<i>ggtranscript</i>: an R package for the visualization and interpretation of transcript isoforms using<i>ggplot2</i>

Gustavsson, Emil K.; Zhang, David; Reynolds, Regina H.; García-Ruiz, Sonia; Ryten, Mina

doi:10.1093/bioinformatics/btac409

Cited by 177 publications

(105 citation statements)

References 9 publications

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“…We classified BC into PAM50-based intrinsic subtypes: luminal A, luminal B, HER2-enriched, basal-like, and normal-like subtype ( Wang et al, 2021 ). Further, the expression data of FLT3 in different phenotypes were analyzed and visualized using ggplot2 ( Gustavsson et al, 2022 ) and ggpubr ( Xia and Li, 2020 ) R packages. Meanwhile, DNA methylation analysis of FLT3 was conducted along with data on clinical features and vital status.…”

Section: Methodsmentioning

confidence: 99%

High FLT3 expression indicates favorable prognosis and correlates with clinicopathological parameters and immune infiltration in breast cancer

Chen

Wang

et al. 2022

Front. Genet.

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Purpose: Breast cancer is a highly heterogeneous malignancy, seriously threatening female health worldwide and inducing higher mortalities. Few have the studies evaluated Fms-like TyrosineKinase-3 (FLT3) in prognostic risk, immunotherapy or any other treatment of breast cancer. Our study focused on investigating the function of FLT3 in breast cancer.Patients and methods: Based on transcriptome and methylation data mined from The Cancer Gene Atlas (TCGA), we explored the clinical features of FLT3 expression in 1079 breast cancer samples. RT-qPCR in cell lines and tissue samples was used to verify the expression difference of FLT3. Kaplan–Meier survival analysis and cox regression models were employed for screening of FLT3 with potential prognostic capacity. Subsequently, functional analysis of the co-expressed genes was conducted using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene-set enrichment analysis (GSEA). The correlation between FLT3 expression and tumor immune infiltration was jointly analyzed with estimate, ssGSEA, TIMER, and TISIDB. Then we employed checkpoint-related molecules, immunophenoscore (IPS), and tumor mutation burden (TMB) to assess the efficacy of immuno-checkpoint inhibitors (ICIs). Pearson correlation coefficient was employed to exam the association between DNA methylation and FLT3 expression.Results: FLT3 displays an elevated expression in breast cancer than normal pairs and is significantly associated with multiple clinical characteristics like age, menopause status, histological type, pathological stage, and molecular subtype as well as increased overall survival (OS). Additionally, FLT3 is a favorable independent prognostic factor. GO, KEGG, and GSEA suggested that FLT3 was associated with diversified immune-related features. FLT3 expression is correlated with the abundance of various immune cells namely CD4+T cell, CD8+ T cell, myeloid dendritic cell, and neutrophil as well as immune inhibitors especially CTLA4, which is positively correlated with FLT3 expression. Moreover, TMB displayed a negative correlation with FLT3 expression while IPS showed adverse tendency. Ultimately, the methylation of FLT3 downregulates the gene expression and closely binds to a few clinical parameters.Conclusion: FLT3 can be used for prognostic prediction and is relevant to immune infiltration in breast cancer. FLT3 may pave the way for future novel immunotherapies.

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Section: Methodsmentioning

confidence: 99%

High FLT3 expression indicates favorable prognosis and correlates with clinicopathological parameters and immune infiltration in breast cancer

Chen

Wang

et al. 2022

Front. Genet.

