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Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

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Big Data Mining and Analytics 2024年第1期7卷 107-130页

作者： Nadezhda Yu.Biziukova Sergey M.Ivanov Oga A.Tarasova Department of bioinformatics Institute of Biomedical ChemistryMoscow 119121Russia Department of bioinformatics Pirogov Russian National Research Medical UniversityMoscow 117997Russia

Analysis of molecular mechanisms that lead to the development of various types of tumors is essential for biology and medicine,because it may help to find new therapeutic opportunities for cancer treatment and cure including personalized treatment *** of the pathways known to be important for the development of neoplastic diseases and pathological processes is the Hedgehog signaling pathway that normally controls human embryonic *** accumulation of various types of biological data,including interactions between proteins,regulation of genes transcription,proteomics,and metabolomics experiments results,allows the application of computational analysis of these big data for identification of key molecular mechanisms of certain diseases and pathologies and promising therapeutic *** aim of this study is to develop a computational approach for revealing associations between human proteins and genes interacting with the Hedgehog pathway components,as well as for identifying their roles in the development of various types of *** automatically collect sets of abstract texts from the NCBI PubMed bibliographic *** recognition of the Hedgehog pathway proteins and genes and neoplastic diseases we use a dictionary-based named entity recognition approach,while for all other proteins and genes machine learning method is *** association extraction,we develop a set of semantic *** complete the results of the text analysis with the gene set enrichment *** identified key pathways that may influence the Hedgehog pathway and their roles in tumor development are then verified using the information in the literature.

关键词： text-mining data mining Hedgehog pathway neoplastic processes enrichment analysis pathology molecularmechanisms

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Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods

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Cancer Biology & Medicine 2024年第4期21卷 312-330页

作者： Qian Zhang Mingran Yang Peng Zhang Bowen Wu Xiaosen Wei Shao Li Institute for TCM-X MOE Key Laboratory of BioinformaticsBioinformatics DivisionBNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China

Gastric cancer(GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development;therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.

关键词： Gastric cancer inflammation-induced tumorigenesis multi-omics artificial intelligence network-based methods

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An enhanced method for predicting and analysing forest fires using an attention-based CNN model

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Journal of Forestry research 2024年第4期35卷 115-127页

作者： Shaifali Bhatt Usha Chouhan Department of Mathematics Bioinformatics and Computer ApplicationsMANIT BhopalBhopalIndia

Prediction,prevention,and control of forest fires are crucial on at all *** effective fire detection systems can aid in their *** study proposes a novel CNN(convolutional neural network)using an attention blocks module which combines an attention module with numerous input layers to enhance the performance of neural *** suggested model focuses on predicting the damage affected/burned areas due to possible wildfires and evaluating the multilateral interactions between the pertinent *** results show the impacts of CNN using attention blocks for feature extraction and to better understand how ecosystems are affected by meteorological *** selected meteorological data,RMSE 12.08 and MAE 7.45 values provide higher predictive power for selecting relevant and necessary features to provide optimal performance with less operational and computational *** findings show that the suggested strategy is reliable and effective for planning and managing fire-prone regions as well as for predicting forest fire damage.

关键词： CNN Attention module Fire prediction Ecosystem Damage prediction

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scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang Keyi Li Shengquan Chen Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease *** fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream *** the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by *** its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

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Genome-wide DNA methylome analysis reveals a critical role of methylation-dysregulated lncRNAs in autophagy regulation in glioblastoma

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Genes & Diseases 2024年第5期11卷 51-54页

作者： Hongying Zhao Ying Liu Meiting Fei Lin Bo Lixia Wang Yaopeng Shu Peiqi Ben Li Wang College of bioinformatics Science and Technology Harbin Medical UniversityHarbinHeilongjiang 150081China

Glioblastoma(GBM)is the most common primary malignant intracranial tumor with a very poor *** this study,we systematically analyzed the DNA methylation alterations of autophagy-related lncRNAs and their association with drug therapies in *** identified 9 DNA methylation-dysregulated lncRNA regulators of autophagy-related genes as autophagy-related lncRNAs.A dysregulated regulatory network consisting of 9 autophagy-related lncRNAs and 237 differentially expressed autophagy-related genes was *** of small molecule drug candidates that may affect DNA methylation dysregulated lncRNA activity,including 45 drug lncRNA pairs,involving 7 DNA methylation dysregulated lncRNAs and 43 ***,we identified a DNA methylation-dysregulated autophagy-related lncRNA MIR155HG as an independent prognostic indicator for GBM.

