Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. https://doi.org/10.1371/journal.pone.0095889. https://doi.org/10.1073/pnas.1613392114. To learn more about some EMBL-EBI databases, try the online tutorial A journey through bioinformatics: Explore resources from EMBL-EBI. 8J showed an essential distinction of CD3D expression in different Grades of HCC patients. 2021. We found that patients with low KLF2 expression levels were more responsive to ICIs therapy and achieved a better prognosis and survival, indicating that advanced HCC patients with lower KLF2 expression levels are more suitable for ICIs therapy. Fig. of major protein bioinformatics databases in this chapter. Cell Physiol Biochem Int J Exp Cell Physiol Biochem Pharmacol. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. 2018;10:530311. WebObjectiveEvidences show that there may be a link between SLE and COVID-19. The book summarizes the popular and innovative bioinformatics repositories currently available, including popular primary genetic and protein sequence databases, phylogenetic databases, structure and pathway databases, microarray databases and boutique databases. Wang R, Geller DA, Wink DA, Cheng B, Billiar TR. The foregoing results support that patients with increased SPP1 expression have a poor prognosis. Examples of Secondary databases are as follows. Tool that allows you to interactively visualize genomic data of various model organisms. And KLF2 has also been shown to inhibit the proliferation and growth of Jurkat T leukemia cells [57, 58]. PubMed https://doi.org/10.1159/000489589. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. Bioinformatics - NCBI Bookshelf - National Center for Your US state privacy rights, 7I, J). This book provides an exploration through the world of Bioinformatics Database Systems.. The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. This highlights the strong influence of KLF2 on the prognosis of HCC patients and its potential use as a dependable marker for prognostication. Mutations indicate the presence of disorders and diseases, sometimes as deadly as cancer. Science Direct is the web site for selected journal titles from the scholarly publisher Elsevier and its affiliates. 4H, I). The human gut microbiota produces diverse, extensive metabolites which have the potential to affect host physiology. The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. See a complete list of databases. A gene that is turned on, or. 2004;199:130515. The gene expression comprehensive database. Global cancer statistics 2020: globocan estimates of incidence and mortality worldwide for 36 cancers in 185 countries. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. 2015;34(45):564861. J The expression distribution of CD3D in the different grades of LIHC. Bioinformatics Tools and databases - Guides at McGill G KaplanMeier survival analysis of KLF2 from ICGC-LIRI dataset. Primary and secondary databases | Bioinformatics for the terrified In conclusion, our study provides a novel clue that KLF2 is a considerable contributor for advanced HCC by affecting the fibrosis and immune infiltration, providing new perspectives on exploring the molecular mechanism for HCC advancement, and emphasizing the potential of KLF2 for improving the prognosis of advanced HCC patients in clinical practice. WebServices Data resources and analysis tools to support life science research EMBLs European Bioinformatics Institute (EMBL-EBI) maintains the worlds most comprehensive range of Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Bioinformatics - National Human Genome Research Institute It obtains unique data obtained from the laboratory and these data are made accessible to normal users without any change. G, H Scatter plots show the correlation of CD3D with PDCD1 and CD274 (PDL1). 4B, enriched items mainly were Focal adhesion, ECM receptor adhesion, Leishmania infection. NCBI, National Center for Biotechnology Information,has a number of useful databases for bioinformatics. J Oncol. C Calibration curve for the overall survival nomogram model in the discovery group. D The distribution of SPP1 expression across different types of tumor and normal tissues. A tool to explore and visualize cancer data generated by Broad GDAC Firehose. In addition to virus discovery, these NGS technologies and bioinformatics resources are currently being employed for ongoing genomic surveillance of SARS-CoV-2 worldwide, tracking its spread, evolution and patterns of variation on a global scale. Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, et al. Yerra VG, Drosatos K. Specificity proteins (SP) and Krppel-like factors (KLF) in liver physiology and pathology. KLF2 inhibits TGF--mediated cancer cell motility in hepatocellular carcinoma. Primary databasesare populated with experimentally derived data such as nucleotide sequence, protein sequence or macromolecular structure. Genome, gene and transcript sequence data Role of Kruppel-like factor 6 in transforming growth factor-beta1-induced epithelial-mesenchymal transition of proximal tubule cells. This means that HCC patients with higher level of KLF2 expression had a significantly better OS, PFS, DFS, and DSS (Fig. These databases collect genome sequences, annotate and analyze them, and provide public access. 