Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV

Luo, Yuanyuan; Yan, Yan; Zhang, Shiqi; Li, Zhen

doi:10.1155/2018/8406857

Cited by 4 publications

(5 citation statements)

References 92 publications

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“…The circRNA functional annotation was based on GO and KEGG annotations in accordance with a previous study. 17 CircRNA Differential Expression Analysis. According to the grouping of samples and FPKM values, differences in circRNA expression were analyzed using the DEseq software package.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Circ007071 Inhibits Unsaturated Fatty Acid Synthesis by Interacting with miR-103-5p to Enhance PPARγ Expression in the Dairy Goat Mammary Gland

Chen

Zhang

et al. 2022

J. Agric. Food Chem.

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Understanding more precisely the mechanisms controlling the metabolism of fatty acid in the mammary gland of dairy goats is essential for future improvements in milk quality. Particularly since recent data have underscored a key role for circular RNAs (circRNAs) in the mammary gland function, high-throughput sequencing technology was used to identify expression levels of circRNAs in the mammary tissue of dairy goats during early and peak lactation in the present study. Compared with early lactation, results demonstrated that the expression level of circ007071 during peak lactation was 12.02-fold up-regulated. Subsequent studies in goat mammary epithelial cells (GMECs) revealed that circ007071 stimulated the synthesis of triglycerides (TAG) and cholesterol, as well as increased the content of saturated fatty acids (C16:0 and C18:0). More importantly, using a double luciferase reporting system allowed us to detect the circ007071 sequence at a binding site of miR-103-5p, indicating that it targeted this miRNA. Overexpression of circ007071 significantly decreased the abundance of miR-103-5p and led to inhibition of TAG synthesis. In contrast, the abundance of peroxisome proliferator-activated receptor γ (PPARγ), a target gene of miR-103-5p, was reinforced with the overexpression of circ007071. Thus, we conclude that one key function of circ007071 in the regulation of milk fat synthesis is to attenuate the inhibitory effect of miR-103-5p on PPARγ via direct interactions with miRNA. As a result, the process of TAG and saturated fatty acid is able to proceed.

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Section: ■ Materials and Methodsmentioning

confidence: 99%

“…Subsequently, the screened circRNAs were annotated according to their positions in the genome and their relationships with protein coding genes. The circRNA functional annotation was based on GO and KEGG annotations in accordance with a previous study …”

Section: Methodsmentioning

confidence: 99%

Circ007071 Inhibits Unsaturated Fatty Acid Synthesis by Interacting with miR-103-5p to Enhance PPARγ Expression in the Dairy Goat Mammary Gland

Chen

Zhang

et al. 2022

J. Agric. Food Chem.

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“…To explore the putative molecular mechanisms linked with the prognostic signature of ERS, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed ( 18 ). The “limma” R package was used to determine the differential gene expressions between the two risk groups (the cutoffs were FDR<0.05 and |log2FC|>1).…”

Section: Methodsmentioning

confidence: 99%

Identification of a novel gene signature of lung adenocarcinoma based on epidermal growth factor receptor-tyrosine kinase inhibitor resistance

Zhou

Guo

et al. 2022

Front. Oncol.

