Genomics & informatics最新文献_第4页

Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment. 确定与两种以上自身免疫性疾病相关的共同遗传因素和免疫相关途径：对风险、诊断和治疗的影响。

Genomics & informatics Pub Date : 2024-07-02 DOI: 10.1186/s44342-024-00004-5

Aruna Rajalingam, Anjali Ganjiwale

{"title":"Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment.","authors":"Aruna Rajalingam, Anjali Ganjiwale","doi":"10.1186/s44342-024-00004-5","DOIUrl":"10.1186/s44342-024-00004-5","url":null,"abstract":"Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system attacking its cells or tissues. Recent studies report shared effects, mechanisms, and evolutionary origins among ADs; however, the possible factors connecting them are unknown. This study attempts to identify gene signatures commonly shared between different autoimmune disorders and elucidate their molecular pathways linking the pathogenesis of these ADs using an integrated gene expression approach. We employed differential gene expression analysis across 19 datasets of whole blood/peripheral blood cell samples with five different autoimmune disorders (rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, Crohn's disease, and type 1 diabetes) to get nine key genes-EGR1, RUNX3, SMAD7, NAMPT, S100A9, S100A8, CYBB, GATA2, and MCEMP1 that were primarily involved in cell and leukocyte activation, leukocyte mediated immunity, IL-17, AGE-RAGE signaling in diabetic complications, prion disease, and NOD-like receptor signaling confirming its role in immune-related pathways. Combined with biological interpretations such as gene ontology (GO), pathway enrichment, and protein-protein interaction (PPI) network, our current study sheds light on the in-depth research on early detection, diagnosis, and prognosis of different ADs.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11221123/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring molecular targets: herbal isolates in cervical cancer therapy. 探索分子靶点：宫颈癌治疗中的草药分离物。

Genomics & informatics Pub Date : 2024-06-26 DOI: 10.1186/s44342-024-00008-1

Maryam Ahmadi, Razieh Abdollahi, Marzieh Otogara, Amir Taherkhani

{"title":"Exploring molecular targets: herbal isolates in cervical cancer therapy.","authors":"Maryam Ahmadi, Razieh Abdollahi, Marzieh Otogara, Amir Taherkhani","doi":"10.1186/s44342-024-00008-1","DOIUrl":"10.1186/s44342-024-00008-1","url":null,"abstract":"Objective: Cervical cancer (CxCa) stands as a significant global health challenge, ranking fourth in cancer-related mortality among the female population. While chemotherapy regimens have demonstrated incremental progress in extending overall survival, the outlook for recurrent CxCa patients remains disheartening. An imperative necessity arises to delve into innovative therapeutic avenues, with molecular targeted therapy emerging as a promising candidate. Previous investigations have shed light on the therapeutic effectiveness of five distinct herbal compounds, epicatechin, curcumin, myricetin, jatrorrhizine, and arborinine, within the context of CxCa.Methods: A systems biology approach was employed to discern differentially expressed genes (DEGs) in CxCa tissues relative to healthy cervical epithelial tissues. A protein-protein interaction network (PPIN) was constructed, anchored in the genes related to CxCa. The central genes were discerned within the PPIN, and Kaplan-Meier survival curves explored their prognostic significance. An assessment of the binding affinity of the selected herbal compounds to the master regulator of prognostic markers in CxCa was conducted.Results: A significant correlation between the overexpression of MYC, IL6, JUN, RRM2, and VEGFA and an adverse prognosis in CxCa was indicated. The regulation of these markers is notably influenced by the transcription factor CEBPD. Molecular docking analysis indicated that the binding affinity between myricetin and the CEBPD DNA binding site was robust.Conclusion: The findings presented herein have unveiled pivotal genes and pathways that play a central role in the malignant transformation of CxCa. CEBPD has emerged as a potential target for harnessing the therapeutic potential of myricetin in this context.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Investigation of missense mutation-related type 1 diabetes mellitus through integrating genomic databases and bioinformatic approach. 通过整合基因组数据库和生物信息学方法研究与错义突变相关的 1 型糖尿病。