2F). Bibliographic database: A searchable platform that contains descriptive records of articles, books, conference proceedings, audio-visual material, maps, newspapers, and more. S4. A single-cell level expression analysis of KLF2 in liver tissue. Open Access Published: 29 June 2023 Multiomics data analyses to identify SLC25A17 as a novel biomarker to predict the prognosis and immune microenvironment in head and neck squamous cell carcinoma Yunbin Shi, Juntao Huang, Yi Hu & Yi Shen BMC Bioinformatics 24, Article number: 269 ( 2023 ) Cite this article 121 Accesses Metrics Cancer Lett. This modification plays a critical role in various biological processes, including mRNA splicing, translation, stability, and degradation. We collected 98 target genes of the KLF2 from the CHEA Transcription Factor Targets dataset in Harmonizome platform, namely KLFTs (Additional file 2: Table S1). WebCNGBdb provides a vast amount of data resources and biological information for research and paper in literature, gene, variation, protein, sequence, project, sample, experiment and assembly database. Schulich Library of Physical Sciences, Life Sciences, and Engineering (Office located in the McLennan Library Building during the Schulich closure), Database Issuecategorizes many of the publicly available online databases related to molecular. To analyze KLF2 expression distribution in different cell types in liver cancer and normal tissue, we used Uniform Manifold Approximation and Projection (UMAP) and t-distributed Stochastic Neighbor Embedding (tSNE) algorithm for the single cell expression analysis in multiple platforms. Data can be downloaded and queried, and Pathway Tools can be installed to create your own local database. Our study identifies the important function of KLF2 for advanced HCC by affecting the fibrosis and immune infiltration, and provides new perspectives on exploring the molecular mechanism for HCC advancement, emphasizing the potential of KLF2 as a new biomarker for improving the prognosis of advanced HCC patients in clinical practice. In addition, we examined the expression distribution of SNAI1, ZEB2, and VIM, which are the top three markers exhibiting strong correlation with KLF2, in the GSE25097 dataset related to cirrhosis development. Continue on to the final pages of this online tutorial for recommendations on what to learn next and to tell us what you thought of this tutorial. Univariate COX regression analysis of CAFs in the C1 subgroup. However, the molecular regulation of lnc-EPS15L1-2:1 in advanced HCC is still unclear. If you have any other comments or suggestions, please let us know at [email protected], Can you spare 5-8 minutes to tell us what you think of this website? 81960525 and 82160591), Science and the Technology Commission of Shanghai Municipality (Grant No. 2021;71(3):20949. 2010;90:133781. Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma, https://doi.org/10.1186/s12859-023-05391-0, https://doi.org/10.1371/journal.pone.0095889, https://doi.org/10.1016/j.gene.2018.07.001, https://doi.org/10.1016/j.cell.2018.01.011, https://doi.org/10.1007/s13277-014-2943-4, https://doi.org/10.1007/s13277-015-4053-3, https://doi.org/10.1016/j.omtn.2018.06.012, https://doi.org/10.1186/s12943-019-1109-9, https://doi.org/10.1186/s12943-019-1066-3, https://doi.org/10.1152/physrev.00058.2009, https://doi.org/10.1053/j.gastro.2017.03.035, https://doi.org/10.1186/s12916-022-02523-w, https://doi.org/10.1186/s13059-019-1906-x, https://doi.org/10.1038/s41467-018-06318-7, https://doi.org/10.1016/j.cmet.2019.05.007, https://doi.org/10.1016/j.jhep.2016.05.007, https://doi.org/10.1146/annurev-pathol-052016-100322, https://doi.org/10.1016/j.ajo.2006.11.040, https://doi.org/10.1038/s41421-020-0157-z, https://doi.org/10.1146/annurev.immunol.021908.132706, https://doi.org/10.1186/s13045-017-0513-0, https://doi.org/10.1016/j.jhep.2012.08.026, https://doi.org/10.1016/j.ajpath.2015.05.019, https://doi.org/10.1152/ajprenal.00055.2008, https://doi.org/10.1158/0008-5472.CAN-05-1702, https://doi.org/10.1016/j.cell.2005.02.034, https://doi.org/10.1016/j.clinbiochem.2018.07.003, https://doi.org/10.1126/science.277.5334.1986, https://doi.org/10.1016/j.canlet.2022.215867, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/. https://doi.org/10.1159/000355743. Biological Databases : These are the databases consisting of biological data like protein sequencing, molecular structure, DNA sequences, etc in an organized form. Based on the RNA sequencing data and corresponding clinical information of 371 HCC samples in the TCGA dataset, consistency clustering was performed