Download SPIDEX annotation database for use in ANNOVAR
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
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.
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.
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.
7. INDEMNIFICATION AND WARRANTIES
7.1. Indemnification. You agree to indemnify Deep Genomics and hold it, its directors, officers, employees, consultants and advisors, harmless from and against any and all claims, threats, loss, liabilities, damages, fees, or expenses, including costs, and attorney's fees and expenses, (individually “Claim” or collectively “Claims”) arising out of or relating to your breach of this EULA and the acts or omissions of your directors, officers, employees, consultants and advisors in connection with the duties under this EULA. In addition, you agree to reimburse Deep Genomics for any and all costs, attorney's fees and expenses incurred by Deep Genomics in enforcing the provisions of this EULA, whether by prosecution of a lawsuit or otherwise. You shall not be required to indemnify Deep Genomics, to the extent allowed by law, where such Claim is caused by the gross negligence or willful misconduct of Deep Genomics.
7.2. Infringement. Deep Genomics warrants that, to the best of its knowledge, SpidexTM Database does not infringe any intellectual property rights of any third party. You will notify Deep Genomics promptly upon becoming aware of any claim or assertion by a third party to the contrary.
8. LIMITATION OF LIABILITY
8.1. IN NO EVENT SHALL DEEP GENOMICS OR ANY OF ITS DIRECTORS, OFFICERS, EMPLOYEES, CONSULTANTS OR ADVISORS BE LIABLE FOR ANY INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES OR EXPENSES OF ANY TYPE (INCLUDING BUT NOT LIMITED TO ANY DAMAGES FOR LOST PROFITS, CORRUPTION OR LOSS OF DATA, FAILURE TO TRANSMIT OR RECEIVE ANY DATA OR INFORMATION, OR ACCESS INTERRUPTION) ARISING OUT OF THIS EULA OR YOUR USE OR INABILITY TO USE THE ANNOVAR SPIDEXTM DATABASE, WHETHER SUCH DAMAGES OR EXPENSES ARISE OUT OF BREACH OF CONTRACT (INCLUDING FUNDAMENTAL BREACH), OR TORT OR ON ANY OTHER STATUTORY OR COMMON LAW BASIS, EVEN IF DEEP GENOMICS OR ANY OF ITS DIRECTORS, OFFICERS, EMPLOYEES, CONSULTANTS OR ADVISORS HAVE BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. DEEP GENOMICS SHALL NOT BE LIABLE FOR CONSEQUENTIAL HARM CAUSED BY DEFECTS AND CLAIMS RAISED BY THIRD PARTIES. LIABILITY OF THE CONTRACTUAL PARTIES SHALL BE RESTRICTED TO DAMAGES CAUSED INTENTIONALLY OR BY GROSS NEGLIGENCE AND IN NO EVENT SHALL DEEP GENOMICS’ TOTAL LIABILITY FOR ALL DAMAGES OF ANY KIND ARISING OUT OF OR RELATING TO THIS EULA EXCEED THE TOTAL AMOUNT OF FIFTY ($50.00) CANADIAN DOLLARS.
9. ACCESS, TERM, AND TERMINATION
9.1. Access. You shall receive access to the ANNOVAR SpidexTM Database on the ANNOVAR servers after completing your profile. The profile submission requires your Institution name, complete mailing address, the internet protocol (IP) address of your Institution (for the purposes of secure authentication as an ANPEU), your name, your Institution email address and your phone number.
9.2. Term and Termination. This EULA is effective as of the activation date of your profile on ANNOVAR, as described in Section 9.1 above, until terminated. Deep Genomics may terminate this EULA with or without cause and without notice. Upon termination of this EULA your access to the ANNOVAR SpidexTM Database will cease immediately. Sections 1.2, 2, 5, 7.1, 8, 9.2 and 10 shall survive termination of this EULA.
10. GENERAL PROVISIONS
10.1. Non-Assignment. You may not assign, delegate or otherwise transfer any of your rights and obligations under this EULA, either by operation of law or otherwise, without the prior written consent of Deep Genomics, which consent shall not be unreasonably withheld.
10.2. Relationship Of The Parties. The Parties are independent contractors under this EULA and this EULA does not and shall not be construed to create a partnership or joint venture, agency relationship, or employment relationship between them. Neither Party has the right or authority to create any obligations on behalf of the other Party.
10.3. No Waiver. No waiver of any provision of this EULA shall be effective unless in writing and signed by an authorized representative of the Party against whom the waiver is sought to be enforced. No failure or delay by either Party in exercising any right under this EULA shall constitute a waiver of that right.
10.4. Cumulative Remedies. Other than as expressly stated in this EULA, the remedies provided herein are in addition to, and without prejudice to, any other remedies of a Party at law or in equity.
10.5. Severability. If any provision of this EULA is held by a court of competent jurisdiction to be void or unenforceable, the provision shall be modified by the court and interpreted so as best to accomplish the objectives of the original provision to the fullest extent permitted by law, and the remaining provisions of this EULA shall remain in full force and effect.
10.6. Governing Law & Attornment. This EULA shall be governed by, and interpreted and enforced in accordance with the laws of the Province of Ontario and the federal laws of Canada applicable therein, and treated in all respects as an Ontario contract. Each Party to this EULA hereby irrevocably and unconditionally attorns and submits to the exclusive jurisdiction of the applicable Ontario or Canadian courts in any action or proceeding arising out of or relating to this EULA. Further, each Party agrees that all such claims in respect of such actions or proceedings shall be heard and determined in Toronto in such Ontario court.
10.7. Entire Agreement. This EULA, including all the documents referenced herein and the schedules and exhibits hereto constitute the complete and final agreement between the Parties as to its subject matter, and supersedes all previous and contemporaneous negotiations, discussions, proposals, agreements, or representations, written or oral, concerning the subject matter of this EULA. No representation, undertaking or promise shall be taken to have been given or be implied from anything said or written in negotiations between the parties prior to this EULA except as expressly stated herein. No amendment to this EULA shall be effective unless in writing and executed by authorized representatives of both Parties.
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).