It is a good bet that the human sequence also is part of a gene that codes 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. 2010;90:133781. 6D), such as BRCA, COAD, KIRP, LUAD, LUSC, READ and so on. Bioinformatics databases or biological databases are computerized and organized storehouses of biological information that provides a standardized way for Kopp F, Mendell JT. Accordingly, lncRNAs regulate both coding and noncoding genes via cis- and trans- regulatory signals [6, 7]. Modern science isnt simply about publishing one set of results and hoping other researchers read it. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance. The databases including GenBank, DDBJ, and EMBL-EBI can be used to retrieve genomic sequences of medicinal plant. Gao X, Wu G, Gu X, Fu L, Mei C. Kruppel-like factor 15 modulates renal interstitial fibrosis by ERK/MAPK and JNK/MAPK pathways regulation. We would therefore find RNA linked to haemoglobin production in the tissues that make red blood cells but not in the tissues where white blood cells are produced. We used cumulative distribution function (CDF) based on consensus clustering and classfied TCGA_LIHC samples into two subtype groups with k=2 selected as the optimum (Fig. Use for citation tracking, finding seminal literature, data visualizations, author alerts, institutional affiliations, and impact factors. LKLF: a transcriptional regulator of single-positive t cell quiescence and survival. 2A, B, KLF2 genomics presented a hypo-mutation condition in most of HCC patients in Firehose Legacy cohort. 2019;21(1):1. https://doi.org/10.1186/s13059-019-1906-x. The different colors represent the trend of gene expression in different samples. The immune scoring results were displayed visually through R software package ggplot2 and pheatmap. DNA sequencing produces huge amounts of data essentially comprising of lots of short sections of DNA letters. 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. D The correlation between KLF2 methylation and the mRNA expression level. Biological databases are free to use and contain a huge collection of a variety of biological data. Xia E, Bhandari A, Shen Y, Zhou X, Wang O. lncRNA LINC00673 induces proliferation, metastasis and epithelial-mesenchymal transition in thyroid carcinoma via Kruppel-like factor 2. 2020;52:48594. Additionally, we assessed the prognostic value of SPP1 in TCGA_LIHC and ICGC_LIRI. Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. Only a small percent (1.4%) patients were accompanied by the KLF2 amplification of copy number variation (CNV). A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. 2018;676:4755. 5E). Despite significant efforts to identify metabolic They can be turned on and off by proteins and chemical messengers. Immunotherapy. Surprisingly, we discovered that methylation, rather than genetic mutations is responsible for the down regulation of KLF2 expression in HCC. [2] Omics Discovery Index can be used to browse and search several biological databases. Mammalian Krppel-like factors in health and diseases. Br J Pharmacol. https://doi.org/10.3322/caac.21660. Accordingly, lymph node metastasis occurs in about half of HCC patients with extrahepatic metastasis, and these patients only have a median survival of less than 1year [3]. ClusterProfiler package (version: 3.18.0) in R was employed to analyze the GO function of potential targets and enrich the KEGG pathway. The data here are highly curated(processing the data before it is presented in the database). The gene expression profile was derived from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov), the International Cancer Genome Consortium database (ICGC, https://daco.icgc.org/), and the Gene Expression Comprehensive Database (GEO, http://www.ncbi.nlm.nih.gov/geo). Acta Biochim Biophys Sin. The role of cancer-associated fibroblasts and fibrosis in liver cancer. Why not share your success on social media? Springer Nature. database More than just medical literature, PubMed was developed by the National Center for Biotechnology Information (NCBI) and publishers of life sciences literature. https://doi.org/10.1016/j.clinbiochem.2018.07.003. (PDF) Bioinformatics Database Resources - ResearchGate The data entered in these types of databases are first compared and then filtered based on desired criteria. 