关键词： regulated alterations drugs

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Integrated analysis of public datasets for the discovery and validation of survival-associated genes in solid tumors

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The Innovation 2024年第3期5卷 129-137页

作者： Balázs Gyorffy Department of Biophysics Medical SchoolUniversity of Pecs7624 PecsHungary Department of bioinformatics Semmelweis University1094 BudapestHungary Cancer Biomarker research Group Institute of Molecular Life SciencesHUN-REN Research Centre for Natural Sciences1117 BudapestHungary

Identifying genes with prognostic significance that can act as biomarkers in solid tumors can help stratify patients and uncover novel therapy ***,our goal was to expand our previous ranking analysis of survival-associated genes in various solid tumors to include colon cancer specimens with available transcriptomic and clinical data.A Gene Expression Omnibus search was performed to identify available datasets with clinical data and raw gene expression measurements.A combined database was set up and integrated into our Kaplan-Meier plotter,making it possible to identify genes with expression changes linked to altered *** a demonstration of the utility of the platform,the most powerful genes linked to overall survival in colon cancer were identified using uni-and multivariate Cox regression *** combined colon cancer database includes 2,137 tumor samples from 17 independent *** most significant genes associated with relapse-free survival with a false discovery rate below 1%in colon cancer carcinoma were RBPMS(hazard rate[HR]=2.52),TIMP1(HR=2.44),and COL4A2(HR=2.36).The three strongest genes associated with shorter survival in stage II colon cancer include CSF1R(HR=2.86),FLNA(HR=2.88),and TPBG(HR=2.65).In summary,a new integrated database for colon cancer is presented.A colon cancer analysis subsystem was integrated into our Kaplan-Meier plotter that can be used to mine the entire database(https://***).The portal has the potential to be employed for the identification and prioritization of promising biomarkers and therapeutic target candidates in multiple solid tumors including,among others,breast,lung,ovarian,gastric,pancreatic,and colon cancers.

关键词： colon tumors analysis

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MicroRNA-630:A potential guardian against inflammation in diabetic kidney disease

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World Journal of Diabetes 2024年第9期15卷 1837-1841页

作者： Ashraf Al Madhoun Department of Genetics and bioinformatics Dasman Diabetes InstituteDasman 15400Kuwait

In this editorial,we comment on the article by Wu et al published“MicroRNA-630 alleviates inflammatory reactions in rats with diabetic kidney disease by targeting toll-like receptor 4”.Diabetic kidney disease(DKD)stands as a significant complication occurring from diabetes mellitus,which contributes substantially to the morbidity and mortality rates *** tubular epithelial cell damage,often accompanied by inflammatory responses and mesenchymal transdifferentiation,plays a pivotal role in the progression of *** extensive research,the intricate molecular mechanisms underlying these processes remain to be *** et al remarkable work identifies microRNA-630(miR-630)as an emerging potential regulator of cell migration,apoptosis,and autophagy,prompting investigation into its association with DKD *** study endeavors to elucidate the impact of miR-630 on TEC injury and the inflammatory response in DKD *** role of miR-630 in human DKD will be of interest for future studies.

关键词： Diabetic kidney disease MicroRNA MicroRNA-630 Toll-like receptor 4 Inflammation

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Age-specific heterogeneity of genetic susceptibility to cardiovascular disease might have opposite outcomes depending on the presence of prediabetes

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World Journal of Diabetes 2024年第6期15卷 1381-1383页

作者： Chaeyoung Lee Department of bioinformatics and Life Science Soongsil UniversitySeoul 06978South Korea

Examining age-specific heterogeneity of susceptibility to cardiovascular disease is also essential in individuals without prediabetes to determine its relative size and direction compared to those with *** particular interest,age-specific heterogeneity in genetic susceptibility may exhibit opposite directions depending on the presence or absence of prediabetes.

