Expression quantitative trait loci for PI3K/AKT pathway

Ryu, Dongchan; Lee, Chaeyoung

doi:10.1097/md.0000000000005817

Cited by 11 publications

(14 citation statements)

References 40 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Moreover, COL4A1 mutations resulted in an excess of the apoptosis of endothelial cells contributing to primary endothelial cell defects and COL4A1 ‐related myopathy in mice . In 2016 it was shown that upregulated COL4A1 had all homozygotes of minor alleles at single nucleotide variants in lymphoblastoid cell lines . Because COL4A1 synthesizes a major complex of plasma membrane and activates fibroblasts through the PI3K/AKT pathway, it might be a candidate gene for predicting patients’ genetic susceptibility to cancer and could be used in targeted cancer therapy .…”

Section: Discussionmentioning

confidence: 99%

“…31 Because COL4A1 synthesizes a major complex of plasma membrane and activates fibroblasts through the PI3K/AKT pathway, it might be a candidate gene for predicting patients' genetic susceptibility to cancer and could be used in targeted cancer therapy. 31 However, a correlation F I G U R E 4 Identification of candidate genes associated with prognosis. A, Kaplan-Meier plot indicates that increased collagen type IV alpha 1 (COL4A1) expression had a poorer prognosis (P = 0.04).…”

Section: Discussionmentioning

confidence: 99%

“…In 2016 it was shown that upregulated COL4A1 had all homozygotes of minor alleles at single nucleotide variants in lymphoblastoid cell lines . Because COL4A1 synthesizes a major complex of plasma membrane and activates fibroblasts through the PI3K/AKT pathway, it might be a candidate gene for predicting patients’ genetic susceptibility to cancer and could be used in targeted cancer therapy . However, a correlation between COL4A1 and tumor has rarely been reported.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence

Wang

Chang

et al. 2019

J of Digest Diseases

View full text Add to dashboard Cite

Objective Cancer recurrence is a complicated problem for clinicians that contributes to poor prognosis. This study aimed to use advanced gastric carcinoma genes profiles to predict increased risk of cancer recurrence in order to identify patients in need of adjuvant therapy for prognosis improvement. Methods Differentially expressed genes were identified for advanced gastric carcinoma by analyzing the GSE2685 from the Gene Expression Omnibus database (GEO) using R package. The candidate genes were then obtained by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein‐protein interaction analysis and survival analysis. Logistic regression analysis was performed to determine the relationship between candidate genes and the recurrence of gastric carcinoma. Results Collagen type IV alpha 1 (COL4A1) was overexpressed in gastric carcinoma tissue by analyzing the GSE2685 gene expression profiles from the Gene Expression Omnibus database. COL4A1 was also overexpressed in gastric carcinoma tissue from the Cancer Genome Atlas dataset and further determined that higher COL4A1 expression led to poorer overall survival. A univariate analysis suggested that COL4A1 was strongly correlated with T stage and gastric carcinoma recurrence (P = 0.014 and 0.041, respectively). Moreover, a multiple logistic regression analysis indicated that COL4A1 was significantly associated with gastric carcinoma recurrence (hazard ratio 1.605, 95% confidence interval 1.063‐2.677, P = 0.008). Conclusions COL4A1 may promote gastric carcinoma recurrence and could be used as a therapeutic target for gastric carcinoma recurrence.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence

Wang

Chang

et al. 2019

J of Digest Diseases

View full text Add to dashboard Cite

show abstract

“…In our pathway figure OCR results, there were over 600 figures with more than 100 genes each. While many of the largest figures are interaction networks, the largest with 385 recognized genes is an augmented KEGG pathway where the authors properly listed the individual gene family and paralog members referenced generically in the original [ 29 ]. At the other end, there was a long tail of just over 20k (37%) figures that had fewer than seven recognized genes.…”

Section: Contentmentioning

confidence: 99%

Pathway information extracted from 25 years of pathway figures

et al. 2020

View full text Add to dashboard Cite

Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and research.

show abstract

“…In our pathway figure OCR results, there were over 600 figures with more than 100 genes each. While many of the largest figures are interaction networks, the largest with 385 recognized genes is an augmented KEGG pathway where the authors properly listed the individual gene family and paralog members referenced generically in the original 26 . At the other end, there was a long tail of just over 20k (37%) figures that had fewer than seven recognized genes.…”

Section: Genes In Pathway Figuresmentioning

confidence: 99%

25 Years of Pathway Figures

Hanspers

Riutta

Kutmon

et al. 2020

Preprint

View full text Add to dashboard Cite

BackgroundPathway diagrams are fundamental tools for describing biological processes in all aspects of science, including training, generating hypotheses, describing new knowledge and ultimately as communication tools in published work. Thousands of pathway diagrams are published each year as figures in papers. But as static images the pathway knowledge represented in figures is not accessible to researchers for computational queries and analyses. In this study, we aimed to identify pathway figures published in the past 25 years, to characterize the human gene content in figures by optical character recognition, and to describe their utility as a resource for pathway knowledge. ApproachTo identify pathway figures representing 25 years of published research, we trained a machine learning service on manually-classified figures and applied it to 235,081 image query results from PubMed Central. Our previously described pipeline 1 was utilized to extract human genes from the pathway figure images. These figures were characterized in terms of their parent papers, human gene content and enriched disease terms. Diverse use cases were explored for this newly accessible pathway resource. ResultsWe identified 64,643 pathway figures published between 1995 and 2019, depicting 1,112,551 instances of human genes (13,464 unique NCBI Genes) in various interactions and contexts. This represents more genes than found in the text of the same papers, as well as genes not found in any pathway database. We developed an interactive web tool to explore the results from the 65k set of figures, and used this tool to explore the history of scientific discovery of the Hippo Signaling pathway. We also defined a filtered set of 32k pathway figures useful for enrichment analysis.

show abstract

Expression quantitative trait loci for PI3K/AKT pathway

Abstract: Supplemental Digital Content is available in the text

Cited by 11 publications

References 40 publications

Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence

Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence

Pathway information extracted from 25 years of pathway figures

25 Years of Pathway Figures

Contact Info

Product

Resources

About