Download SPIDEX annotation database for use in ANNOVAR
Background
This webpage provides links to download the SPIDEX 1.0 - Deep Genomics : (Xiong et al, Science 2015) Machine-learning prediction on how genetic variants affect RNA splicing. This dataset is described below:
ABSTRACT: To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation-driven aberrant splicing. Intronic disease mutations that are more than 30 nucleotides from any splice site alter splicing nine times as often as common variants, and missense exonic disease mutations that have the least impact on protein function are five times as likely as others to alter splicing. We detected tens of thousands of disease-causing mutations, including those involved in cancers and spinal muscular atrophy. Examination of intronic and exonic variants found using whole-genome sequencing of individuals with autism revealed misspliced genes with neurodevelopmental phenotypes. Our approach provides evidence for causal variants and should enable new discoveries in precision medicine.
REFERNCE: Xiong HY, Alipanahi B, Lee LJ, Bretschneider H, Merico D, Yuen RK, Hua Y, Gueroussov S, Najafabadi HS, Hughes TR, Morris Q, Barash Y, Krainer AR, Jojic N, Scherer SW, Blencowe BJ, Frey BJ. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science 347(6218):1254806, 2015.
Please read the User License Agreement below, and if you agree with it, you can fill out the download form.
User License Agreement
PLEASE READ THIS END USER LICENSE AGREEMENT (“EULA”) CAREFULLY BEFORE USING THE ANNOVAR SPIDEXTM DATABASE (AS DEFINED BELOW). BY USING THE ANNOVAR SPIDEXTM DATABASE YOU CERTIFY THAT YOU ARE AN ACADEMIC OR NOT-FOR-PROFIT END USER (AS DEFINED BELOW) AND YOU AGREE TO BE BOUND BY THE TERMS OF THIS EULA, AS THESE MAY BE UPDATED FROM TIME TO TIME. IF YOU DO NOT AGREE TO THESE TERMS, DO NOT USE THE ANNOVAR SPIDEXTM DATABASE AND WHEN PRESENTED WITH THE OPTION TO “AGREE” OR “DECLINE” THE TERMS OF THIS EULA, CLICK “DECLINE”.
This END USER LICENSE AGREEMENT (“EULA”) for Academic or Not-for-Profit end users (“ANPEU”) is a legally binding contract between you, an ANPEU, and Deep Genomics. In this EULA, an ANPEU means a scientist undertaking research activities in an academic institution, government research laboratory, or not-for-profit organization (“Institution”) where neither the scientist not the Institution is engaged with a commercial entity in any manner, including undertaking research and development on behalf of a commercial organization, related to the subject matter of this EULA. Deep Genomics and you may be individually referred to in this EULA as a “Party” and collectively as “Parties.”
Deep Genomics has developed a proprietary genome-wide database of scores that predict the functional effects of single nucleotide variants (SNVs) on cassette splicing (“SpidexTM Database”). Deep Genomics has made the SpidexTM Database freely available for use by ANPEUs on ANNOVAR (“ANNOVAR SpidexTM Database”) for scientific research purposes only.
THE FOLLOWING TERMS WILL GOVERN YOUR USE OF THE ANNOVAR SPIDEXTM DATABASE.
1. GRANT AND SCOPE OF LICENSE
1.1. Permitted uses. Deep Genomics grants you a non-exclusive, revocable, non-transferable, and limited right to use the ANNOVAR SpidexTM Database for the purpose of undertaking academic, governmental, or non-for-profit research (“Scope of License”).
1.2. Prohibited uses. Your use of the ANNOVAR SpidexTM Database is limited to the Scope of License as described in Section 1.1 above. For clarity, you may not:
a) at any time, directly or indirectly, dispute or contest the exclusive licensing rights of Deep Genomics in SpidexTM Database; transfer or assign any of your rights or obligations under this EULA to any third party without the prior written consent of Deep Genomics; disclose, provide, or to otherwise make SpidexTM Database or access thereto available in full or in part and in any form to any third party or natural or legal person (“Person”);
b) use SpidexTM Database or data generated therefrom for any non-academic purposes or applications of any kind;
c) copy, translate or modify SpidexTM Database and any other copyrighted work or confidential information provided by Deep Genomics in relations to SpidexTM Database or grant third parties access or rights to changed or modified versions of SpidexTM Database;
d) reproduce, make, have made, use, import, export, or sell any product or service derived from the use of SpidexTM Database without express written permission from Deep Genomics under separate license;
e) in whole or in part, whether modified or unmodified, incorporate SpidexTM Database into other programs or sublicense SpidexTM Database to any third parties;
f) work around, reverse engineer, decompile, disassemble SpidexTM Database, publish for others to copy, rent, lease, lend, or host SpidexTM Database to or for third parties for any reason; and
2. OWNERSHIP
Without prejudice to the permitted uses granted to you in Section 1.1 above, Deep Genomics has the exclusive rights in all copies of SpidexTM Database, including the copy hosted on ANNOVAR, in full or in part, as well as the right to distribute, sub-license, display, and make derivative works of SpidexTM Database, as uploaded into ANNOVAR or in any other form. All aspects and parts of SpidexTM Database are the property of Deep Genomics and nothing in this EULA shall serve to, or should be construed to transfer any ownership rights whatsoever in SpidexTM Database to you.
