ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish.

IF 1.4 4区生物学 Q4 DEVELOPMENTAL BIOLOGY

Zebrafish Pub Date : 2020-10-01 Epub Date: 2020-09-15 DOI:10.1089/zeb.2020.1869

Seniye Targen, Tuğberk Kaya, M Ender Avci, Damla Gunes, Ayse Gokce Keskus, Ozlen Konu

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引用次数: 6

Abstract

Rapidly accumulating literature has proven feasibility of the zebrafish xenograft models in cancer research. Nevertheless, online databases for searching the current zebrafish xenograft literature are in great demand. Herein, we have developed a manually curated database, called ZenoFishDb v1.1 (https://konulab.shinyapps.io/zenofishdb), based on R Shiny platform aiming to provide searchable information on ever increasing collection of zebrafish studies for cancer cell line transplantation and patient-derived xenografts (PDXs). ZenoFishDb v1.1 user interface contains four modules: DataTable, Visualization, PDX Details, and PDX Charts. The DataTable and Visualization pages represent xenograft study details, including injected cell lines, PDX injections, molecular modifications of cell lines, zebrafish strains, as well as technical aspects of the xenotransplantation procedures in table, bar, and/or pie chart formats. The PDX Details module provides comprehensive information on the patient details in table format and can be searched and visualized. Overall, ZenoFishDb v1.1 enables researchers to effectively search, list, and visualize different technical and biological attributes of zebrafish xenotransplantation studies particularly focusing on the new trends that make use of reporters, RNA interference, overexpression, or mutant gene constructs of transplanted cancer cells, stem cells, and PDXs, as well as distinguished host modifications.

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ZenoFishDb v1.1:斑马鱼异种移植研究数据库。

快速积累的文献已经证明了斑马鱼异种移植模型在癌症研究中的可行性。然而，搜索当前斑马鱼异种移植文献的在线数据库需求量很大。在此，我们开发了一个人工管理的数据库，名为ZenoFishDb v1.1 (https://konulab.shinyapps.io/zenofishdb)，基于R Shiny平台，旨在为不断增加的斑马鱼研究提供可搜索的信息，用于癌细胞系移植和患者来源的异种移植(PDXs)。ZenoFishDb v1.1用户界面包含四个模块:DataTable、Visualization、PDX Details和PDX Charts。DataTable和Visualization页面展示了异种移植研究的细节，包括注射细胞系，PDX注射，细胞系的分子修饰，斑马鱼菌株，以及表格，条形图和/或饼状图格式的异种移植程序的技术方面。PDX Details模块以表格形式提供有关患者详细信息的全面信息，并且可以进行搜索和可视化。总体而言，ZenoFishDb v1.1使研究人员能够有效地搜索、列出和可视化斑马鱼异种移植研究的不同技术和生物学属性，特别是关注利用移植癌细胞、干细胞和pdx的报告基因、RNA干扰、过表达或突变基因构建的新趋势，以及区分宿主修饰。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Zebrafish DEVELOPMENTAL BIOLOGY-ZOOLOGY

CiteScore

3.60

自引率

5.00%

发文量

审稿时长

3 months

期刊介绍： Zebrafish is the only peer-reviewed journal dedicated to the central role of zebrafish and other aquarium species as models for the study of vertebrate development, evolution, toxicology, and human disease. Due to its prolific reproduction and the external development of the transparent embryo, the zebrafish is a prime model for genetic and developmental studies. While genetically more distant from humans, the vertebrate zebrafish nevertheless has comparable organs and tissues, such as heart, kidney, pancreas, bones, and cartilage. Zebrafish introduced the new section TechnoFish, which highlights these innovations for the general zebrafish community. TechnoFish features two types of articles: TechnoFish Previews: Important, generally useful technical advances or valuable transgenic lines TechnoFish Methods: Brief descriptions of new methods, reagents, or transgenic lines that will be of widespread use in the zebrafish community Zebrafish coverage includes: Comparative genomics and evolution Molecular/cellular mechanisms of cell growth Genetic analysis of embryogenesis and disease Toxicological and infectious disease models Models for neurological disorders and aging New methods, tools, and experimental approaches Zebrafish also includes research with other aquarium species such as medaka, Fugu, and Xiphophorus.