If a gene is traced to multiple probes, the average expression value was taken to representative gene expression levels when using microarray data from the GEO database. D The distribution of SPP1 expression across different types of tumor and normal tissues. database The authors declare no conflicts of interest in this work. Results Accession number identifies each data uniquely and it never changes. 2013;37(6):63140. 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. NCBI provides a variety of resources that allow developers to access and manipulate NCBI data in their applications. 81960525 and 82160591), Science and the Technology Commission of Shanghai Municipality (Grant No. Moreover, KLF2 expression was negatively correlated with tumor mutational burden (TMB) (=0.29, P<0.001) (Fig. 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. https://doi.org/10.1158/0008-5472.CAN-05-1702. Cancer Sci. All answers are anonymous. The results showed that T cells accounted for the major proportion among all immune infiltration cells in the liver tissue. We observed that the top several enrichment entries were concentrated in the biological characteristics related to tumor matrix and immunity. WebWhat makes a good bioinformatics database? 8G, H). Bioinformatics is fundamental to much biological research and involves biologists who learn programming, or computer programmers, mathematicians or database managers who learn the foundations of biology. 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. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. Cookies policy. They collaborate with Sequence Read Archive (SRA), which archives raw reads from high-throughput sequencing instruments. And cancer associated fibroblasts (CAFs) are the primary cells involved in this process. Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. Am J Transl Res. C The correlations between KLF2 and relevant pathway score. 2018;10:530311. 2022;2022:6571272. https://doi.org/10.1155/2022/6571272. databases Databases. Analysis of KLF2 targets (KLFTs) and KLF2 expression in different cohorts. 3C, D). 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. Therefore, this paper will analyze the relevant data of HNSCC patients in online databases by bioinformatics methods and explore the role of DFLC2022012) and Key Specialty Construction Project of Shanghai Pudong New Area Health Commission (Grant No. Whats more, we noticed that SPP1, also known as osteopontin (OPN), had been reported to be a promising tumor marker for detecting metastatic disease in many tumors [38, 39]. Orimo A, Gupta PB, Sgroi DC, Arenzana-Seisdedos F, Delaunay T, Naeem R, et al. Single-cell sequencing data were analyzed in CeDR Atlas platform (https://ngdc.cncb.ac.cn/cedr/) and the Human Protein Atlas (HPA, https://www.proteinatlas.org/). https://doi.org/10.1007/s13277-014-2943-4. Over 20,000 pathway/genome databases (PGDBs). 8B, a network of cell types and drug response was constructed, and for CXCR6 CD8+ T cells, the drug Isoflupredone showed the most significant statistical significance (Spearman cor: 0.25: P value: 0.042). https://doi.org/10.1186/s12943-019-1109-9. 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. Once given a database accession number, the data in primary databases are never changed: they form part of the scientific record. LKLF: a transcriptional regulator of single-positive t cell quiescence and survival. Zhang D, Dai Y, Cai Y, Suo T, Liu H, Wang Y, et al. C Calibration curve for the overall survival nomogram model in the discovery group. Li Y, Xiao J, Bai J, Tian Y, Qu Y, Chen X, et al. https://doi.org/10.1038/nm843. 6B). Scientists can use RNA sequencing to compare gene expression in different cell types, for example between healthy and diseased cells. UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). SP and KLF transcription factors in digestive physiology and diseases. In addition to archiving variation discovery, dbVar also stores associations of defined variants with phenotype information. The various bioinformatics resources covered in this chapter will be helpful in several ways in medicinal plant research. Gene expression profiles were obtained from Gene Expression Omnibus (GEO) database. Biological databases emerged as a response to the huge data generated by low-cost DNA sequencing technologies. Article A The distribution of KLF2 expression across different types of tumor and normal tissues. KLF2 is downregulated in pancreatic ductal adenocarcinoma and inhibits the growth and migration of cancer cells. Google Scholar. These results suggest that KLF2 expression levels are significantly different in different cell types in the liver tissue, mainly focusing on fibroblasts, epithelial cells and immune cells, which are the main components of liver tissue. We found that an important T-cell receptor (TCR) molecule, CD3D, plays a significant role in KLF2 affecting the immune microenvironment. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles. CD3D, an essential part of the T-cell receptor/CD3 complex (TCR/CD3 complex), is involved in development and signal transduction of T-cell [41]. A powerful scientific workflow system that provides access to hundreds of genomic analysis tools. WebBioinformatics is used to analyze and interpret biological data, develop computer programs to efficiently access, manage, and use biological information and create mathematical formulas and statistical approaches to evaluate relationships in large datasets. In general, the input is the Gene ID, DNA sequence in a Fasta format, organism, antigen name, haplotype, disease name, or ontology. To learn more about some EMBL-EBI databases, try the online tutorial A journey through bioinformatics: Explore resources from EMBL-EBI. S4). [metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. Using ontologies to provide controlled vocabularies, Bioinformatics as an experimental science, Guided example 1: ZAP70 as a potential target for immunosuppressive therapy. These results further demonstrate an essential role that KLF2 performed during development of HCC associated with liver fibrosis/cirrhosis. 2019;30(2):37484. Part of https://doi.org/10.1038/nrc.2016.73. Wu J, Lingrel JB. 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 And we also assessed the differential levels of KLF2 expressed in cirrhosis tissue and HCC tissue. [2] Omics Discovery Index can be used to browse and search several biological databases. Springer Nature. 