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2013 ; 7 Suppl 5
(Suppl 5
): S7
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English Wikipedia
Gene and isoform expression signatures associated with tumor stage in kidney
renal clear cell carcinoma
#MMPMID24564989
Liu Q
; Zhao S
; Su PF
; Yu S
BMC Syst Biol
2013[]; 7 Suppl 5
(Suppl 5
): S7
PMID24564989
show ga
BACKGROUND: Identification of expression alternations between early and late
stage cancers is helpful for understanding cancer development and progression.
Much research has been done focusing on stage-dependent gene expression profiles.
In contrast, relatively fewer studies on isoform expression profiles have been
performed due to the difficulty of quantification and noisy splicing. Here we
conducted both gene- and isoform-level analysis on RNA-seq data of 234 stage I
and 81 stage IV kidney renal clear cell carcinoma patients, aiming to uncover the
stage-dependent expression signatures and investigate the advantage of isoform
expression profiling for identifying advanced stage cancers and predicting
clinical outcome. RESULTS: Both gene and isoform expression signatures are useful
for distinguishing cancer stages. They provide common and unique information
associated with cancer progression and metastasis. Combining gene and isoform
signatures even improves the classification performance and reveals additional
important biological processes, such as angiogenesis and TGF--beta signaling
pathway. Moreover, expression abundance of a number of genes and isoforms is
predictive of the risk of cancer death in an independent dataset, such as gene
and isoform expression of ITPKA, the expression of a functional important isoform
of UPS19. CONCLUSION: Isoform expression profiling provides unique and important
information which cannot be detected by gene expression profiles. Combining gene
and isoform expression signatures helps to identify advanced stage cancers,
predict clinical outcome, and present a comprehensive view of cancer development
and progression.