using the R software package ConsensesclusterPlus (v1.54.0), and the parameters were set as follows: the maximum number of clusters was 6, 80% of the total samples were extracted 100 times, clusterAlg=HC, innerlinkage=ward, D2'. https://doi.org/10.1016/j.jhep.2012.08.026. For example, your body makes haemoglobin to carry oxygen in red blood cells, but its not needed in white blood cells. dbVar (Database of Genomic Structural Variation) has been developed to archive information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. The Broad Institute of Harvard and MIT shares some data and software tools produced with the larger scientific community. I GSEA-Hallmark analysis on the CD3D-related genes in HCC. Scientists can use RNA sequencing to compare gene expression in different cell types, for example between healthy and diseased cells. Chen, XQ., Ma, J., Xu, D. et al. 1CG, Additional file 1: Fig. Furthermore, many studies have reported CD3D as a promising prognostic and therapeutic biomarker [59,60,61]. D, E GSEA enrichment plot of CXCR6 CD8+-T-cell marker genes from GSE125188 scRNA dataset and differential genes expressed in CXCR6 CD8+-T-cell induced by the drug Isoflupredone. Most Hepatocellular carcinoma (HCC) patients are in advanced or metastatic stage at the time of diagnosis. REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Genome Biol. D Correlation analysis between KLF2 gene expression and TMB. WebBioinformatics is the emerging field that deals with the application of computers to the collection, organization, analysis, manipulation, presentation, and sharing of biologic data. 1997;277(5334):198690. The above results suggest that KLF2 is involved in the regulation of biological processes associated with tumor matrix. 2020;12(1):2535. The identified KLF2 transcription factor target gene sets were collected from Harmonizome platform (https://maayanlab.cloud/Harmonizome/) to go further analyzing. Then survival prognosis of the analyzed genes was assessed using KaplanMeier curves in TCGA_LIHC and ICGC- LIRI. Characteristics of Biological Data (Genome Data Management), Create a database on Relational Database Service (RDS) of Amazon Web Services(AWS), How to pre populate database in Android using SQLite Database, Difference between Database Administrator (DBA) and Database Engineer, Difference between Centralized Database and Distributed Database, Difference between Open Source Database and Commercial Database, Difference between Database Administrator vs Database Architect. 00:00. Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma. Protein sequences are the fundamental determinants of biological structure and function. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies. 2007;143(4):7057. Kopp F, Mendell JT. E GSEA-Hallmark analysis on the Spp1-related genes in HCC. Toggle Amino acid / protein databases subsection, Gene expression databases (mostly microarray data), Metabolic pathway and protein function databases, National Center for Biotechnology Information, International Nucleotide Sequence Database, Database of computationally identifies transcripts from the same locus, Database of intrinsically disordered and mobile proteins, Database of Comparative Protein Structure Models, Pictorial database of 3D structures in the Protein Data Bank, Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase, Database of annotated 3D protein structure models, Neuroimaging Informatics Tools and Resources Clearinghouse, The Comprehensive Antibiotic Resistance Database, RAC: Repository of Antibiotic resistance Cassettes, Housekeeping and Reference Transcript Atlas (HRT Atlas), "Databases, data tombs and dust in the wind", "Volume 46 Issue D1 | Nucleic Acids Research | Oxford Academic", "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information", "SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis", "eggNOG v4.0: nested orthology inference across 3686 organisms", "eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses", "Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family", "SoyBase, the USDA-ARS soybean genetics and genomics database", "PDBe: towards reusable data delivery infrastructure at protein data bank in Europe", "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures", "The RCSB protein data bank: integrative view of protein, gene and 3D structural information", "IntAct: an open source molecular interaction database", "A call for public archives for biological image data", "The Digital Brain Bank, an open access platform for post-mortem imaging datasets", "A structure-based nomenclature for Bacillus thuringiensis and other bacteria-derived pesticidal proteins", "BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins", "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets", "MetOSite: an integrated resource for the study of methionine residues sulfoxidation", Nucleic Acid Research Molecular Biology Database Collection, Nucleic Acid