Genomics & informatics Pub Date : 2024-06-26 DOI: 10.1186/s44342-024-00005-4

Dyonisa Nasirochmi Pakha, Ratih Dewi Yudhani, Lalu Muhammad Irham

{"title":"Investigation of missense mutation-related type 1 diabetes mellitus through integrating genomic databases and bioinformatic approach.","authors":"Dyonisa Nasirochmi Pakha, Ratih Dewi Yudhani, Lalu Muhammad Irham","doi":"10.1186/s44342-024-00005-4","DOIUrl":"10.1186/s44342-024-00005-4","url":null,"abstract":"Though genes are already known to be responsible for type 1 diabetes mellitus (T1DM), the knowledge of missense mutation of that disease gene has still to be under covered. A genomic database and a bioinformatics-based approach are integrated in the present study in order to address this issue. Initially, nine variants associated with T1DM were retrieved from the GWAS catalogue. Different genomic algorithms such as PolyPhen2.0, SNPs and GTEx analyser programs were used to study the structural and functional effects of these mutations. Subsequently, SNPnexus was also employed to understand the effect of these mutations on the function of the expressed protein. Nine missense variants of T1DM were identified using the GWAS catalogue database. Among these nine SNPs, three were predicted to be related to the progression of T1DM disease by affecting the protein level. TYK2 gene variants with SNP rs34536443 were thought to have a probably damaging effect. Meanwhile, both COL4A3 and IFIH1 genes with SNPs rs55703767 and rs35667974, respectively, might alter protein function through a possibly damaging prediction. Among the variants of the three genes, the TYK2 gene with SNP rs34536443 had the strongest contribution in affecting the development of T1DM, with a score of 0.999. We sincerely hope that the results could be of immense importance in understanding the genetic basis of T1DM.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Survey on large language model annotation of cellular senescence from figures in review articles. 从综述文章中的数字对细胞衰老进行大语言模型注释的调查。

Genomics & informatics Pub Date : 2024-06-17 DOI: 10.1186/s44342-024-00011-6

Yuki Yamagata, Ryota Yamada

引用次数: 0

Overexpression of heat shock protein 47 is associated with increased proliferation and metastasis in gastric cancer. 热休克蛋白 47 的过表达与胃癌的增殖和转移有关。

Genomics & informatics Pub Date : 2024-06-17 DOI: 10.1186/s44342-024-00010-7

Jieun Lee, Jung-Ah Hwang, Seung-Hyun Hong, Seon-Young Kim, Donghyeok Seol, Il Ju Choi, Yeon-Su Lee

{"title":"Overexpression of heat shock protein 47 is associated with increased proliferation and metastasis in gastric cancer.","authors":"Jieun Lee, Jung-Ah Hwang, Seung-Hyun Hong, Seon-Young Kim, Donghyeok Seol, Il Ju Choi, Yeon-Su Lee","doi":"10.1186/s44342-024-00010-7","DOIUrl":"10.1186/s44342-024-00010-7","url":null,"abstract":"Here, we investigated that the heat shock protein 47 (HSP47) plays a crucial role in the progression of gastric cancer (GC). We analyzed HSP47 gene expression in GC cell lines and patient tissues. The HSP47 mRNA and protein expression levels were significantly higher in GC cell lines and tumor tissues compared to normal gastric mucosa. Using siRNA to silence the expression of HSP47 in GC cells resulted in a significant reduction in their proliferation, wound healing, migration, and invasion capacities. Additionally, we also showed that the mRNA expression of matrix metallopeptidase-7 (MMP-7), a metastasis-promoting gene, was significantly reduced in HSP47 siRNA-transfected GC cells. We confirmed that the HSP47 promoter region was methylated in the SNU-216 GC cell line expressing low levels of HSP47 and in most non-cancerous gastric tissues. It means that the expression of HSP47 is regulated by epigenetic regulatory mechanisms. These findings suggest that targeting HSP47, potentially through its promoter methylation, could be a useful new therapeutic strategy for treating GC.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022. 2022 年两次 COVID-19 波期间，SARS-CoV-2 系 BA.5.1.25 及其后代在秘鲁的扩散情况。

