Papers and Publications
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Papers and Publications
Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods
June 07, 2021
Prognostic value and co-expression patterns of metabolic pathways in cancers
Dan Zhang , Yan Guo and Ni Xie |
December 29, 2020
Background: Abnormal metabolic pathways have been considered as one of the hallmarks of cancer. While
numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway
gene expression and cancer prognosis has not been established.
Results: Using two recently developed bioinformatics analysis methods, we evaluated the prognosis potential of
metabolic pathway expression and tumor-vs-normal dysregulations for up to 29 metabolic pathways in 33 cancer
types. Results show that increased metabolic gene expression within tumors corresponds to poor cancer prognosis.
Meta differential co-expression analysis identified four metabolic pathways with significant global co-expression
network disturbance between tumor and normal samples. Differential expression analysis of metabolic pathways
also demonstrated strong gene expression disturbance between paired tumor and normal samples.
Conclusion: Taken together, these results strongly suggested that metabolic pathway gene expressions are
disturbed after tumorigenesis. Within tumors, many metabolic pathways are upregulated for tumor cells to activate
corresponding metabolisms to sustain the required energy for cell division.
Keywords: Metabolic pathway, Meta co-expression analysis, Gene expression composite score, Cancer
numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway
gene expression and cancer prognosis has not been established.
Results: Using two recently developed bioinformatics analysis methods, we evaluated the prognosis potential of
metabolic pathway expression and tumor-vs-normal dysregulations for up to 29 metabolic pathways in 33 cancer
types. Results show that increased metabolic gene expression within tumors corresponds to poor cancer prognosis.
Meta differential co-expression analysis identified four metabolic pathways with significant global co-expression
network disturbance between tumor and normal samples. Differential expression analysis of metabolic pathways
also demonstrated strong gene expression disturbance between paired tumor and normal samples.
Conclusion: Taken together, these results strongly suggested that metabolic pathway gene expressions are
disturbed after tumorigenesis. Within tumors, many metabolic pathways are upregulated for tumor cells to activate
corresponding metabolisms to sustain the required energy for cell division.
Keywords: Metabolic pathway, Meta co-expression analysis, Gene expression composite score, Cancer
Global Autozygosity Is Associated with Cancer Risk, Mutational Signature and Prognosis
Limin Jiang, Fei Guo, Jijun Tang , Shuguan Leng, Scott Ness, Fei Ye, Huining Kang, David C. Samuels and Yan Guo |
December 04, 2020
Global autozygosity in the form of runs of homozygosity is associated with various diseases. Heterozygosity ratio, an alternative measure of global autozygosity, is used to assess cancer risk in this study. Our analysis shows strong and consistent associations between heterozygosity ratios and various cancer types. Further analysis reveals the heterozygosity ratio’s potential connections to mutational signatures and cancer prognosis.