Research (NAR) Database Summary Paper Category List, Microsoft Research - University of Trento Centre for Computational and Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, US National Center for Biotechnology Information, African Society for Bioinformatics and Computational Biology, International Nucleotide Sequence Database Collaboration, International Society for Computational Biology, Institute of Genomics and Integrative Biology, European Conference on Computational Biology, Intelligent Systems for Molecular Biology, International Conference on Bioinformatics, International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics, ISCB Africa ASBCB Conference on Bioinformatics, Research in Computational Molecular Biology, https://en.wikipedia.org/w/index.php?title=List_of_biological_databases&oldid=1149964893, Short description is different from Wikidata, Wikipedia articles needing clarification from February 2022, Creative Commons Attribution-ShareAlike License 4.0, Research Collaboratory for Structural Bioinformatics (RCSB), NCBI Taxonomy: a taxonomic database operated by, Electron Microscopy Public Image Archive (EMPIAR), Extracellular RNA Atlas: a repository of small RNA-seq and qPCR-derived exRNA profiles from human and mouse biofluids, This page was last edited on 15 April 2023, at 14:45. Nature. Types of biological Database in Bioinformatics - GeeksforGeeks BMC Bioinformatics The Encyclopedia of DNA Elements (ENCODE) Consortium is an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI). To analyze the expression regulation of KLF2 in HCC comprehensively, we used cBioPortal platform to investigate the genetic mutation status of KLF2. Although a large number of protein bioinformatics databases and resources have been developed to catalog and store different information about proteins, there are challenges and opportunities to develop Next-Generation databases and resources to facilitate data integration, data-driven hypothesis generation, and biological knowledge discovery. KM survival analysis reveals that HCC patients with decreased KLF2 expression tend to achieve a much worse OS, DSS, PFS, and RFS. 2005;115:20918. Several studies have reported that KLF2 plays an important role in maintaining hepatic endothelial cell homeostasis and vascular integrity, and protects the liver from fibrosis or cirrhosis [43, 44]. Volunteers in big studies like UK Biobank mean that there is ready-made bioinformatics data available to researchers who apply for permission to use it. 33-genes related with cancer associated fibroblasts (CAFs) were collected to identify the significant association of KLF2 with fibrosis. Bioinformatics databases or biological databases are computerized and organized storehouses of biological information that provides a standardized way for searching and updating data. They can be defined as libraries containing data collected from scientific experiments, published literature and computational analysis. 2D showed KLF2 expression was negatively correlated with its methylation (Spearman=0.57, P<0.001). G1: liver cirrhosis tissue; G2: early HCC tissue; G3: advanced HCC tissue. Surprisingly, we found that KLF2 was a predictive target gene of lnc-EPS15L1-2:1 from both cis- and trans- analysis, which implied a potential interaction between KLF2 and the progress of HCC. These three databases are primary databases, as they house original sequence data. S3AH, the study findings revealed a positive association between KLF2 expression levels and these EMT markers. Finally, according to the annotation of the corresponding microarray platform, probe IDs were converted to gene symbols. To further derive promising markers associated with CAFs in HCC progression, we selected the C1 subgroup with the most striking features of KLFTs-17 to analyze the important role of CAF. Acta Biochim Biophys Sin. For the overall expression level of the gene signature, the single sample Gene Set Enrichment Analysis (ssGSEA) algorithm is applied to evaluate the gene enrichment fraction in each sample, thus differentiating high and low expression groups of the gene signature. Using the CeDR Atlas, we further analyzed the single-cell sequencing data of hepatic cells derived from GSE115469 [30] and GSE130073 [31]. DataSet records contain additional resources including cluster tools and differential expression queries. The data stored in these types of databases are the analyzed result of the primary database. A phenotype might be risk of diabetes or eye colour. Table S1: Target genes of the KLF2 from the CHEA Transcription Factor Targets dataset in Harmonizome platform, namely KLFTs. B A network of the correlation between the cell type and drug response is also shown on the right (datasets are marked in red, cell types are marked in yellow, and drugs are marked in blue). D The correlation between KLF2 methylation and the mRNA expression level. Databases. The Database for Annotation, Visualization and