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X Demographics
Mendeley readers
Attention Score in Context
| Title |
In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants
|
|---|---|
| Published in |
BMC Genomics, May 2017
|
| DOI | 10.1186/s12864-017-3750-2 |
| Pubmed ID | |
| Authors |
Lenora W. M. Loo, Mathieu Lemire, Loïc Le Marchand |
| Abstract |
Genome-wide association studies have identified 55 genetic variants associated with colorectal cancer risk to date. However, potential causal genes and pathways regulated by these risk variants remain to be characterized. Therefore, we performed gene ontology enrichment and pathway analyses to determine if there was an enrichment of genes in proximity to the colorectal cancer risk variants that could further elucidate the probable causal genes and pathways involved in colorectal cancer biology. For the 65 unique genes that either contained, or were immediately neighboring up- and downstream, of these variants there was a significant enrichment for the KEGG pathway, Pathways in Cancer (p-value = 2.67 × 10(-5)) and an enrichment for multiple biological processes (FDR < 0.05), such as cell junction organization, tissue morphogenesis, regulation of SMAD protein phosphorylation, and odontogenesis identified through Gene Ontology analysis. To identify potential causal genes, we conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using gene expression and genotype data from the Genotype-Tissue Expression (GTEx) Project portal in normal sigmoid (n = 124) and transverse (n = 169) colon tissue. In addition, we also did a cis-eQTL analysis on colorectal tumor tissue (n = 147) from The Cancer Genome Atlas (TCGA). We identified two risk alleles that were significant cis-eQTLs for FADS2 (rs1535) and COLCA1 and 2 (rs3802842) genes in the normal transverse colon tissue and two risk alleles that were significant cis-eQTLs for the CABLES2 (rs2427308) and LIPG (rs7229639) genes in the normal sigmoid colon tissue, but not tumor tissue. Our data reaffirm the potential to identify an enrichment for biological processes and candidate causal genes based on expression profiles correlated with genetic risk alleles of colorectal cancer, however, the identification of these significant cis-eQTLs is context and tissue specific. |
X Demographics
The data shown below were collected from the profiles of 2 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 2 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 2 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 39 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 39 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 6 | 15% |
| Researcher | 6 | 15% |
| Student > Master | 6 | 15% |
| Student > Bachelor | 4 | 10% |
| Other | 2 | 5% |
| Other | 5 | 13% |
| Unknown | 10 | 26% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 11 | 28% |
| Agricultural and Biological Sciences | 11 | 28% |
| Medicine and Dentistry | 4 | 10% |
| Pharmacology, Toxicology and Pharmaceutical Science | 2 | 5% |
| Unspecified | 1 | 3% |
| Other | 0 | 0% |
| Unknown | 10 | 26% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 17 May 2017.
All research outputs
#15,459,013
of 22,971,207 outputs
Outputs from BMC Genomics
#6,720
of 10,686 outputs
Outputs of similar age
#194,845
of 309,986 outputs
Outputs of similar age from BMC Genomics
#147
of 216 outputs
Altmetric has tracked 22,971,207 research outputs across all sources so far. This one is in the 22nd percentile – i.e., 22% of other outputs scored the same or lower than it.
So far Altmetric has tracked 10,686 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 28th percentile – i.e., 28% of its peers scored the same or lower than it.
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We're also able to compare this research output to 216 others from the same source and published within six weeks on either side of this one. This one is in the 25th percentile – i.e., 25% of its contemporaries scored the same or lower than it.