Genomics & informatics Pub Date : 2024-05-31 DOI: 10.1186/s44342-024-00006-3

Victor Jimenez-Vasquez, Natalia Vargas-Herrera, Luis Bárcena-Flores, Verónica Hurtado, Carlos Padilla-Rojas, Roger V Araujo-Castillo

引用次数: 0

A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene. 对人类 CYLD 基因中与疾病相关的突变进行结构和功能分析的计算方法。

Genomics & informatics Pub Date : 2024-05-31 DOI: 10.1186/s44342-024-00007-2

Arpita Singha Roy, Tasmiah Feroz, Md Kobirul Islam, Md Adnan Munim, Dilara Akhter Supti, Nusrat Jahan Antora, Hasan Al Reza, Supriya Gosh, Newaz Mohammed Bahadur, Mohammad Rahanur Alam, Md Shahadat Hossain

{"title":"A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene.","authors":"Arpita Singha Roy, Tasmiah Feroz, Md Kobirul Islam, Md Adnan Munim, Dilara Akhter Supti, Nusrat Jahan Antora, Hasan Al Reza, Supriya Gosh, Newaz Mohammed Bahadur, Mohammad Rahanur Alam, Md Shahadat Hossain","doi":"10.1186/s44342-024-00007-2","DOIUrl":"10.1186/s44342-024-00007-2","url":null,"abstract":"Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein-protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Visualization of scientific production in Caenorhabditis elegans: a bibliometric analysis (1980-2023). 草履虫科研成果的可视化：文献计量分析（1980-2023 年）。

Genomics & informatics Pub Date : 2024-05-31 DOI: 10.1186/s44342-024-00002-7

Şeyda Berk, Serkan Özdemir, Ayşe Nur Pektaş

{"title":"Visualization of scientific production in Caenorhabditis elegans: a bibliometric analysis (1980-2023).","authors":"Şeyda Berk, Serkan Özdemir, Ayşe Nur Pektaş","doi":"10.1186/s44342-024-00002-7","DOIUrl":"10.1186/s44342-024-00002-7","url":null,"abstract":"Caenorhabditis elegans (C. elegans) is a nematode and model organism whose entire genome has been mapped, which allows for easy observation of the organism's development due to its transparent structure, and which is appealing due to its ease of crossover, ease of culture, and low cost. Despite being separated by nearly a billion years of evolution, C. elegans homologs have been identified for the vast majority of human genes and are associated with C. elegans for many biological processes such as apoptosis, cell signaling, cell cycle, cell polarity, metabolism, and aging. A detailed bibliometric study is performed here to examine publication trends in this field. Data were taken from the Web of Science database and analyzed using the bibliometric application Biblioshiny (RStudio). In terms of publication, the results indicated a gradual increase each year between 1980 and 2023. A total of 20,322 records were issued in 96 countries, the majority of which were in the USA, China, and Japan. The most prolific writers, the journals most engaged in the area, the nations, institutions, and keywords used by authors were all determined using the Web of Science database and bibliometric rules. The number of papers in the C. elegans research field is increasing exponentially, and Genetics is the journal with the highest number of articles. This study presents how research patterns have evolved throughout time. As a result, worldwide cooperation and a potential field can be developed.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao). 在可可树（Theobroma cacao）的子代和体细胞胚胎成熟过程中，对小辅酶上调 RNA 基因家族进行全基因组鉴定、表征和表达分析。

Genomics & informatics Pub Date : 2024-05-28 DOI: 10.1186/s44342-024-00003-6

Ngoc Thi Bich Chu, Man Thi Le, Hong Viet La, Quynh Thi Ngoc Le, Thao Duc Le, Huyen Thi Thanh Tran, Lan Thi Mai Tran, Chi Toan Le, Dung Viet Nguyen, Phi Bang Cao, Ha Duc Chu

