2022;2022:6571272. https://doi.org/10.1155/2022/6571272. PubMed 2022;20:335. https://doi.org/10.1186/s12916-022-02523-w. Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, et al. The first step is to check that the sequence is of the highest quality before we start to piece the sections together. They can be turned on and off by proteins and chemical messengers. A novel 12-marker panel of cancer-associated fibroblasts involved in progression of hepatocellular carcinoma. This unit provides a brief overview of major sequence databases and p 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. Ma Z, Peng P, Zhou J, Hui B, Ji H, Wang J, et al. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature. Open Source and Free Bioinformatics Tools List VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. Epub 2013 Nov 12. Privacy Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. What happens to DNA sequence when it comes off a sequencing machine? The function enrichment analysis of KLF2 targets indicated the crucial association between KLF2 and tumor matrix. Integrated analysis of long noncoding RNA expression profiles in lymph node metastasis of hepatocellular carcinoma. Google Scholar. This book provides an exploration through the world of Bioinformatics Database Systems.. An increasing number of studies have reported that CAFs play a crucial role in promoting solid tumorigenesis. Specifically, the functional enrichment analysis in Fig. Therefore, developing databases to deal with gigantic volumes of biological data is a fundamentally essential task in bioinformatics. It is maintained by the National Institutes of Health (NIH) and the National Center for Biotechnology Information Data acquisition was carried out by XC, JM and DX. Moreover, it has been implicated in numerous physiological and pathological processes, such as cancer, immune responses, and viral infection [21, 22]. J Cell Physiol. Target genes of the KLF2 from the CHEA Transcription Factor Targets dataset in Harmonizome platform, namely KLFTs. Lin J, Tan H, Nie Y, Wu D, Zheng W, Lin W, et al. 2016;16(9):58298. Most of these databases are cross-referenced with UniProt / UniProtK https://doi.org/10.1016/j.cmet.2019.05.007. B The level of KLF2 expression was significantly lower in tumor tissue in ICGC-LIRI (G1: normal liver tissue; G2: primary tumor tissue). 2023;24:4682. https://doi.org/10.3390/ijms24054682. Structured and natural language searching. Its about linking everything that is out there, to provide new insights that we can only spot if we can see the big picture. CF KaplanMeier survival analysis showed patients with higher KLF2 expression had a significantly better overall survival (OS), progression free survival (PFS), disease free survival (DFS) and disease specific survival (DSS) from TCGA-LIHC. bioinformatics Article SenBanerjee S, Lin Z, Atkins GB, Greif DM, Rao RM, Kumar A, et al. The data entered here remains uncurated(no modifications are performed over the data). The common CAFs-related marker genes by consulting relevant references. Elevated serum bone sialoprotein and osteopontin in colon, breast, prostate, and lung cancer. Manavski Y, Abel T, Hu J, Kleinltzum D, Buchholz CJ, Belz C, et al. For example, your body makes haemoglobin to carry oxygen in red blood cells, but its not needed in white blood cells. Positive lymph node metastasis has a marked impact on the long-term survival of patients with hepatocellular carcinoma with extrahepatic metastasis. The results in Fig. Marrone G, Russo L, Rosado E, Hide D, Garca-Cardea G, Garca-Pagn JC, et al. Select relevant databases are linked below. In our study, we focus on the exploration of KLF2, a predictive target gene of lnc-EPS15L1-2:1, which has been identified to have a strong association with HCC advancement in our previous research [5]. J Enrichment results, the enriched KEGG signaling pathways [24] and Gene Ontology (GO) analysis, of the differential genes expression between the two subgroups. The expression distribution of these genes in TCGA database and LIRI databases was initially examined. Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated sdf-1/cxcl12 secretion. Annu Rev Immunol. 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). 8O, P). Fig. Try using Northeastern'sInterlibrary Loansystem torequest books or articles not available at NU. Accession number identifies each data uniquely and it never changes. Aino H, Sumie S, Niizeki T, Kuromatsu R, Tajiri N, Nakano M, et al. KLF2 inhibits Jurkat T leukemia cell growth via upregulation of cyclin-dependent kinase inhibitor p21WAF1/CIP1. Images play a critical role in biomedicine, ranging from images of anthropological specimens to zoology. KLF2 is an important transcription factor from the Krppel-like family of proteins, which exerts regulation in various cell types in the processes of activation, differentiation and migration by targeting different downstream genes. E GSEA-Hallmark analysis on the Spp1-related genes in HCC. G1: normal liver tissue; G2: liver cirrhosis tissue; G3: HCC tissue. The contribution of the tumor microenvironment to tumor prognosis cannot be negligible. 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. volume24, Articlenumber:270 (2023) The include: DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. The expression distribution of KLF family members and regulators of NOS enzymes in tumor tissues and normal tissues of TCGA-LIHC and ICGC-LIRI. Mammalian Krppel-like factors in health and diseases. 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. Organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution. 81960525 and 82160591), Science and the Technology Commission of Shanghai Municipality (Grant No. Article D TSNE plot shows KLF2 expression in different cell lines of liver cancer. B Relative change in the area under the CDF curve (CDF delta area). https://doi.org/10.1158/0008-5472.CAN-05-1702. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. A tool to explore and visualize cancer data generated by Broad GDAC Firehose. M The ROC curve for SPP1 diagnosis. Single-cell level expression analyses revealed KLF2 was highly expressed in immune cells and fibroblasts. Examples of Secondary databases are as follows. Comprehensive analysis of KLF2 as a prognostic biomarker McConnell BB, Yang VW. The various bioinformatics resources covered in this chapter will be helpful in several ways in medicinal plant research. Searching the Nucleotide Database will yield available results from each of its component databases. 2019;11(11):692437. Databases 6B). 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. Gene integrates information from a wide range of species. These results further demonstrate an essential role that KLF2 performed during development of HCC associated with liver fibrosis/cirrhosis. Functional classification and experimental dissection of long noncoding RNAs. Nat Commun. 2001;2(8):698704. statement and As we expected, KLF2 was in a high positive correlation with these pathways, such as EMT_markers, ECM_related genes, collagen_ formation, degradation_of_ECM and TGF (Fig. Article All authors contributed toward data analysis, drafting and critically revising the paper and agree to be accountable for all aspects of the work. 00:38. Yerra VG, Drosatos K. Specificity proteins (SP) and Krppel-like factors (KLF) in liver physiology and pathology. on the molecular characterization and clinical significance of m6A modulators across 33 cancer types [23]. The foregoing results support that patients with increased SPP1 expression have a poor prognosis. Li Y, Tu S, Zeng Y, Zhang C, Deng T, Luo W, et al. Genes provide the information our cells use to make proteins, which are the machinery of the cell. Once given a database accession number, the data in primary databases are never changed: they form part of the scientific record. F KaplanMeier survival analysis of the two subgroups. These three databases are primary databases, as they house original sequence data. Comprehensive analysis of KLF2 as a prognostic biomarker J The expression distribution of CD3D in the different grades of LIHC. Liver fibrosis. Why not share your success on social media? PubMed Kuo et al. Yang Y, Zang Y, Zheng C, Li Z, Gu X, Zhou M, et al. Fig. 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. have demonstrated that KLF2 is expressed in both CD4+ and CD8+ T cells. 5F). 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. The Cancer Genome Atlas (TCGA) catalyzed considerable growth and advancement in the computational biology field by supporting the development of high-throughput genomic characterization technologies, generating a massive quantity of data, and fielding teams of researchers to analyze the data. 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. 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. Nat Rev Cancer. Google Scholar. In addition, as Fig. 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. This resource organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations. G, H Scatter plots show the correlation of CD3D with PDCD1 and CD274 (PDL1). There are basically 3 types of biological databases are as follows. Embase includes unique non-English content and coverage of the most important types of evidence, such as randomized controlled trials, controlled clinical trials, Cochrane reviews and meta-analyses. It obtains unique data obtained from the laboratory and these data are made accessible to normal users without any change. 7D). Kim C, He P, Bialkowska AB, Yang VW. Fibrosis of the tumor stroma is an important biological process contributing to the advancement of solid tumors. https://doi.org/10.1159/000355743. Genomic sequencing tests identify differing levels of expression in a group of genes to understand their interactions. The data stored in these types of databases are the analyzed result of the primary database. Mol Ther Nucleic Acids. KLF2 is a novel transcriptional regulator of endothelial proinflammatory activation. 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). 2019;13(1):1817094795. https://doi.org/10.1177/1557988318816907. Additionally, we assessed the prognostic value of SPP1 in TCGA_LIHC and ICGC_LIRI. Ma J, Zhang L, Yang P, Zeng ZC, Xiang ZL. The data entered in these types of databases are first compared and then filtered based on desired criteria. https://doi.org/10.1152/ajprenal.00055.2008. It helps in searching sequences rapidly. BioCyc encyclopedias integrate a diverse range of data and provide a high level of curation for important microbes. Modern science isnt simply about publishing one set of results and hoping other researchers read it. C The correlations between KLF2 and relevant pathway score. Osteopontin (OPN), encoded by SPP1, has been implicated in multiple human diseases and has been shown to play an important regulatory role in HCC progression [53,54,55]. Tumour Biol J Int Soc Oncodev Biol Med. These studies further confirmed our findings that CD3D is prospective to be an emerging marker for HCC immunotherapy. ArrayExpress Archive of Functional Genomics Data stores data from high-throughput functional genomics experiments, and provides these data for reuse to the research community. TGF-, a strong inducer of EMT, has been implicated as a key cytokine mediating liver fibrosis [45]. 2013;37(6):63140. 2021;40:e105977. *P<0.05, **P<0.01, ***P<0.001. 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. HK KaplanMeier survival analysis show patients from TCGA_LIHC with high level of SPP1 expression had a significantly worse OS, PFS, DSS, and DFS. B Putative copy number alterations of KLF2 in HCC. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral variations and clinical mutations. 2014;2(3):3938. D The correlation between KLF2 methylation and the mRNA expression level. Therefore, this study does not require ethical approval. Based on our previous microarray results [4], we identified several lncRNAs as important factors in HCC progress.
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