UP-TORR: online tool for accurate and Up-to-Date annotation of RNAi Reagents.
نویسندگان
چکیده
RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent-gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent-gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.
منابع مشابه
Functional Genetics in the Post-genomics Era: Building a Better Roadmap in Drosophila
In this commentary, Rob Kulathinal describes two papers from the Perrimon laboratory, each describing a new online resource that can assist geneticists with the design of their RNAi experiments. Hu et al.'s "UP-TORR: online tool for accurate and up-to-date annotation of RNAi reagents" and "FlyPrimerBank: An online database for Drosophila melanogaster gene expression analysis and knockdown evalu...
متن کاملIranian EFL Learners L2 Reading Comprehension: The Effect of Online Annotations via Interactive White Boards
This study explores the effect of online annotations via Interactive White Boards (IWBs) on reading comprehension of Iranian EFL learners. To this aim, 60 students from a language institute were selected as homogeneous based on their performance on Oxford Placement Test (2014).Then, they were randomly assigned to 3 experimental groups of 20, and subsequently exposed to the research treatment af...
متن کاملUp-to-date Treatments of Primary Hyperhidrosis with Focus on Sympathectomy and Sympathicotomy; a Narrative Review
Background: Primary hyperhidrosis (PH) refers to excessive sweating, beyond normal physiological levels, in specific sites of the body for unknown reasons. It is usually bilateral and is most prominent in the palms, axillae, feet, and face. PH prevalence is estimated to be 0%-6.1% in different populations. It usually begins in childhood and is more frequent in women. In 57% of ...
متن کاملDesign and psychometric evaluation of measurement tools for Institutional research functions
Introduction: Universities in the path of survival, development, and excellence will inevitably be continually aligned with complex, ambiguous and turbulent environmental changes which will not be achieved by managing, planning, and deciding on scientific, research-based and accurate, up-to-date, and accurate information. The purpose of this study was to design and psychometric evaluation of me...
متن کاملارزیابی منابع اطلاعاتی پزشکی مبتنی بر شواهد براساس میزان پاسخدهی به پرسشهای بالینی
Introduction: This study was to identify the best accessible electronic information resources for finding answers to clinical questions in Iranian National Medical Digital Library. Methods: 20 clinical questions were randomly selected from four areas: prevention and treatment, diagnosis, etiology and prognosis from American National Library of Medicine (NLM). The keywords were searched in info...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Genetics
دوره 195 1 شماره
صفحات -
تاریخ انتشار 2013