ArticleBMC medicine2015
Improved survival among colon cancer patients with increased differentially expressed pathways.
Article in BMC medicine, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it, 22 citations in OpenAlex.
- Personalized identification of differentially expressed pathways in pediatric sepsis.Molecular medicine reports · 2017Pooled it
- A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials.Nature communications · 2024Article
- Next-generation sequencing: recent applications to the analysis of colorectal cancer.Journal of translational medicine · 2017Review
- Article
- A five-gene based risk score with high prognostic value in colorectal cancer.Oncology letters · 2017Article
- Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2017Article
- Prognosis of stage III colorectal carcinomas with FOLFOX adjuvant chemotherapy can be predicted by molecular subtype.Oncotarget · 2017Article
- Personalized Analysis by Validation of Monte Carlo for Application of Pathways in Cardioembolic Stroke.Medical science monitor : international medical journal of experimental and clinical research · 2017Article
- Personalized Identification of Differentially Expressed Modules in Osteosarcoma.Medical science monitor : international medical journal of experimental and clinical research · 2017Article
- DNA copy number alterations, gene expression changes and disease-free survival in patients with colorectal cancer: a 10 year follow-up.Cellular oncology (Dordrecht, Netherlands) · 2016Article
- Transcriptome profiling of the rat retina after optic nerve transection.Scientific reports · 2016Article
- Dietary intake alters gene expression in colon tissue: possible underlying mechanism for the influence of diet on disease.Pharmacogenetics and genomics · 2016Article
- Altered pathways and colorectal cancer prognosis.BMC medicine · 2015Article
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5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundStudies of colorectal cancer (CRC) have shown that hundreds to thousands of genes are differentially expressed in tumors when compared to normal tissue samples. In this study, we evaluate how genes that are differentially expressed in colon versus normal tissue influence survival.
methodsWe performed RNA-seq on tumor/normal paired samples from 175 colon cancer patients. We implemented a cross validation strategy to determine genes that were significantly differentially expressed between tumor and normal samples. Differentially expressed genes were evaluated with Ingenuity Pathway Analysis to identify key pathways that were de-regulated. A summary differential pathway expression score (DPES) was developed to summarize hazard of dying while adjusting for age, American Joint Committee on Cancer (AJCC) stage, sex, and tumor molecular phenotype, i.e., MSI, TP53, KRAS, and CIMP.
resultsA total of 1,138 genes were up-regulated and 695 were down-regulated. These de-regulated genes were enriched for 19 Ingenuity Canonical Pathways, with the most significant pathways involving cell signaling and growth. Of the enriched pathways, 16 were significantly associated with CRC-specific mortality, including 1 metabolic pathway and 15 signaling pathways. In all instances, having a higher DPES (i.e., more de-regulated genes) was associated with better survival. Further assessment showed that individuals diagnosed at AJCC Stage 1 had more de-regulated genes than individuals diagnosed at AJCC Stage 4.
conclusionsOur data suggest that having more de-regulated pathways is associated with a good prognosis and may be a reaction to key events that are disabling to tumor progression. Please see related article: http://dx.doi.org/10.1186/s12916-015-0307-6 .
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