{"title":"Genome-wide identification, characterization, and expression analysis of the small auxin-up RNA gene family during zygotic and somatic embryo maturation of the cacao tree (Theobroma cacao).","authors":"Ngoc Thi Bich Chu, Man Thi Le, Hong Viet La, Quynh Thi Ngoc Le, Thao Duc Le, Huyen Thi Thanh Tran, Lan Thi Mai Tran, Chi Toan Le, Dung Viet Nguyen, Phi Bang Cao, Ha Duc Chu","doi":"10.1186/s44342-024-00003-6","DOIUrl":"10.1186/s44342-024-00003-6","url":null,"abstract":"Small auxin-up RNA (SAUR) proteins were known as a large family that supposedly participated in various biological processes in higher plant species. However, the SAUR family has been still not explored in cacao (Theobroma cacao L.), one of the most important industrial trees. The present work, as an in silico study, revealed comprehensive aspects of the structure, phylogeny, and expression of TcSAUR gene family in cacao. A total of 90 members of the TcSAUR gene family have been identified and annotated in the cacao genome. According to the physic-chemical features analysis, all TcSAUR proteins exhibited slightly similar characteristics. Phylogenetic analysis showed that these TcSAUR proteins could be categorized into seven distinct groups, with 10 sub-groups. Our results suggested that tandemly duplication events, segmental duplication events, and whole genome duplication events might be important in the growth of the TcSAUR gene family in cacao. By re-analyzing the available transcriptome databases, we found that a number of TcSAUR genes were exclusively expressed during the zygotic embryogenesis and somatic embryogenesis. Taken together, our study will be valuable to further functional characterizations of candidate TcSAUR genes for the genetic engineering of cacao.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":"22 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184954/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141437954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unraveling the hypoxia modulating potential of VEGF family genes in pan-cancer. 揭示血管内皮生长因子家族基因在泛癌细胞中对缺氧调节的潜力。

Genomics & informatics Pub Date : 2023-12-01 Epub Date: 2023-09-27 DOI: 10.5808/gi.23061

So-Hyun Bae, Taewon Hwang, Mi-Ryung Han

{"title":"Unraveling the hypoxia modulating potential of VEGF family genes in pan-cancer.","authors":"So-Hyun Bae, Taewon Hwang, Mi-Ryung Han","doi":"10.5808/gi.23061","DOIUrl":"10.5808/gi.23061","url":null,"abstract":"Tumor hypoxia, oxygen deprivation state, occurs in most cancers and promotes angiogenesis, enhancing the potential for metastasis. The vascular endothelial growth factor (VEGF) family genes play crucial roles in tumorigenesis by promoting angiogenesis. To investigate the malignant processes triggered by hypoxia-induced angiogenesis across pan-cancers, we comprehensively analyzed the relationships between the expression of VEGF family genes and hypoxic microenvironment based on integrated bioinformatics methods. Our results suggest that the expression of VEGF family genes differs significantly among various cancers, highlighting their heterogeneity effect on human cancers. Across the 33 cancers, VEGFB and VEGFD showed the highest and lowest expression levels, respectively. The survival analysis showed that VEGFA and placental growth factor (PGF) were correlated with poor prognosis in many cancers, including kidney renal cell and liver hepatocellular carcinoma. VEGFC expression was positively correlated with glioma and stomach cancer. VEGFA and PGF showed distinct positive correlations with hypoxia scores in most cancers, indicating a potential correlation with tumor aggressiveness. The expression of miRNAs targeting VEGF family genes, including hsa-miR-130b-5p and hsa-miR-940, was positively correlated with hypoxia. In immune subtypes analysis, VEGFC was highly expressed in C3 (inflammatory) and C6 (transforming growth factor β dominant) across various cancers, indicating its potential role as a tumor promotor. VEGFC expression exhibited positive correlations with immune infiltration scores, suggesting low tumor purity. High expression of VEGFA and VEGFC showed favorable responses to various drugs, including BLU-667, which abrogates RET signaling, an oncogenic driver in liver and thyroid cancers. Our findings suggest potential roles of VEGF family genes in malignant processes related with hypoxia-induced angiogenesis.","PeriodicalId":94288,"journal":{"name":"Genomics & informatics","volume":" ","pages":"e44"},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10788353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49687003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0