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IntroductionTyrosine kinase inhibitors (TKIs) that target epidermal growth factor receptor (EGFR) mutations are commonly administered to EGFR-positive lung cancer patients. However, resistance to EGFR-TKIs (mostly gefitinib and erlotinib) is presently a significant problem. Limited studies have focused on an EGFR-TKI resistance-related gene signature (ERS) in lung adenocarcinoma (LUAD).MethodsGefitinib and erlotinib resistance-related genes were obtained through the differential analyses of three Gene Expression Omnibus datasets. These genes were investigated further in LUAD patients from The Cancer Genome Atlas (TCGA). Patients in the TCGA-LUAD cohort were split into two groups: one for training and one for testing. The training cohort was used to build the ERS, and the testing cohort was used to test it. GO and KEGG analyses were explored for the enriched pathways between the high-risk and low-risk groups. Various software, mainly CIBERSORT and ssGSEA, were used for immune infiltration profiles. Somatic mutation and drug sensitivity analyses were also explored.ResultsAn ERS based on five genes (FGD3, PCDH7, DEPDC1B, SATB2, and S100P) was constructed and validated using the TCGA-LUAD cohort, resulting in the significant stratification of LUAD patients into high-risk and low-risk groups. Multivariable Cox analyses confirmed that ERS had an independent prognostic value in LUAD. The pathway enrichment analyses showed that most of the genes that were different between the two risk groups were related to the immune system. Further immune infiltration results revealed that a lower immune infiltration score was observed in high-risk patients, and that various leukocytes were significantly related to the ERS. Importantly, samples from the high-risk group showed lower levels of PD-1, PD-L1, and CTLA-4, which are important biomarkers for immunotherapy responses. Patients in the high-risk group also had more gene mutation changes and were more sensitive to chemotherapy drugs like docetaxel and sorafenib. The ERS was also validated in the GSE30219, GSE11969 and GSE72094, and showed a favorable prognostic value for LUAD patients.DiscussionThe ERS established during this study was able to predict a poor prognosis for LUAD patients and had great potential for predicting drug responses.

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“…The points distributed outside the two vertical borders and above the horizontal border represented the proteins with significant differences; proteins with at least a 1.5-fold change in expression and P<0.05 were considered significant. Subsequently, bioinformatics analysis, including GO and KEGG pathway analysis, was performed to identify differentially expressed proteins ( 18 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of differentially expressed proteins involved in fetal scarless wound healing using a rat model of cleft lip

Liu

et al. 2021

Mol Med Rep

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in early pregnancy, fetal skin wounds can heal quickly and undergo a transition period from scarless healing to scar formation. The aim of the present study was to identify potential biomarkers associated with scarless repair of cleft lips, in order to determine the intrinsic factors leading to scar formation in embryonic tissue. a stable model of cleft lip was established using microsurgery by constructing a wedge-shaped cleft lip-like defect in fetal rats at gestational age (Ga) 16.5 and Ga18.5. The Ga16.5 and Ga18.5 groups were used to model scarless healing and scar formation, respectively. The fetuses were returned to the uterus following surgery, then removed 72 h after the procedure. Macroscopic observation of the cleft defect and histological examination were carried out. reverse transcription-quantitative (rT-q) Pcr and parallel reaction monitoring (PrM) were used to detect mrna and protein expression levels, respectively. The upper-left lip completely healed 72 h after surgery in the Ga16.5 group of fetal rats. However, this was not the case in the Ga18.5 group. Histological examination indicated new follicles visible under the epidermis of the scarless group (Ga16.5). Scarring was visible on the upper-left cleft lip wound of the fetal rats in the Ga18.5 group. The expression of some growth and pro-inflammatory factors, including TnF-α, were also different between two groups. Label-free quantification was used to identified differentially expressed proteins and five differentially expressed proteins (Smad4, Fabp5, S100a4, S100a8 and S100a9) were identified. The relative expression of these molecules at the mrna and protein levels were measured using rT-qPcr and PrM. These molecules may represent potential biomarkers for the scarless repair of fetal rat cleft lip wounds.

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Computational Approach to Investigating Key GO Terms and KEGG Pathways Associated with CNV

Cited by 4 publications

References 92 publications

Circ007071 Inhibits Unsaturated Fatty Acid Synthesis by Interacting with miR-103-5p to Enhance PPARγ Expression in the Dairy Goat Mammary Gland

Circ007071 Inhibits Unsaturated Fatty Acid Synthesis by Interacting with miR-103-5p to Enhance PPARγ Expression in the Dairy Goat Mammary Gland

Identification of a novel gene signature of lung adenocarcinoma based on epidermal growth factor receptor-tyrosine kinase inhibitor resistance

Identification of differentially expressed proteins involved in fetal scarless wound healing using a rat model of cleft lip

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