Supplementary Data for 'Transformers Significantly Improve Splice Site Prediction'

Description: This repository contains supplementary data accompanying the manuscript "Transformers Significantly Improve Splice Site Prediction". The data includes annotations used for training our splice site prediction models and the predictions made by our model and SpliceAI 10k. These datasets are provided to facilitate replication of our results and to support further research in RNA splicing and machine learning applications in genomics. Contents: Annotations Used for Model Training: clinvar_splice_variants.tsv Description: Contains detailed information about ClinVar splice variants used in our study. Contents Include: Variant identifiers, genomic coordinates, associated clinical significance, and relevant annotations. splice_site_annotation_gtex.tsv Description: Splice site annotations derived from all tissues in GTEx V8. Contents Include: Coordinates of splice sites and transcript information. splice_site_annotation_icelandic_whole_blood_plus_gtex.tsv Description: Splice site annotations derived from a combination of Icelandic whole blood samples and samples from all tissues in GTEx V8. Contents Include: Coordinates of splice sites and transcript information. Model Predictions: a. SpliceAI 10k Model Predictions: spliceai_10k_clinvar_delta.vcf Description: SpliceAI 10k delta scores for ClinVar splice variants. Contents Include: Variant Call Format (VCF) file containing delta scores that indicate the predicted impact on splicing for ClinVar variants. spliceai_10k_no_sqtl_delta.vcf Description: SpliceAI 10k delta scores for variants unlikely to be splicing quantitative trait loci (sQTLs) in Icelandic whole blood. Contents Include: VCF file with delta scores for variants not associated with sQTLs. spliceai_10k_sqtl_delta.vcf Description: SpliceAI 10k delta scores for sQTLs detected in Icelandic whole blood. Contents Include: VCF file with delta scores for variants identified as sQTLs. b. Transformer 45k Model Predictions: transformer_45k_clinvar_delta.vcf Description: Transformer 45k delta scores for ClinVar splice variants. Contents Include: VCF file with delta scores from our Transformer model, indicating the predicted impact on splicing. transformer_45k_no_sqtl_delta.vcf Description: Transformer 45k delta scores for variants unlikely to be sQTLs in Icelandic whole blood. Contents Include: VCF file with delta scores for variants not associated with sQTLs, as predicted by our model. transformer_45k_sqtl_delta.vcf Description: Transformer 45k delta scores for sQTLs detected in Icelandic whole blood. Contents Include: VCF file with delta scores for variants identified as sQTLs, based on our Transformer model predictions. Additional Information: Delta Scores and Their Interpretation: Each variant is assessed for its potential impact on splicing through four delta scores: Acceptor Site Creation (top_a_creation_delta): Predicts the likelihood of creating a new acceptor site. Acceptor Site Disruption (top_a_disruption_delta): Predicts the likelihood of disrupting an existing acceptor site. Donor Site Creation (top_d_creation_delta): Predicts the likelihood of creating a new donor site. Donor Site Disruption (top_d_disruption_delta): Predicts the likelihood of disrupting an existing donor site. Final Delta Score Calculation: The overall impact of a variant is determined by taking the maximum of these four delta scores: final_delta_score = max(top_a_creation_delta, top_a_disruption_delta, top_d_creation_delta, top_d_disruption_delta) A higher final delta score indicates a