scholarly journals NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis

2017 ◽  
Vol 11 (S4) ◽  
Author(s):  
Duanchen Sun ◽  
Yinliang Liu ◽  
Xiang-Sun Zhang ◽  
Ling-Yun Wu
Keyword(s):  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Generative Model ◽  
Functional Enrichment ◽  
Gene Set ◽  
Probabilistic Generative Model

scholarly journals Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores

2021 ◽  
Author(s):  
Rui Fan ◽  
Qinghua Cui
Keyword(s):  
Functional Analysis ◽  
Gene List ◽  
Lung Squamous Cell Carcinoma ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Hypergeometric Test ◽  
Exact Test ◽  
Gene Set ◽  
Gene Functional Analysis

ABSTRACTGene functional enrichment analysis represents one of the most popular bioinformatics methods for annotating the pathways and function categories of a given gene list. Current algorithms for enrichment computation such as Fisher’s exact test and hypergeometric test totally depend on the category count numbers of the gene list and one gene set. In this case, whatever the genes are, they were treated equally. However, actually genes show different scores in their essentiality in a gene list and in a gene set. It is thus hypothesized that the essentiality scores could be important and should be considered in gene functional analysis. For this purpose, here we proposed WEAT (https://www.cuilab.cn/weat/), a weighted gene set enrichment algorithm and online tool by weighting genes using essentiality scores. We confirmed the usefulness of WEAT using two case studies, the functional analysis of one aging-related gene list and one gene list involved in Lung Squamous Cell Carcinoma (LUSC). Finally, we believe that the WEAT method and tool could provide more possibilities for further exploring the functions of given gene lists.

Identification and Functional Enrichment Analysis of Differentially Expressed Genes in Osteoarthritis

2020 ◽  
Author(s):  
Chen Xu ◽  
Ling-bing Meng ◽  
Yu Xiao ◽  
Yong Qiu ◽  
Ying-jue Du ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Differentially Expressed Genes ◽  
Cellular Response ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Ppi Network ◽  
Gene Set Enrichment ◽  
Gene Set

Abstract Background Osteoarthritis (OA) is a chronic, progressive, inflammatory, degenerative disease, which has become an osteoarthropathy that seriously affects physical health and quality of life of elderly people. However, the etiology and pathogenesis of OA remains unclear. Therefore, the study purposed to utilize bioinformatics technology to perform identification and functional enrichment analysis of differentially expressed genes in osteoarthritis. Method The main methods of this study consist of access to microarray data (GSE82107 and GSE55235), identification of differently expressed genes (DEGs) by GEO2R between OA and normal synovium samples, enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) by Gene Set Enrichment Analysis (GSEA), construction and analysis of protein-protein interaction (PPI) network, significant module and hub genes. Result A total of 300 DEGs were identified, consisting of 64 up-regulated genes and 11 down-regulated genes in OA samples compared to normal synovium tissues. Gene set enrichment analysis of DEGs provided a comprehensive overview of some major pathophysiological mechanisms in OA: cellular response to hydrogen peroxide, P53 signaling pathway and so on. The study also built the PPI network, and a total of 10 key genes were identified: CYR61, PENK, GOLM1, DUSP1, ATF3, STC2, FOSB, PRSS23, TF, and TNC. Conclusion DEGs exists between OA patients and normal cartilage tissue, which may be involved in the related mechanism of OA development, especially cellular response to hydrogen peroxide and CYR61.

Gene Set to Diseases (GS2D): disease enrichment analysis on human gene sets with literature data

2016 ◽  
Vol 2 (1) ◽  
pp. 33 ◽  
Author(s):  
Jean Fred Fontaine ◽  
Miguel A Andrade-Navarro
Keyword(s):  
Experimental Data ◽  
Enrichment Analysis ◽  
Cost Effective ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Protein Coding ◽  
Gene Set ◽  
Gene Sets ◽  
Cost Effective Method ◽  
Disease Associations