Integrated Discovery () provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes.These tools are powered by the comprehensive DAVID Knowledgebase built upon the DAVID Gene concept which pulls Hepatocellular carcinoma (HCC), one of the most common and invasive solid malignancies, accounts for the most proportion of liver cancers. [metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. Google Scholar. The bar graph results exhibited that KLF2 was mostly expressed in fibroblasts, epithelial cells and immune cells (T-cells, B-cells, plasma cell, NK-cells and so on) (Fig. C Heat map of consistent clustering results when k=2, rows and columns represent samples, and different colors represent different subtype groups. The cluster heatmap in Fig. In addition, KaplanMeier survival analysis of subgroups presented those patients with higher KLFTs-17 expression achieved the worse OS (Fig. Figure4G showed the strong association of KLF2 with CAFs-related marker genes. Cookies policy. For GO analysis shown in Fig. KLF2 is involved in many major biological processes, including proinflammatory activation, cell proliferation, apoptosis, and metabolism (such as glucose metabolism, fatty acid and cholesterol metabolism, amino acid and protein metabolism and so on) [9,10,11,12,13]. Differential gene analysis, machine learning algorithms, gene set enrichment analysis, and immune cell infiltration analysis were conducted using R software. 7E, F). https://doi.org/10.1002/jcp.1111. Multiomics data analyses to identify SLC25A17 as a novel https://doi.org/10.1186/s12943-019-1109-9. Predicting hepatitis B virus-positive metastatic hepatocellular carcinomas using gene expression profiling and supervised machine learning. 2017;10:11. By using this website, you agree to our *P<0.05, **P<0.01, ***P<0.001. The Cancer Genome Atlas (TCGA), Cancer Genome Consortium database (ICGC), and the Gene Expression Comprehensive Database (GEO) provided the raw data of this study research. This study was based on our previous microarray results, and aimed to explore the promising diagnostic and prognostic markers for advanced HCC by focusing on the important function of KLF2. Tumour Biol J Int Soc Oncodev Biol Med. In addition, as a supplement, we also explore the expression distribution and prognostic value of several KLF family members (including zinc finger transcription factors) and regulators of NOS enzymes, including KLF2, KLF4, KLF5, KLF6, KLF8, KLF9, KLF10, KLF11, KLF12, NOS2 and NOS3 [25,26,27,28]. Furthermore, we analyzed the association between SPP1 expression and clinical characteristics. S3. dbSNP (Database of Short Genetic Variations) includes single nucleotide variations, microsatellites, and small-scale insertions and deletions. Modern biological databases comprise not only data, but also sophisticated query facilities and bioinformatics data analysis tools. Model organism databases provide in-depth biological data for intensively studied organisms. https://doi.org/10.1016/j.omtn.2018.06.012. This article is being improved by another user right now. https://doi.org/10.15252/embj.2020105977. The role of cancer-associated fibroblasts and fibrosis in liver cancer. Fibroblasts account for the major stromal cell type in the microenvironment of liver diseases, including liver cirrhosis and liver cancers. The present study aimed to identify novel serum 2018;12:68497. Li Y, Xiao J, Bai J, Tian Y, Qu Y, Chen X, et al. COX regression analysis was applied, and SPP1 was identified as an independent prognostic factor associated with HCC fibrosis (Additional file 5: Table S4, Fig. Therefore, we speculate CD3D is a key mediator of KLF2 involvement in HCC immune response. There are two main approaches: Projects like the UK Biobank bring together lots of types of health data from patients, ready for use by bioinformaticians to study health outcomes of patients. A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Int J Mol Sci. As expected, a significantly higher percentage of m6A genes expression was detected in cancer tissues (Fig. C Heat map of the correlation between the expression of KLF2 and immune-checkpoint-related genes. Additionally, we assessed the prognostic value of SPP1 in TCGA_LIHC and ICGC_LIRI. 8A, the UMAP and the Cell Fraction plots showed the clustering of cell types and the proportion of cell types. The TIDE database was applied to predict the possibility of immune escape in the TCGA-HNSC cohort. https://doi.org/10.1111/cas.13961. Target genes of the KLF2 from the CHEA Transcription Factor Targets dataset in Harmonizome platform, namely KLFTs. EMBO J. Genes provide the information our cells use to make proteins, which are the machinery of the cell. Results showed that KLF2 was the only gene found to have a significant correlation with overall survival (OS), progression free survival (PFS), disease free survival (DSS), and disease specific survival (DSS).

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