KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Bu, Dechao; Luo, Haitao; Huo, Peipei; Wang, Zhihao; Zhang, Shan; He, Zihao; Wu, Yang; Zhao, Lianhe; Liu, Jingjia; Guo, Jincheng; Fang, Shuangsang; Cao, Wanchen; Yi, Lei; Zhao, Yi; Kong, Lei

doi:10.1093/nar/gkab447

Cited by 984 publications

(664 citation statements)

References 46 publications

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“…ClusterProfiler package in Bioconductor was used to perform GO analysis ( Yu et al, 2012 ) and q -values < 0.05 were considered statistically significant. KEGG pathways were enriched by KOBAS online software 2 ( Bu et al, 2021 ) and the corrected P -values < 0.05 were considered statistically significant.…”

Section: Methodsmentioning

confidence: 99%

Identification of Circular RNA Expression Profiles in White Adipocytes and Their Roles in Adipogenesis

et al. 2021

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Obesity and its related metabolic diseases have become great public health threats worldwide. Although accumulated evidence suggests that circRNA is a new type of non-coding RNAs regulating various physiological and pathological processes, little attention has been paid to the expression profiles and functions of circRNAs in white adipose tissue. In this study, 3,771 circRNAs were detected in three stages of white adipogenesis (preadipocyte, differentiating preadipocyte, and mature adipocyte) by RNA-seq. Experimental validation suggested that the RNA-seq results are highly reliable. We found that nearly 10% of genes which expressed linear RNAs in adipocytes could also generate circRNAs. In addition, 40% of them produced multiple circRNA isoforms. We performed correlation analysis and found that a great deal of circRNAs (nearly 50%) and their parental genes were highly correlated in expression levels. A total of 41 differential expression circRNAs (DECs) were detected during adipogenesis and an extremely high ratio of them (80%) were correlated with their parental genes, indicating these circRNAs may potentially play roles in regulating the expression of their parental genes. KEGG enrichment and GO annotation of the parental genes suggesting that the DECs may participate in several adipogenesis-related pathways. Following rigorous selection, we found that many up-regulated circRNAs contain multiple miRNAs binding sites, such as miR17, miR-30c, and miR-130, indicating they may potentially facilitate their regulatory functions by acting as miRNA sponges. These results suggest that plenty of circRNAs are expressed in white adipogenesis and the DECs may serve as new candidates for future adipogenesis regulation.

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Section: Methodsmentioning

confidence: 99%

Identification of Circular RNA Expression Profiles in White Adipocytes and Their Roles in Adipogenesis

et al. 2021

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“…genome.jp/kegg, accessed on 15 May 2021). For the KEGG enrichment or pathway analysis, the KOBAS3.0 [29] method was used, and visualized by Pathview package of R/Bioconductor.…”

Section: Genome Wide Identification Of the Mshsp90 Gens And Gene Sequence Analysismentioning

confidence: 99%

Genome-Wide Characterization of HSP90 Gene Family in Malus sieversii and Their Potential Roles in Response to Valsa mali Infection

Haxim

Liu

et al. 2021

Forests

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Heat shock protein 90 (HSP90) is highly conservative molecular chaperon produced by plants in response to adverse environmental stresses including fungal infection. In China, canker disease, caused by Valsa mali, is the main threat for Malus sieversii, an ancestor of the cultivated apple. In this study, a total of eight HSP90 genes were identified from the M. sieversii genome and randomly distributed on eight chromosomes. According to gene structure and phylogenetic analysis, the MsHSP90s can be divided into five categories. The transcriptome analysis of M. sieversii under V. mali infection showed that the plant pathogen interaction pathway was identified as significantly enriched. RNA-seq data and qRT-PCR analysis demonstrated that the MsHSP90-6a gene was significantly repressed by V. mali infection. We further predicted cis-regulatory elements on the promotor region of MsHSP90 genes and identified canonical SHE motifs. Our results improve our understanding of the HSP90 gene family and provide a foundation for further studies of disease prevention in M. sieversii.

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“…We use the GAQ score to determine the value added to functional information, particularly when compared with well-annotated model species, such as D. melanogaster, and to a lesser extent, Apis mellifera and Triboleum castaneum. [26,27] assigns input proteins to known pathways in KEGG. It also includes a gene set enrichment function (Table S3) to find statistically enriched genes in a disease or experimental condition with respect to the background of all annotated proteins in the organism.…”

Section: Combining and Qc Of Go Annotationsmentioning

confidence: 99%

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

Saha

Cooksey

Childers

et al. 2021

Insects

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Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply ‘omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in genome sequences (structural annotation); and associating a function with genetic elements (functional annotation). While there are well-established and freely available workflows for structural annotation of gene identification in newly assembled genomes, workflows for providing the functional annotation required to support functional genomics studies are less well understood. Genome-scale functional annotation is required for functional modeling (enrichment, networks, etc.). A first-pass genome-wide functional annotation effort can rapidly identify under-represented gene sets for focused community annotation efforts. We present an open-source, open access, and containerized pipeline for genome-scale functional annotation of insect proteomes and apply it to various arthropod species. We show that the performance of the predictions is consistent across a set of arthropod genomes with varying assembly and annotation quality.

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KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

Cited by 984 publications

References 46 publications

Identification of Circular RNA Expression Profiles in White Adipocytes and Their Roles in Adipogenesis

Identification of Circular RNA Expression Profiles in White Adipocytes and Their Roles in Adipogenesis

Genome-Wide Characterization of HSP90 Gene Family in Malus sieversii and Their Potential Roles in Response to Valsa mali Infection

Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes

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