Large sets of candidate genes derived from high-throughput biological experiments can be characterized by functional enrichment analysis. The analysis consists of comparing the functions of one gene set against that of a background gene set. Then, functions related to a significant number of genes in the gene set are expected to be relevant. Web tools offering disease enrichment analysis on gene sets are often based on gene-disease associations from manually curated or experimental data that is accurate but does not cover all diseases discussed in the literature. Using associations automatically derived from literature data could be a cost effective method to improve the coverage of diseases for enrichment analysis at comparable levels of accuracy. We have implemented a method named Gene set to Diseases, GS2D, as a web tool performing disease enrichment analysis on human protein coding gene sets. It uses an automatically built dataset of more than 63 thousand gene-disease associations defined as statistically significant co-occurrences of genes and diseases in annotations of biomedical citations from PubMed. The dataset covers more diseases for enrichment analysis than the largest comparable curated database, Comparative Toxicogenomics Database, and its performance compared favourably to similar approaches based on manually curated or experimental data. Graphical and programmatic interfaces are available at http://cbdm.uni-mainz.de/geneset2diseases.

scholarly journals CEA: Combination-based gene set functional enrichment analysis

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Duanchen Sun ◽  
Yinliang Liu ◽  
Xiang-Sun Zhang ◽  
Ling-Yun Wu
Keyword(s):  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Gene Set

Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Wrky Transcription Factor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Callose Deposition ◽  
Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

scholarly journals Structural variations in papaya genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhenyang Liao ◽  
Xunxiao Zhang ◽  
Shengcheng Zhang ◽  
Zhicong Lin ◽  
Xingtan Zhang ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Enrichment Analysis ◽  
Copy Number Variant ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Structural Variations ◽  
Reproduction Traits ◽  
Depth Study ◽  
Environmental Adaptability ◽  
The Impact

Abstract Background Structural variations (SVs) are a type of mutations that have not been widely detected in plant genomes and studies in animals have shown their role in the process of domestication. An in-depth study of SVs will help us to further understand the impact of SVs on the phenotype and environmental adaptability during papaya domestication and provide genomic resources for the development of molecular markers. Results We detected a total of 8083 SVs, including 5260 deletions, 552 tandem duplications and 2271 insertions with deletion being the predominant, indicating the universality of deletion in the evolution of papaya genome. The distribution of these SVs is non-random in each chromosome. A total of 1794 genes overlaps with SV, of which 1350 genes are expressed in at least one tissue. The weighted correlation network analysis (WGCNA) of these expressed genes reveals co-expression relationship between SVs-genes and different tissues, and functional enrichment analysis shows their role in biological growth and environmental responses. We also identified some domesticated SVs genes related to environmental adaptability, sexual reproduction, and important agronomic traits during the domestication of papaya. Analysis of artificially selected copy number variant genes (CNV-genes) also revealed genes associated with plant growth and environmental stress. Conclusions SVs played an indispensable role in the process of papaya domestication, especially in the reproduction traits of hermaphrodite plants. The detection of genome-wide SVs and CNV-genes between cultivated gynodioecious populations and wild dioecious populations provides a reference for further understanding of the evolution process from male to hermaphrodite in papaya.

scholarly journals CCTs as new biomarkers for the prognosis of head and neck squamous cancer

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 672-688
Author(s):  
Yanbo Dong ◽  
Siyu Lu ◽  
Zhenxiao Wang ◽  
Liangfa Liu
Keyword(s):  
Head And Neck ◽  
Survival Data ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Advanced Tumor Stage ◽  
Expression Levels ◽  
T Complex ◽  
Advanced Tumor ◽  
Squamous Cancer

AbstractThe chaperonin-containing T-complex protein 1 (CCT) subunits participate in diverse diseases. However, little is known about their expression and prognostic values in human head and neck squamous cancer (HNSC). This article aims to evaluate the effects of CCT subunits regarding their prognostic values for HNSC. We mined the transcriptional and survival data of CCTs in HNSC patients from online databases. A protein–protein interaction network was constructed and a functional enrichment analysis of target genes was performed. We observed that the mRNA expression levels of CCT1/2/3/4/5/6/7/8 were higher in HNSC tissues than in normal tissues. Survival analysis revealed that the high mRNA transcriptional levels of CCT3/4/5/6/7/8 were associated with a low overall survival. The expression levels of CCT4/7 were correlated with advanced tumor stage. And the overexpression of CCT4 was associated with higher N stage of patients. Validation of CCTs’ differential expression and prognostic values was achieved by the Human Protein Atlas and GEO datasets. Mechanistic exploration of CCT subunits by the functional enrichment analysis suggests that these genes may influence the HNSC prognosis by regulating PI3K-Akt and other pathways. This study implies that CCT3/4/6/7/8 are promising biomarkers for the prognosis of HNSC.

