ArticleBritish journal of cancer2018
Colon-specific eQTL analysis to inform on functional SNPs.
Article in British journal of cancer, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Mixed-model and transcriptome-wide association analyses identify transcription factors and genes associated with colorectal cancer susceptibility.Nature communications · 2026Article
- Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention.American journal of human genetics · 2026Article
- Multi-omics analysis of the biological function of the VEGF family in colon adenocarcinoma.Functional & integrative genomics · 2024Article
- Analysis of sex-biased gene expression in a Eurasian admixed population.Briefings in bioinformatics · 2024Article
- Germline genetic regulation of the colorectal tumor immune microenvironment.BMC genomics · 2024Article
- Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective.Human genetics · 2023Review
- Methylenetetrahydrofolate reductase polymorphic variants C677T and A1298C in rectal cancer in Slavic population: significance for cancer risk and response to chemoradiotherapy.Frontiers in genetics · 2023Article
- Endoplasmic reticulum-resident protein Sec62 drives colorectal cancer metastasis via MAPK/ATF2/UCA1 axis.Cell proliferation · 2022Article
- Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis.Clinical epigenetics · 2022Review
- Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue.Clinical epigenetics · 2021Article
- Multi-omics analysis to identify susceptibility genes for colorectal cancer.Human molecular genetics · 2021Article
- Article
- Differential Expression Analysis Revealing CLCA1 to Be a Prognostic and Diagnostic Biomarker for Colorectal Cancer.Frontiers in oncology · 2020Article
- Identifying Putative Susceptibility Genes and Evaluating Their Associations with Somatic Mutations in Human Cancers.American journal of human genetics · 2019Article
- Moving the needle on colorectal cancer genetics: it takes more than two to TANGO.British journal of cancer · 2018Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide association studies on colorectal cancer have identified more than 60 susceptibility loci, but for most of them there is no clear knowledge of functionality or the underlying gene responsible for the risk modification. Expression quantitative trail loci (eQTL) may provide functional information for such single nucleotide polymorphisms (SNPs).
methodsWe have performed detailed eQTL analysis specific for colon tissue on a series of 97 colon tumours, their paired adjacent normal mucosa and 47 colon mucosa samples donated by healthy individuals. R package MatrixEQTL was used to search for genome-wide cis-eQTL and trans-eQTL fitting linear models adjusted for age, gender and tissue type to rank transformed expression data.
resultsThe cis-eQTL analyses has revealed 29,073 SNP-gene associations with permutation-adjusted P-values < 0.01. These correspond to 363 unique genes. The trans-eQTL analysis identified 10,665 significant SNP-gene associations, most of them in the same chromosome, further than 1 Mb of the gene. We provide a web tool to search for specific SNPs or genes. The tool calculates Pearson or Spearman correlation, and allows to select tissue type for analysis. Data and plots can be exported.
conclusionsThis resource should be useful to prioritise SNPs for further functional studies and to identify relevant genes behind identified loci.
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