Gene set enrichment analysis
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This study aims to identify functionally relevant lncRNAs impacting OS proliferation and lipid metabolism and seeks to shed light on the upstream regulatory mechanisms governing lipogenic enzyme activity. Based on comprehensive bioinformatic analysis and the establishment of a risk model, we identified seven lncRNAs signifcantly associated with clinical characteristics and lipid metabolism-related genes in patients with OS.
15p vikoch 27-06-2024 1 1 Download
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This study developed a gene signature associated with a malignant and common tumor of the urinary system, the Bladder Urothelial Carcinoma (BLCA). Methods: The Cancer Genome Atlas (TCGA) database was searched to obtain 414 BLCA samples and the expression spectra of 19 normal samples. Single-sample Gene Set Enrichment Analysis (ssGSEA) was conducted to determine the enrichment levels in the BLCA samples of the 29 immune genes.
18p vialfrednobel 23-12-2023 4 3 Download
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Tumor acidosis, a common phenomenon in solid cancers such as breast cancer, is caused by the abnormal metabo‑ lism of cancer cells. The low pH affects cells surrounding the cancer, and tumor acidosis has been shown to inhibit the activity of immune cells.
11p vialfrednobel 23-12-2023 6 3 Download
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Thyroid cancer (TC) is one of the most common endocrine malignancies, and its morbidity continues to rise. N6 -methyladenosine (m6 A) RNA methylation, an epigenetic modification, is an important regulator of gene expression in TC.
13p vioracle 29-09-2023 5 3 Download
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Multiple myeloma (MM) is a fatal malignant tumor in hematology. Mitophagy plays vital roles in the pathogenesis and drug sensitivity of MM. We acquired transcriptomic expression data and clinical index of MM patients from NCI public database, and 36 genes involved in mitophagy from the gene set enrichment analysis (GSEA) database.
18p vioracle 29-09-2023 2 2 Download
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Executive function (EF) is vital to human beings. It has been linked to many genes and family environmental factors in separate studies, but few studies have examined the potential interactions between gene(s) and environmental factor(s).
11p vihagrid 30-01-2023 4 3 Download
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Emerging evidence has proven the robust role of tumor mutation burden (TMB) and immune cell infltration (ICI) in cancer immunotherapy. However, the precise efect of TMB and ICI on clear cell renal cell carcinoma (ccRCC) remains elusive and merits further investigation.
14p vihagrid 30-01-2023 12 3 Download
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Biochemical recurrence (BCR) after initial treatment, such as radical prostatectomy, is the most frequently adopted prognostic factor for patients who suffer from prostate cancer (PCa). In this study, we aimed to construct a prognostic model consisting of gene expression profiles to predict BCR-free survival.
11p viangelamerkel 27-07-2022 6 3 Download
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Single-cell transcriptomics reveals gene expression heterogeneity but suffers from stochastic dropout and characteristic bimodal expression distributions in which expression is either strongly non-zero or non-detectable. We propose a two-part, generalized linear model for such bimodal data that parameterizes both of these features.
13p viaristotle 29-01-2022 13 0 Download
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DNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions.
26p viarchimedes 26-01-2022 8 0 Download
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Alternative splicing (AS) is an important aspect of gene regulation. Nevertheless, its role in molecular processes and pathobiology is far from understood. A roadblock is that tools for the functional analysis of AS-set events are lacking.
22p viarchimedes 26-01-2022 21 0 Download
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A bottleneck in high-throughput functional genomics experiments is identifying the most important genes and their relevant functions from a list of gene hits. Gene Ontology (GO) enrichment methods provide insight at the gene set level.
35p viarchimedes 26-01-2022 6 0 Download
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There is no unified treatment standard for patients with extranodal NK/T-cell lymphoma (ENKTL). Cancer neoantigens are the result of somatic mutations and cancer-specific. Increased number of somatic mutations are associated with anti-cancer effects.
12p vielonmusk 21-01-2022 11 0 Download
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Neuroligin1 (NLGN1) is a main component of excitatory glutamatergic synapses complex and is important for synapse assembly and function. The clinical value of NLGN1 in colorectal cancer (CRC) is not clear.
11p vimahuateng 26-11-2021 10 1 Download
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A promising approach for solving this problem is to compare gene networks built using experimental gene sets with random networks. One of the resources that make such an analysis possible is CrossTalkZ, which uses the FunCoup database. However, existing methods, including CrossTalkZ, do not take into account individual types of interactions, such as protein/protein interactions, expression regulation, transport regulation, catalytic reactions, etc., but rather work with generalized types characterizing the existence of any connection between network members.
14p vibeauty 23-10-2021 9 0 Download
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The key idea behind enrichment analysis is: given a set of significantly expressed genes (or metabolites), use that set to infer a smaller set of perturbed biological pathways or processes, in which those genes (or metabolites) play a role.
11p vilichoo2711 23-06-2021 8 1 Download
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Rosaceae species are economically highly relevant crops. Their cultivation systems are constrained by phytopathogens causing severe losses. Plants respond to invading pathogens through signaling mechanisms, a component of which are of them being plant elicitor peptides (Peps).
18p vilichoo2711 23-06-2021 8 1 Download
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Significance analysis plays a major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regions, and other high-throughput features associated with illness. We propose a new approach, called gene set bagging, for measuring the probability that a gene set replicates in future studies.
8p viwyoming2711 16-12-2020 11 1 Download
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Gaining biological insights into molecular responses to treatments or diseases from omics data can be accomplished by gene set or pathway enrichment methods. A plethora of diferent tools and algorithms have been developed so far. Among those, the gene set enrichment analysis (GSEA) proved to control both type I and II errors well.
13p viwyoming2711 16-12-2020 16 1 Download
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Despite the widespread use of high throughput expression platforms and the availability of a desktop implementation of Gene Set Enrichment Analysis (GSEA) that enables non-experts to perform gene set based analyses, the availability of the necessary precompiled gene sets is rare for species other than human.
6p vikentucky2711 26-11-2020 10 3 Download