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“…( C ) Summary of the cardinality between the annotated introns and novel junctions in IntroVerse. ( D ) Visualisation of a novel junction and the mis-splicing activity occurring within the MANE transcript of a selected gene using ggtranscript ( 35 ).…”

Section: Methodsmentioning

confidence: 99%

IntroVerse: a comprehensive database of introns across human tissues

García-Ruiz

Zhang

Reynolds

et al. 2022

Nucleic Acids Research

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Dysregulation of RNA splicing contributes to both rare and complex diseases. RNA-sequencing data from human tissues has shown that this process can be inaccurate, resulting in the presence of novel introns detected at low frequency across samples and within an individual. To enable the full spectrum of intron use to be explored, we have developed IntroVerse, which offers an extensive catalogue on the splicing of 332,571 annotated introns and a linked set of 4,679,474 novel junctions covering 32,669 different genes. This dataset has been generated through the analysis of 17,510 human control RNA samples from 54 tissues provided by the Genotype-Tissue Expression Consortium. IntroVerse has two unique features: (i) it provides a complete catalogue of novel junctions and (ii) each novel junction has been assigned to a specific annotated intron. This unique, hierarchical structure offers multiple uses, including the identification of novel transcripts from known genes and their tissue-specific usage, and the assessment of background splicing noise for introns thought to be mis-spliced in disease states. IntroVerse provides a user-friendly web interface and is freely available at https://rytenlab.com/browser/app/introverse.

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“…DEGs with the threshold criterion of |log2FC| >1 and p < 0.05 from NOA and normal control samples in GSE45885 and GSE45887 datasets were screened with the limma package ( Walker, 2009 ). Subsequently, heatmaps and volcano plots of DEGs from each dataset were plotted using the pheatmap package ( Ning et al, 2022 ) and ggplot2 package ( Gustavsson et al, 2022 ) in the R analysis platform.…”

Section: Methodsmentioning

confidence: 99%

Integrative analyses of potential biomarkers and pathways for non-obstructive azoospermia

et al. 2022

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Background: Non-obstructive azoospermia (NOA) is the most severe form of male infertility. Currently, the molecular mechanisms underlying NOA pathology have not yet been elucidated. Hence, elucidation of the mechanisms of NOA and exploration of potential biomarkers are essential for accurate diagnosis and treatment of this disease. In the present study, we aimed to screen for biomarkers and pathways involved in NOA and reveal their potential molecular mechanisms using integrated bioinformatics.Methods: We downloaded two gene expression datasets from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) in NOA and matched the control group tissues were identified using the limma package in R software. Subsequently, Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA), protein-protein interaction (PPI) network, gene-microRNAs network, and transcription factor (TF)-hub genes regulatory network analyses were performed to identify hub genes and associated pathways. Finally, we conducted immune infiltration analysis using CIBERSORT to evaluate the relationship between the hub genes and the NOA immune infiltration levels.Results: We identified 698 common DEGs, including 87 commonly upregulated and 611 commonly downregulated genes in the two datasets. GO analysis indicated that the most significantly enriched gene was protein polyglycylation, and KEGG pathway analysis revealed that the DEGs were most significantly enriched in taste transduction and pancreatic secretion signaling pathways. GSEA showed that DEGs affected the biological functions of the ribosome, focaladhesion, and protein_expor. We further identified the top 31 hub genes from the PPI network, and friends analysis of hub genes in the PPI network showed that NR4A2 had the highest score. In addition, immune infiltration analysis found that CD8+ T cells and plasma cells were significantly correlated with ODF3 expression, whereas naive B cells, plasma cells, monocytes, M2 macrophages, and resting mast cells showed significant variation in the NR4A2 gene expression group, and there were differences in T cell regulatory immune cell infiltration in the FOS gene expression groups.Conclusion: The present study successfully constructed a regulatory network of DEGs between NOA and normal controls and screened three hub genes using integrative bioinformatics analysis. In addition, our results suggest that functional changes in several immune cells in the immune microenvironment may play an important role in spermatogenesis. Our results provide a novel understanding of the molecular mechanisms of NOA and offer potential biomarkers for its diagnosis and treatment.

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ggtranscript: an R package for the visualization and interpretation of transcript isoforms usingggplot2

Cited by 177 publications

References 9 publications

High FLT3 expression indicates favorable prognosis and correlates with clinicopathological parameters and immune infiltration in breast cancer

High FLT3 expression indicates favorable prognosis and correlates with clinicopathological parameters and immune infiltration in breast cancer

IntroVerse: a comprehensive database of introns across human tissues

Integrative analyses of potential biomarkers and pathways for non-obstructive azoospermia

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