4D, the results analyzed from GSE 25097 showed KLF2 expression level continued to decreasing, as liver tissue became progressively cirrhotic and then progressed to HCC (G1: normal liver tissue; G2: liver cirrhosis tissue; G3: HCC tissue). An independent online publishing house; provides immediate free access to the peer-reviewed biological and medical research. Modern biological databases comprise not only data, but also sophisticated query facilities and bioinformatics data analysis tools. No and hepatocellular cancer. originally ,metadata was only common term referring simply to data about data such a tags ,keywords, and markup headers. For KEGG analysis in Fig. Learn how to download articles directly to your mobile device. The result showed that SPP1 was increased not only in LIHC tumor tissue, but also in multiple cancers (Fig. Local regulation of gene expression by lncRNA promoters, transcription and splicing. The cBioPortal platform, CeDR Atlas platform, and the Human Protein Atlas (HPA) website were applied to analyze the mutational landscape and single-cell sequencing data of KLF2. Mol Ther Nucleic Acids. Which of these best describes your occupation? Immune checkpoint inhibits (ICIs) therapy have dramatically improved outcomes of cancer patients in clinical practice, especially for PD-1 and PD-L1 (CD274). [13] The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. You will be notified via email once the article is available for improvement. Most importantly, our study identifies a CAFs-related marker, SPP1, which is strongly associated with clinical characteristics and prognostic survival of HCC patients. Nat Commun. The foundations of bioinformatics were laid in the early 1960s with the application of computational methods to protein sequence analysis (notably, de novo sequence assembly, biological sequence databases and substitution models). A tool to explore and visualize cancer data generated by Broad GDAC Firehose. Revision of the manuscript was done by ZX. bioinformatics The heatmap in Fig. The results showed that T cells accounted for the major proportion among all immune infiltration cells in the liver tissue. Once the tumor has been advanced and metastasized, the HCC patient's prognosis is very bleak [2]. PubMed consists of 26 million citations for biomedical literature from Medline, life science journals and online books. The results indicated that, as depicted in the Additional file 1: Fig. https://doi.org/10.1038/nm843. 5AC). A gene that is turned on, or. Oncogene. Tumour Biol J Int Soc Oncodev Biol Med. Taken together, the above results suggest that KLF2 is highly correlated with the immune microenvironment in HCC, and advanced HCC patients with lower KLF2 expression derive greater benefit from ICIs treatments. Moreover, it has been implicated in numerous physiological and pathological processes, such as cancer, immune responses, and viral infection [21, 22]. 2016;37(3):342531. Int J Oncol. The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Secondary databases are:[clarification needed]. The importance of biological databases in biological discovery Decreased KLF2 expression was discovered to be mainly regulated by hypermethylation, and indicated a poor prognosis of HCC. Table 2Essential aspects of primary and secondary databases. BMC Bioinformatics 5D showed that the expression level of genes of the subgroup C1 were higher than that in the subgroup C2. Multiomics data analyses to identify SLC25A17 as a novel An overview of KLF2 genetic alterations landscape in HCC. Krppel-like factor 2 inhibits hepatocarcinogenesis through negative regulation of the hedgehog pathway. Mol Cancer. E, F Scatter plots show KLF2 expression is associated with PDCD1 and CD274. Transcription factor LKLF is sufficient to program T cell quiescence via a c-Myc-dependent pathway. 2018;59:1724. Aino H, Sumie S, Niizeki T, Kuromatsu R, Tajiri N, Nakano M, et al. XC conducted the data analysis. Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. 