scholarly journals Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes

2011 ◽  
Vol 20 (14) ◽  
pp. 2879-2888 ◽  
Author(s):  
Luis G. Carvajal-Carmona ◽  
Jean-Baptiste Cazier ◽  
Angela M. Jones ◽  
Kimberley Howarth ◽  
Peter Broderick ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Fine Mapping ◽  
In Silico ◽  
Target Genes ◽  
Cancer Susceptibility ◽  
In Silico Analysis ◽  
Susceptibility Loci ◽  
Functional Variation ◽  
Candidate Target ◽  
Silico Analysis

scholarly journals TP73 G4C14-A4T14 polymorphism and cancer susceptibility: evidence from 36 case–control studies

2018 ◽  
Vol 38 (6) ◽  
Author(s):  
Jialin Meng ◽  
Shuo Wang ◽  
Meng Zhang ◽  
Song Fan ◽  
Li Zhang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cervical Cancer ◽  
In Silico ◽  
Cancer Susceptibility ◽  
Meta Analysis ◽  
In Silico Analysis ◽  
Case Control ◽  
Genetic Models ◽  
Case Control Studies ◽  
Silico Analysis

G4C14-A4T14 polymorphism of TP73 gene has been reported with a potential association in cancer risks through affected cell homeostasis; however the results were not consistent. We performed a comprehensive meta-analysis to explore the associations between G4C14-A4T14 polymorphism and cancer susceptibility. Extensive retrieve was performed in PubMed, EMBASE, Google Scholar, Web of Science, Wanfang database and CNKI database up to May 20, 2018. Odds ratios (ORs) and 95% confidence intervals (CIs) were conducted to evaluate the overall strength of the associations in five genetic models, as well as in subgroup analyses. Q-test, false-positive report probability analysis and trial sequential analysis, Egger’s test and Begg’s funnel plot were applied to evaluate the robustness of the results. In silico analysis was managed to demonstrate the relationship of TP73 expression correlated with cancer tissues. Finally, 36 case–control studies with a total of 9493 cancer cases and 13,157 healthy controls were enrolled into the meta-analysis. The pooled results present a significantly higher risk of G4C14-A4T14 polymorphism in all the five genetic models, as well as in the subgroups of Caucasian, cervical cancer, colorectal cancer, H-B subgroup and comfort to Hardy–Weinberg equilibrium subgroup. In silico analysis revealed that the expression of TP73 in cervical cancer tissue is higher than it in corresponding normal tissue, as well as in cervical cancer. All in all, TP73 G4C14-A4T14 polymorphism causes an upgrade cancer risk, especially in Caucasian population. G4C14-A4T14 polymorphism might be a potential biomarker for judging the tumorigenesis of cervical cancer and colorectal cancer.

Serum Micrornas can Detect Colorectal Cancer; two Validation Study after In-Silico Analysis

2017 ◽  
Vol 152 (5) ◽  
pp. S1018
Author(s):  
Hiroyuki Takamaru ◽  
Yutaka Saito ◽  
Taku Sakamoto ◽  
Seiichiro Abe ◽  
Masayoshi Yamada ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Validation Study ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis ◽  
Serum Micrornas

lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis

2020 ◽  
Vol 89 ◽  
pp. 107370
Author(s):  
Tayyebeh Ghasemi ◽  
Mohammad Khalaj-Kondori ◽  
Mohammad Ali Hosseinpour feizi ◽  
Parviz Asadi
Keyword(s):  
Colorectal Cancer ◽  
In Silico ◽  
Interaction Network ◽  
In Silico Analysis ◽  
Silico Analysis

The role of cell surface proteins gene expression in diagnosis, prognosis, and drug resistance of colorectal cancer: In silico analysis and validation

2021 ◽  
Vol 123 ◽  
pp. 104688
Author(s):  
Nasrin Nazempour ◽  
Mohammad Hossein Taleqani ◽  
Navid Taheri ◽  
Amir Hossein Haji Ali Asgary Najafabadi ◽  
Alireza Shokrollahi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Drug Resistance ◽  
Cell Surface ◽  
In Silico ◽  
In Silico Analysis ◽  
Surface Proteins ◽  
Cell Surface Proteins ◽  
Silico Analysis

scholarly journals The Expression Patterns of BECN1, LAMP2, and PINK1 Genes in Colorectal Cancer Are Potentially Regulated by Micrornas and CpG Islands: An In Silico Study

2020 ◽  
Vol 9 (12) ◽  
pp. 4020
Author(s):  
Martyna Bednarczyk ◽  
Edyta Fatyga ◽  
Sylwia Dzięgielewska-Gęsiak ◽  
Dariusz Waniczek ◽  
Beniamin Grabarek ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
In Silico ◽  
Expression Patterns ◽  
Cpg Islands ◽  
In Silico Analysis ◽  
Epigenetic Changes ◽  
Grid Infrastructure ◽  
In Silico Study ◽  
Silico Analysis

Background: Autophagy plays a dual role of tumor suppression and tumor promotion in colorectal cancer. The study aimed to find those microRNAs (miRNAs) important in BECN1, LAMP2, and PINK1 regulation and to determine the possible role of the epigenetic changes in examined colorectal cancer using an in silico approach. Methods: A total of 44 pairs of surgically removed tumors at clinical stages I‒IV and healthy samples (marginal tissues) from patients’ guts were analyzed. Analysis of the obtained results was conducted using the PL-Grid Infrastructure and Statistica 12.0 program. The miRNAs and CpG islands were estimated using the microrna.org database and MethPrimer program. Results: The autophagy-related genes were shown to be able to be regulated by miRNAs (BECN1—49 mRNA, LAMP2—62 mRNA, PINK1—6 mRNA). It was observed that promotion regions containing at least one CpG region were present in the sequence of each gene. Conclusions: The in silico analysis performed allowed us to determine the possible role of epigenetic mechanisms of regulation gene expression, which may be an interesting therapeutic target in the treatment of colorectal cancer.

scholarly journals MicroRNAs Modulate the Pathogenesis of Alzheimer’s Disease: An In Silico Analysis in the Human Brain

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 983
Author(s):  
Agnese Gugliandolo ◽  
Luigi Chiricosta ◽  
Virginia Boccardi ◽  
Patrizia Mecocci ◽  
Placido Bramanti ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Nervous System ◽  
In Silico ◽  
Target Genes ◽  
Amyloid Β ◽  
In Silico Analysis ◽  
Protein Translation ◽  
Mirnas Expression ◽  
Silico Analysis

MicroRNAs (miRNAs) are small RNAs involved in the post-transcriptional regulation of their target genes, causing a decrease in protein translation from the mRNA. Different miRNAs are found in the nervous system, where they are involved in its physiological functions, but altered miRNAs expression was also reported in neurodegenerative disorders, including Alzheimer’s disease (AD). AD is characterized by memory loss, cognitive function abnormalities, and various neuropsychiatric disturbances. AD hallmarks are amyloid β (Aβ) aggregates, called senile plaques, and neurofibrillary tangles (NFTs) formed by hyperphosphorylated Tau protein. In this study, we performed an in silico analysis to evaluate altered patterns of miRNAs expression in the brains of AD patients compared to healthy subjects. We found 12 miRNAs that were differentially expressed in AD compared to healthy individuals. These miRNAs have target genes involved in AD pathogenesis. In particular, some miRNAs influence Aβ production, having as target secretase and amyloid precursor protein (APP). Some miRNAs were reported to be involved in nervous system functions, and their alteration can cause neuronal dysfunction.

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