greater predicted impact on splicing. Positions: The positions (*_pos) indicate the genomic coordinates where the predicted splicing events occur, providing insight into the specific locations affected by the variant. Interpreting Delta Scores: Delta scores range from 0 to 1. Scores closer to 1 suggest a higher probability of the variant affecting splicing. Purpose: These datasets support the findings reported in our manuscript by providing the raw data used for model training and evaluation. Researchers can use these datasets to replicate our experiments, compare model performances, or conduct further studies on splice site prediction. Citation: Please cite this dataset as: B.A. Jónsson, G.H. Halldórsson, S. Árdal, S. Rögnvaldsson, E. Einarsson, P. Sulem, D.F. Guðbjartsson, P. Melsted, K. Stefánsson, M.Ö. Úlfarsson (2023). Supplementary Data for "Transformers Significantly Improve Splice Site Prediction". Zenodo. https://doi.org/10.5281/zenodo.14109868 Contact Information: For questions or further information, please contact: Benedikt A. Jónsson Affiliation: deCODE Genetics/Amgen, Inc., Reykjavik, Iceland Email: [e-mail]本仓库包含与论文《Transformer显著优化剪接位点预测》（"Transformers Significantly Improve Splice Site Prediction"）配套的补充数据。本数据集涵盖用于训练我们的剪接位点预测模型的注释信息，以及我们的模型与SpliceAI 10k生成的预测结果。提供这些数据集旨在便于复现本研究结果，并为RNA剪接领域及基因组学机器学习应用的后续研究提供支撑。 ### 模型训练所用注释 1. `clinvar_splice_variants.tsv` 描述：包含本研究中使用的ClinVar剪接变异体的详细信息。 内容包含：变异体标识符、基因组坐标、关联的临床意义及相关注释信息。 2. `splice_site_annotation_gtex.tsv` 描述：源自GTEx V8数据库所有组织的剪接位点注释。 内容包含：剪接位点坐标及转录本信息。 3. `splice_site_annotation_icelandic_whole_blood_plus_gtex.tsv` 描述：源自冰岛全血样本与GTEx V8数据库所有组织的组合数据集的剪接位点注释。 内容包含：剪接位点坐标及转录本信息。 ### 模型预测结果 #### a. SpliceAI 10k模型预测结果 1. `spliceai_10k_clinvar_delta.vcf` 描述：ClinVar剪接变异体的SpliceAI 10k delta得分文件。 内容包含：以变异识别格式（Variant Call Format，VCF）存储的delta得分，用于表征ClinVar变异体对剪接过程的预测影响。 2. `spliceai_10k_no_sqtl_delta.vcf` 描述：冰岛全血中不太可能为剪接数量性状位点（splicing quantitative trait loci, sQTL）的变异体的SpliceAI 10k delta得分。 内容包含：存储未关联sQTL的变异体delta得分的VCF文件。 3. `spliceai_10k_sqtl_delta.vcf` 描述：冰岛全血中检测到的sQTL的SpliceAI 10k delta得分。 内容包含：存储已鉴定为sQTL的变异体delta得分的VCF文件。 #### b. Transformer模型（Transformer）45k预测结果 1. `transformer_45k_clinvar_delta.vcf` 描述：ClinVar剪接变异体的Transformer 45k delta得分。 内容包含：存储我们的Transformer模型生成的delta得分的VCF文件，用于表征变异体对剪接过程的预测影响。 2. `transformer_45k_no_sqtl_delta.vcf` 描述：冰岛全血中不太可能为sQTL的变异体的Transformer 45k delta得分。 内容包含：存储未被本模型预测为关联sQTL的变异体delta得分的VCF文件。 3. `transformer_45k_sqtl_delta.vcf` 描述：冰岛全血中检测到的sQTL的Transformer 45k delta得分。 内容包含：存储基于本Transformer模型预测已鉴定为sQTL的变异体delta得分的VCF文件。 ### 附加信息 #### Delta得分及其解读 每个变异体通过四类delta得分评估其对剪接过程的潜在影响： - 受体位点创建得分（top_a_creation_delta）：预测生成新剪接受体位点的可能性。 - 受体位点破坏得分（top_a_disruption_delta）：预测破坏现有剪接受体位点的可能性。 - 供体位点创建得分（top_d_creation_delta）：预测生成新剪接供体位点的可能性。 - 供体位点破坏得分（top_d_disruption_delta）：预测破坏现有剪接供体位点的可能性。 #### 最终Delta得分计算 变异体的整体影响通过取上述四类delta得分的最大值确定： `final_delta_score = max(top_a_creation_delta, top_a_disruption_delta, top_d_creation_delta, top_d_disruption_delta)` 最终delta得分越高，代表该变异体对剪接过程的预测影响越大。 #### 坐标位置 带`*_pos`后缀的字段代表预测剪接事件发生的基因组坐标，可用于解析变异体影响的具体基因组区域。 #### Delta得分解读 Delta得分取值范围为0至1。得分越接近1，代表该变异体影响剪接过程的概率越高。 #### 研究用途 本数据集提供了模型训练与评估所用的原始数据，可支撑本论文的研究结论。研究人员可利用本数据集复现本实验、对比不同模型的性能，或开展剪接位点预测相关的后续研究。 ### 引用方式 请按照以下格式引用本数据集： B.A. Jónsson, G.H. Halldórsson, S. Árdal, S. Rögnvaldsson, E. Einarsson, P. Sulem, D.F. Guðbjartsson, P. Melsted, K. Stefánsson, M.Ö. Úlfarsson (2023). Supplementary Data for "Transformers Significantly Improve Splice Site Prediction". Zenodo. https://doi.org/10.5281/zenodo.14109868 ### 联系方式 如有疑问或进一步信息需求，请联系： Benedikt A. Jónsson 所属机构：deCODE Genetics/Amgen, Inc., 冰岛雷克雅未克 邮箱：[e-mail]