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. It helps in searching sequences rapidly. ClusterProfiler package (version: 3.18.0) in R was employed to analyze the GO function of potential targets and enrich the KEGG pathway. For functional enrichment, Gene Ontology (GO), a widely-used tool, is utilized to annotate genes with functions, especially molecular function, biological pathways, and cellular components, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis [24], a practical resource, is used to study gene functions and associated high-level genome functional information. Meta databases are databases of databases that collect data about data to generate new data. G1: normal liver tissue; G2: liver cirrhosis tissue; G3: HCC tissue. PATRIC, the bacterial bioinformatics database and analysis What happens to DNA sequence when it comes off a sequencing machine? Databases https://doi.org/10.1073/pnas.1613392114. These three databases are primary databases, as they house original sequence data. WebGISAID is a pathogenic virus database that provides options to search for SARS-CoV-2 sequences based on their location and date of collection alongside an analytical tool for sequence alignment and visualization ( 5 ). Giannelli G, Koudelkova P, Dituri F, Mikulits W. Role of epithelial to mesenchymal transition in hepatocellular carcinoma. To explore comprehensively the methylation of KLF2 promoter, we used the deoxyribonucleic acid (DNA) methylation data from the online MethSurv tool (https://biit.cs.ut.ee/methsurv/) to analyze different methylation sites of KLF2 and the survival data in TCGA cohort of HCC. It helps scientists to understand the concepts of biological phenomena. 2019;18(1):137. https://doi.org/10.1186/s12943-019-1066-3. Genome, gene and transcript sequence data 33-genes related with cancer associated fibroblasts (CAFs) were collected to identify the significant association of KLF2 with fibrosis. 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Nat Immunol. 2018;172(3):393407. The above results suggest that KLF2 negatively regulates the expression of those downstream genes associated with fibrosis. 2016;16(9):58298. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.[13]. Based on our previous microarray results [4], we identified several lncRNAs as important factors in HCC progress. Firstly, we analyzed KLF2 expression distribution between different human tumor and normal tissues in TCGA database. Select relevant databases are linked below. The sequence features of KLF2 presented that there were highly conserved classical Cys2/His2 zinc fingers (Fig. Bioinformatics is the science of both storing lots of complex biological data, and of analysing it to find new insights, which we use in many different ways. 2019;13(1):1817094795. https://doi.org/10.1177/1557988318816907. 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). 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). G, H Scatter plots show the correlation of CD3D with PDCD1 and CD274 (PDL1). G, H Comparison of response to ICB treatments in KLF2 high- and low-expression groups. Immune checkpoint molecules expressed on the immune cells play a critical role in the immune responses and immunotherapy. https://doi.org/10.1007/s13277-015-4053-3. This book provides an exploration through the world of Bioinformatics Database Systems.. D KLF2 expression is analyzed in different tissues from GSE25097. Tools like HumanMine and OpenTargets allow scientists to start from a gene and see what proteins it is the blueprint for. Google Scholar. As Fig. 2010;90:133781. Enteropathway: the metabolic pathway database for the human Interestingly, we found that KLF2 is highly expressed in fibroblasts and immune cells, but low in hepatocytes. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome analysis, modeling, systems biology and education. Ask us!Privacy notice. 2019;18:115. Correspondence to Diversity and Anti-Racism in Bioinformatics, https://subjectguides.lib.neu.edu/bioinformatics, 'best bets'literature databases relevant to Bioinformatics, Complete list of databases at Northeastern, Web of Science, Core Collection 1975-present, Genome Analysis Toolkit - Broad Institute, KEGG: Kyoto Encyclopedia of Genes and Genomes, TCGA Computational Tools - National Cancer Institute, Data, Statistics, and Information Science. However, UniProt also infers peptide sequences from genomic information, and it provides a wealth of additional information, some derived from automated annotation (TrEMBL), and even more from careful manual analysis (SwissProt). J Clin Investig. originally ,metadata was only common term referring simply to data about data such a tags ,keywords, and markup headers. McGill University is located in Tiohti:ke (Montreal) on uncededKanien'keh:ka traditional territory. Scatter plots results showed a significantly positive correlation between KLF2 expression and immune cells infiltration in HCC based on the TIMER algorithm (Fig. The prognostic survival value of KLF family members and regulators of NOS enzymes from TCGA-LIHC and ICGC-LIRI. Then we used HPA platform to further analyze the single-cell expression level of KLF2 in liver tissues. https://doi.org/10.3892/ijo.2018.4524. Numerous databases collect information about species and other taxonomic categories. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. In the anti-tumor immune response, CD8+ cytotoxic T lymphocytes (CTLs) played a main cellular effector role. 4A, the major items were External encapsulating structure organization, Collagen fibril organization, Lymph vessel development. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide. Open Source and Free Bioinformatics Tools List Role of Kruppel-like factor 6 in transforming growth factor-beta1-induced epithelial-mesenchymal transition of proximal tubule cells. Try using Northeastern'sInterlibrary Loansystem torequest books or articles not available at NU. Kuo CT, Veselits ML, Leiden JM. More than just medical literature, PubMed was developed by the National Center for Biotechnology Information (NCBI) and publishers of life sciences literature. ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. J Hepatol. Topics explored included the importance of database curation, database integration and interoperability, consistency and standards in terminology, error prevention and correction, data provenance, ontology, the importance of maintaining privacy, data mining, and the need for more computer scientists with specialty training in bioinformatics.
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