the co-genes of HOXA11-AS in squamous cell carcinoma. Here, PPDPFL is linked to squamous cell carcinoma.