The differential expression patterns and co-expression networks of paralogs as an indicator of the TNM stages of lung adenocarcinoma and squamous cell carcinoma

Highlights

• Paralogous gene pairs (1870) were identified from 9605 pairs of 29 coexisting vertebrate species by homology analysis.

• The expression of most paralogs (~60%) were cancer type-dependent.

• The differentially expressed TF pairs (>50%) showed positive expression correlations across cancers.

• Down-regulation patterns of paralogs and TFs in LUAD and LUSC were highly linked with the M, and N stages.

• TF pairs (CDX1, CDX2) and (ZNF85, ZNF724) were key TFs of LUAD and LUSC.

Abstract

Cancers constitute a severe threat to human health. Elucidating the association between the expression patterns of the paralogous genes and transcription factors (TF) and the progression of cancers by comprehensively investigating the expression patterns and co-expression networks will contribute to the in-depth understanding of the pathogenesis of cancers. Here, we identified the paralogous gene pairs and systematically analyzed the expression patterns of these paralogs and the known TFs to elucidate the associations with Tumor, Node, Metastasis (TNM) staging information across ten cancers. We found that the expression of ~60% paralogs was cancer-dependent, and more than 50% of the differentially expressed TFs pairs showed positive expression correlations. The down-regulation patterns of paralogs and TFs were closely associated with the M and N developmental stages of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Our results will help to understand the roles of paralogs and TFs in cancer progression and to screen prognostic biomarkers for early cancer diagnosis.