关键词： Age-specific difference Cardiovascular disease Genetic heterogeneity by age Genetic susceptibility Prediabetes

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Novel insights on oral squamous cell carcinoma management using long non-coding RNAs

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Oncology research 2024年第10期32卷 1589-1612页

作者： SUBHAYAN SUR DIMPLE DAVRAY SOUMYA BASU SUPRIYA KHEUR JAYANTA KUMAR PAL SHUCHI NAGAR AVINASH SANAP BHIMAPPA MRUDAGI SAMIR GUPTA Cancer and Translational research Centre Dr.D.Y.Patil Biotechnology and Bioinformatics InstituteDr.D.Y.Patil VidyapeethTathawadePune411033India bioinformatics Centre Dr.D.Y.Patil Biotechnology and Bioinformatics InstituteDr.D.Y.Patil VidyapeethPune411033India Department of Oral Pathology and Microbiology Dr.D.Y.Patil Dental College&HospitalDr.D.Y.Patil VidyapeethPune411018India Department of Surgical Oncology Dr.D.Y.Patil Medical CollegeHospital&Research CentreDr.D.Y.Patil VidyapeethPune411018India

Oral squamous cell carcinoma(OSCC)is one of the most prevalent forms of head and neck squamous cell carcinomas(HNSCC)with a poor overall survival rate(about 50%),particularly in cases of ***-based cancer biomarkers are a relatively advanced concept,and non-coding RNAs currently have shown promising roles in the detection and treatment of various *** review underlines the function of long non-coding RNAs(lncRNAs)in the OSCC and its subsequent clinical ***,a class of non-coding RNAs,are larger than 200 nucleotides and resemble mRNA in numerous ***,unlike mRNA,lncRNA regulates multiple druggable and non-druggable signaling molecules through simultaneous interaction with DNA,RNA,proteins,or microRNAs depending on concentration and localization in *** of oncogenic lncRNAs and downregulation of tumor suppressor lncRNAs are evident in OSCC tissues and body fluids such as blood and saliva indicating their potential as valuable *** inhibition of candidate oncogenic lncRNAs or overexpression of tumor suppressor lncRNAs showed potential therapeutic roles in in-vivo animal *** types of lncRNAs that are expressed differentially in OSCC tissue and bodily fluids have been systematically documented with specificity and *** review thoroughly discusses the biological functions of such lncRNAs in OSCC cell survival,proliferation,invasion,migration,metastasis,angiogenesis,metabolism,epigenetic modification,tumor immune microenvironment,and drug ***,we addressed the diagnostic and therapeutic importance of lncRNAs in OSCC pre-clinical and clinical systems,providing details on ongoing research and outlining potential future directions for advancements in this *** essence,this review could be a valuable resource by offering comprehensive and current insights into lncRNAs in OSCC for researchers in fundamental and clinical domains.

关键词： Oral squamous cell carcinoma(OSCC) Head and neck cancer Non-coding RNA Long non-coding RNA(lncRNA) Cancer diagnosis

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Recurrent evolution of seaweed body plan complexity among photosynthetic eukaryotes

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Molecular Plant 2024年第7期17卷 999-1001页

作者： Elisa S.Goldbecker Iker Irisarri Jan de Vries Department of Applied bioinformatics Institute for Microbiology and GeneticsUniversity of GottingenGoldschmidtstr.137077 GottingenGermany Section Phylogenomics Center for Molecular Biodiversity ResearchLeibniz Institute for the Analysis of Biodiversity Change(LIB)Museum of Nature HamburgMartin-Luther-King-Platz 320146 HamburgGermany Department of Applied bioinformatics Campus Institute Data Science(CIDAS)University of GottingenGoldschmidtstr.137077 GottingenGermany Department of Applied bioinformatics Gottingen Center for Molecular Biosciences(GZMB)University of GottingenGoldschmidtstr.137077 GottingenGermany

The evolutionary origin of multicellularity is an age-old question in biological *** studies have delved into the evolutionary processes that led to the evolution of multicellular life forms from unicellular *** beauty and the challenge about this topic are that evolution has brought forth various forms of multicellular life,multiple times independently,scattered across the evolutionary tree of *** to the challenge,multicellular organisms exist in a diversity of forms and complexities,and the mechanisms by which multicellularity emerged are also likely different between animals,algae,or fungi(Niklas and Newman,2020).Recently,Nelson et al.(2024)presented a large-scale comparative genomics study focused on particularly intricate multicellular organisms:macroalgae(seaweeds),which emerged independently in three distinct eukaryotic lineages-green algae(Chlorophyta),red algae(Rhodophyta),and brown algae(Phaeophyceae).

关键词： algae seaweed evolution

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