2017;10:11. These foregoing results indicate that the low expression level of KLF2 in HCC mainly is regulated by hypermethylation, instead of genetic mutation. https://doi.org/10.1111/bph.14838. SenBanerjee S, Lin Z, Atkins GB, Greif DM, Rao RM, Kumar A, et al. *P<0.05, **P<0.01, ***P<0.001. The single sample Gene Set Enrichment Analysis (ssGSEA) was used to calculate absolute enrichment scores, and Gene Set Enrichment Analysis (GSEA) was used to demonstrate the biological processes. Biomed Res Int. Yang F, Tuxhorn JA, Ressler SJ, McAlhany SJ, Dang TD, Rowley DR. Stromal expression of connective tissue growth factor promotes angiogenesis and prostate cancer tumorigenesis. Holian J, Qi W, Kelly DJ, Zhang Y, Mreich E, Pollock CA, et al. The m6A-related genes were derived from the research by Juan Xu et al. The threshold was defined as adjusted P<0.05 and log2 (Fold Change)>1 or log2 (Fold Change)<1 for the differential expression of mRNAs. volume24, Articlenumber:270 (2023) Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. Bioinformatics resources for SARS-CoV 4E (G1: liver cirrhosis tissue; G2: early HCC tissue; G3: advanced HCC tissue). 2018;53(5):192738. EMBO J. The results also showed that CD3D has a strong predictive role in HCC immunotherapy. The transcription factor KLF2 mediates hepatic endothelial protection and paracrine endothelial-stellate cell deactivation induced by statins. J Clin Investig. CA Cancer J Clin. Computational algorithms are applied to the primary database and meaningful and informative data is stored inside the secondary database. Here, we focus on exploring how KLF2 influences biological changes to promote HCC progression. The Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). 00:38. Clinical characteristics and prognostic factors for advanced hepatocellular carcinoma with extrahepatic metastasis. Experimental results are submitted directly into the database by researchers, and the data are essentially archival in nature. Ouchi R, Togo S, Kimura M, Shinozawa T, Koido M, Koike H, et al. The cBioPortal platform, CeDR Atlas platform, and the Human Protein Atlas (HPA) website were applied to analyze the mutational landscape and single-cell This book provides an exploration through the world of Bioinformatics Database Systems.. The TIDE database was applied to predict the possibility of immune escape in the TCGA-HNSC cohort. Intriguingly, Fig. The data are given accession numbers when they are entered into the database. D Correlation analysis between KLF2 gene expression and TMB. S3IK). Fibrosis of the tumor stroma is an important biological process contributing to the advancement of solid tumors. 6L,M). https://doi.org/10.1371/journal.pone.0095889. A suite of databases and tools to conducting genome and metagenome studies. The initial data are taken from the primary database, and then they are merged together based on certain conditions. https://doi.org/10.1007/s13277-014-2943-4. PubMed Chen WC, Lin HH, Tang MJ. To further demonstrate the role of SPP1 in HCC, we explored the distribution of SPP1 expression across different types of tumor and normal tissues in TCGA. And SPP1 was validated as a promising prognostic and diagnostic marker for advanced HCC patients. This unit provides a brief overview of major sequence databases and p https://doi.org/10.1016/j.ajo.2006.11.040. E GSEA-Hallmark analysis on the Spp1-related genes in HCC. E The heatmap of the methylation level of KLF2 in HCC and normal samples. Google Scholar. A novel 12-marker panel of cancer-associated fibroblasts involved in progression of hepatocellular carcinoma. 2023;24:4682. https://doi.org/10.3390/ijms24054682. H The heatmap of the differential gene expression between the two subgroups. H The correlation between KLF2 expression and m6A-related genes in HCC. Your US state privacy rights, All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles. 4H, I). The authors declare no conflicts of interest in this work. Accordingly, we selected CXCR6 CD8+ T cells for further analysis. Frontiers | IDbSV: An Open-Access Repository for Monitoring SARS Fedarko NS, Jain A, Karadag A, Van Eman MR, Fisher LW. To assess the immune score evaluation, we used immuneeconv, an R software package integrating six latest algorithms, including TIMER, xCell, MCP-counter, CIBERSORT, EPIC and quanTIseq. Examples of Secondary databases are as follows. This population data lets researchers see if a phenotype is linked to a disease, or locate a gene that might be influencing the phenotype. Figure3A and B showed the single-cell expression level of KLF2 in different cell lines of the SCP542 analysis [29] in the Cellular Drug Response (CeDR) Atlas and Single cell portal (SCP) database. We noticed that the higher expression of CD3D was more responsive to ICIs (Fig. Kim C, He P, Bialkowska AB, Yang VW. How has the site influenced you (or others)? Bioinformatics Databases - Bioinformatics - Research Results 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. https://libraryguides.mcgill.ca/bioinformatics, BLAST (Basic Local Alignment Search Tool). We found that an important T-cell receptor (TCR) molecule, CD3D, plays a significant role in KLF2 affecting the immune microenvironment. Databases. Ma J, Zhang L, Yang P, Zeng ZC, Xiang ZL. Cancer Manag Res. 2G). PubMed Central https://doi.org/10.1038/onc.2015.18. However, whether SPP1 is a potential target of KLF2 involved in fibrosis deserves to be investigated experimentally. This study identified that KLF2 is an important factor promoting HCC progression by affecting the fibrosis and immune infiltration, highlighting its great potential as a novel prognostic biomarker for advanced HCC. Then we obtained 17 prognostic significant genes, named KLFTs-17. Google Scholar. An up-to-date biomedical research database covering the most important international biomedical literature from 1947 to the present day. 2023 BioMed Central Ltd unless otherwise stated. Confirmation of the prognostic factor SPP1. This can be done via a database called a genome browser. Database of Genotypes and Phenotypes (dbGaP) is an archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. Am J Transl Res. Select relevant databases are linked below. Fig. Select relevant databases are linked below. Interestingly, we found that KLF2 is highly expressed in fibroblasts and immune cells, but low in hepatocytes. The purpose of this study is to screen out the diagnostic biomarkers of systemic lupus erythematosus (SLE) with COVID-19 and explore the possible related mechanisms by the bioinformatics approach.MethodsSLE and COVID-19 datasets were extracted separately from the NCBI The foregoing results support that patients with increased SPP1 expression have a poor prognosis. Secondary databases have become the molecular biologists reference library over the past decade or so, providing a wealth of (often daunting) information on just about any gene or gene product that has been investigated by the research community. https://doi.org/10.1186/s13045-017-0513-0. McGill Library Questions? https://doi.org/10.1074/jbc.M211337200. In general, the input is the Gene ID, DNA sequence in a Fasta format, organism, antigen name, haplotype, disease name, or ontology. Furthermore, area under curve (AUC) of ROC curves revealed CD3D had a moderate capacity to predicate HCC patients response to ICB therapy (Fig. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. Tumour Biol J Int Soc Oncodev Biol Med. https://doi.org/10.1136/gut.2010.220913. The sequencing data and clinical prognosis data of the HCC multi-cohorts were aggregated by the BEST tool (https://rookieutopia.com/) with batch effects removed to analyze the correlation of gene expression with drug susceptibility, immune infiltration, and prognosis of ICI treatment. 6A). Cell. Gracia-Sancho J, Russo L, Garca-Calder H, Garca-Pagn JC, Garca-Cardea G, Bosch J. Endothelial expression of transcription factor Kruppel-like factor 2 and its vasoprotective target genes in the normal and cirrhotic rat liver. Then, we assessed the responsive of KLF2 in the immunotherapy cohorts, IMvigor210 cohort 2018 and Kim cohort 2019. DataSet records contain additional resources including cluster tools and differential expression queries. A The distribution of KLF2 expression across different types of tumor and normal tissues. 2016;16(9):58298. Li Y, Tu S, Zeng Y, Zhang C, Deng T, Luo W, et al. Oncogene. on the molecular characterization and clinical significance of m6A modulators across 33 cancer types [23]. Mol Cancer. The International Human Epigenome Consortium (IHEC) makes available comprehensive sets of reference epigenomes relevant to health and disease. ZX conceived the study design. 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. Its our job in this course to reduce your activation energy to make more of these resources for your research. 2018;9(1):4383. https://doi.org/10.1038/s41467-018-06318-7. 15 Free Bioinformatics Tools List 2022 What is Genomic Testing? A suite of tools and pipelines developed for processing and analyzing various types of large-scale genomic and proteomic data.
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