Non-exonic read content reorganises lncRNA co-expression networks in renal and other cancers
- 1University of Cambridge
Abstract
Co-expression networks are used to find prognostic lncRNA programmes, but lncRNA quantification depends on unprocessed RNA in the library. In renal cancer (1,062 patients), the leading lncRNA axis tracked the non-exonic (non-feature) read fraction, a routine alignment metric, at Spearman rho 0.90. Without adjustment, most of the lncRNA network merged into one module. Adjustment preserved agreement with single-cell tumour-normal differences. Under rules fixed with the renal results known, 9 of 25 TCGA cancer types had a lncRNA-specific axis and 4 had network collapse (8 and 2 of 23 non-renal types). Intronic lncRNAs tracked the metric more than intergenic ones in all 25, and the metric was not consistently prognostic. All five renal modules that survived adjustment kept their direction in an external cohort, two nominally significant and none at a 5% false discovery rate. Three localised to malignant or epithelial cells. Together they added no discrimination over TNM and grade.
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BibTeX
@misc{youssef2026nonexonic,
title = {{Non-exonic read content reorganises lncRNA co-expression networks in renal and other cancers}},
author = {G. Youssef and N. Han},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.09.757827},
url = {https://www.biorxiv.org/content/10.64898/2026.10.09.757827v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Non-exonic read content reorganises lncRNA co-expression networks in renal and other cancers
AU - G. Youssef
AU - N. Han
PY - 2026
DA - 2026/10/09
PB - bioRxiv
DO - 10.64898/2026.10.09.757827
UR - https://www.biorxiv.org/content/10.64898/2026.10.09.757827v1
AB - Co-expression networks are used to find prognostic lncRNA programmes, but lncRNA quantification depends on unprocessed RNA in the library. In renal cancer (1,062 patients), the leading lncRNA axis tracked the non-exonic (non-feature) read fraction, a routine alignment metric, at Spearman rho 0.90. Without adjustment, most of the lncRNA network merged into one module. Adjustment preserved agreement with single-cell tumour-normal differences. Under rules fixed with the renal results known, 9 of 25 TCGA cancer types had a lncRNA-specific axis and 4 had network collapse (8 and 2 of 23 non-renal types). Intronic lncRNAs tracked the metric more than intergenic ones in all 25, and the metric was not consistently prognostic. All five renal modules that survived adjustment kept their direction in an external cohort, two nominally significant and none at a 5% false discovery rate. Three localised to malignant or epithelial cells. Together they added no discrimination over TNM and grade.
ER -