3. DATABASE UPGRADES
Deep Genomics, at its discretion, may make available future upgrades to the ANNOVAR SpidexTM Database. The terms of this EULA will govern any future upgrades or updates provided by Deep Genomics in relation to the ANNOVAR SpidexTM Database unless such updates or upgrades are accompanied by separate license.
4. PUBLICATIONS
You have the right to publish experimental data or results generated through your use of the ANNOVAR SpidexTM Database in scientific manuscripts and conference abstracts, posters, or presentations (“Publication Events”). You shall acknowledge your use of the SpidexTM Database as the source of such data or results in all Publication Events by citing the following publication:
H.Y.Xiong,B.Alipanahi,L.J.Lee,H.Bretschneider,D.Merico,R.K.C.Yuen,Y.Hua,S.Gueroussov, H. S. Najafabadi, T. R. Hughes, Q. D. Morris, Y. Barash, A. R. Krainer, N. Jojic, S. W. Scherer, B. J. Blencowe and B. J. Frey. The human splicing code reveals new insights into the genetic determinants of disease. Science Express DOI: 10.1126/science.1254806, December 2014, Science 347:6218, January 2015. (Deep Genomics is the exclusive licensee of the intellectual property contained therein and associated therewith).
5. PROTECTION OF SPIDEXTM DATABASE
5.1. Confidentiality. You acknowledge that SpidexTM Database is protected by Copyright law, it is proprietary information of Deep Genomics, and is hereby explicitly identified as confidential information. You agree to treat all confidential information with at least the same degree of care with which you treat your own confidential information and in no event with less care than is reasonably required to protect the confidentiality of SpidexTM Database. You shall take precautionary measures in order to prevent third parties from taking possession of, gain access to, or use ANNOVAR SpidexTM Database, in whole or in part. Third parties may include any other ANPEU, companies, or organizations known to or collaborating with you in any capacity, including in matters not related to the subject matter of this EULA.
5.2. Remedies For Breach Of Confidential Information. You acknowledge and agree that the confidentiality provisions of this EULA are necessary to protect the trade, commercial, and financial interests of Deep Genomics and that the unauthorized disclosure or use of any confidential information contrary to this EULA by you or your trainees, staff, or collaborators (“Representatives”) and your or your Representatives’ failure to comply with the terms and conditions of this EULA will give rise to irreparable harm and significant injury to Deep Genomics that is inadequately compensable in monetary damages. Accordingly, Deep Genomics may, in addition to any other remedy available at law, enforce the performance of this EULA by injunction or specific performance upon application to a court of competent jurisdiction without proof of actual damage and without the requirement of posting a bond or other security, and notwithstanding that damages may be readily quantifiable. You agree not to plead sufficiency of damages as a defence in any proceeding.
6. DISCLAIMER
DEEP GENOMICS LICENSES, AND YOU ACCEPT THE ANNOVAR SPIDEXTM DATABASE UNDER THE TERMS OF THIS EULA "AS IS." DEEP GENOMICS PROVIDES NO WARRANTIES AS TO THE FUNCTION OR USE OF THE ANNOVAR SPIDEXTM DATABASE, WHETHER EXPRESS, IMPLIED, OR STATUTORY, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF ANNOVAR SPIDEXTM DATABASE RESTS WITH YOU. DEEP GENOMICS DOES NOT WARRANT THAT THE FUNCTIONS CONTAINED IN OR PERFORMED BY THE ANNOVAR SPIDEXTM DATABASE WILL MEET YOUR REQUIREMENTS OR THAT THE ANNOVAR SPIDEXTM DATABASE WILL FUNCTION ERROR FREE.
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Download form for SPIDEX 1.0 - Deep Genomics : (Xiong et al, Science 2015) Machine-learning prediction on how genetic variants affect RNA splicing
If you agree to these terms above, please fill out the form and you will receive an email with URL to download the datasets within 10 minutes (if not, email me and I will check this).