scholarly journals Investigation and Functional Enrichment Analysis of the Human Host Interaction Network with Common Gram-Negative Respiratory Pathogens Predicts Possible Association with Lung Adenocarcinoma

2021 ◽  
Vol 28 (1) ◽  
pp. 20-33
Author(s):  
Lydia-Eirini Giannakou ◽  
Athanasios-Stefanos Giannopoulos ◽  
Chrissi Hatzoglou ◽  
Konstantinos I. Gourgoulianis ◽  
Erasmia Rouka ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Cell Junctions ◽  
Respiratory Pathogens ◽  
Gram Negative ◽  
Human Proteins ◽  
Apoptotic Pathways

Haemophilus influenzae (Hi), Moraxella catarrhalis (MorCa) and Pseudomonas aeruginosa (Psa) are three of the most common gram-negative bacteria responsible for human respiratory diseases. In this study, we aimed to identify, using the functional enrichment analysis (FEA), the human gene interaction network with the aforementioned bacteria in order to elucidate the full spectrum of induced pathogenicity. The Human Pathogen Interaction Database (HPIDB 3.0) was used to identify the human proteins that interact with the three pathogens. FEA was performed via the ToppFun tool of the ToppGene Suite and the GeneCodis database so as to identify enriched gene ontologies (GO) of biological processes (BP), cellular components (CC) and diseases. In total, 11 human proteins were found to interact with the bacterial pathogens. FEA of BP GOs revealed associations with mitochondrial membrane permeability relative to apoptotic pathways. FEA of CC GOs revealed associations with focal adhesion, cell junctions and exosomes. The most significantly enriched annotations in diseases and pathways were lung adenocarcinoma and cell cycle, respectively. Our results suggest that the Hi, MorCa and Psa pathogens could be related to the pathogenesis and/or progression of lung adenocarcinoma via the targeting of the epithelial cellular junctions and the subsequent deregulation of the cell adhesion and apoptotic pathways. These hypotheses should be experimentally validated.

scholarly journals Isolation and identification of a novel bacterium, Pseudomonas sp. ZyL-01, involved in the biodegradation of CL-20

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Zhiyong Liu ◽  
Kai Dang ◽  
Cunzhi Li ◽  
Junhong Gao ◽  
Hong Wang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Fate ◽  
Draft Genome ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Community Diversity ◽  
Functional Enrichment ◽  
Metagenomic Sequencing ◽  
Isolation And Identification ◽  
Novel Bacterium

Abstract Hexanitrohexaazaisowurtzitane (CL-20) is a compound with a polycyclic cage and an N-nitro group that has been shown to play an unfavorable role in environmental fate, biosafety, and physical health. The aim of this study was to isolate the microbial community and to identify a single microbial strain that can degrade CL-20 with desirable efficiency. Metagenomic sequencing methods were performed to investigate the dynamic changes in the composition of the community diversity. The most varied genus among the microbial community was Pseudomonas, which increased from 1.46% to 44.63% during the period of incubation (MC0–MC4). Furthermore, the new strain was isolated and identified from the activated sludge by bacterial morphological and 16s rRNA sequencing analyses. The CL-20 concentrations decreased by 75.21 μg/mL and 74.02 μg/mL in 48 h by MC4 and Pseudomonas sp. ZyL-01, respectively. Moreover, ZyL-01 could decompose 98% CL-20 of the real effluent in 14 day’s incubation with the glucose as carbon source. Finally, a draft genome sequence was obtained to predict possible degrading enzymes involved in the biodegradation of CL-20. Specifically, 330 genes that are involved in energy production and conversion were annotated by Gene Ontology functional enrichment analysis, and some of these candidates may encode enzymes that are responsible for CL-20 degradation. In summary, our studies indicate that microbes might be a valuable biological resource for the treatment of environmental contamination caused by CL-20 and that Pseudomonas sp. ZyL-01 might be a promising candidate for eradicating CL-20 to achieve a more biosafe environment and improve public health.

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