cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19311235.v1
title: Additional file 7 of Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease

description: Additional file 7. Supplemental Table 7: Genetic colocalization with CAD.
DOI: 10.6084/m9.figshare.19311238.v1
title: Additional file 8 of Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease

description: Additional file 8. Supplemental Table 8: gene ontology enrichment for genes with colocalization.
DOI: 10.6084/m9.figshare.19311241
title: Additional file 9 of Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease

description: Additional file 9. Supplemental Table 9: Mendelian randomization of 3D and eQTL mapped genes.
DOI: 10.6084/m9.figshare.19311241.v1
title: Additional file 9 of Enhancer promoter interactome and Mendelian randomization identify network of druggable vascular genes in coronary artery disease

description: Additional file 9. Supplemental Table 9: Mendelian randomization of 3D and eQTL mapped genes.
DOI: 10.25345/c5f766847
title: MassIVE Reanalysis RMSV000000355.305 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PLEKHN1 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c59k45v3d
title: MassIVE Reanalysis RMSV000000355.315 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RNF215 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5x921m07
title: MassIVE Reanalysis RMSV000000355.316 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, ACOT13 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5222r757
title: MassIVE Reanalysis RMSV000000355.314 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PLA2G2D [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c55t3g192
title: MassIVE Reanalysis RMSV000000355.311 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, HIST1H4L [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5ns0m02r
title: MassIVE Reanalysis RMSV000000355.313 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, CARD9 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5sj19s6g
title: MassIVE Reanalysis RMSV000000355.310 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, C18orf54 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5j09w597
title: MassIVE Reanalysis RMSV000000355.312 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PAGE2B [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311305
title: Additional file 11 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 10: Table S7. Biological process enrichment of class-specific proteins.
DOI: 10.6084/m9.figshare.19311308
title: Additional file 12 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 11: Table S8. Coverage comparison between the Ras signaling network reconstructed in this work and 3 experimental network sources.
DOI: 10.6084/m9.figshare.19311311
title: Additional file 2 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 1: Table S1. All protein-protein interactions (PPI) of the Ras-network sorted by layer.
DOI: 10.6084/m9.figshare.19311305.v1
title: Additional file 11 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 10: Table S7. Biological process enrichment of class-specific proteins.
DOI: 10.6084/m9.figshare.19311308.v1
title: Additional file 12 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 11: Table S8. Coverage comparison between the Ras signaling network reconstructed in this work and 3 experimental network sources.
DOI: 10.6084/m9.figshare.19311311.v1
title: Additional file 2 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 1: Table S1. All protein-protein interactions (PPI) of the Ras-network sorted by layer.
DOI: 10.6084/m9.figshare.19311317
title: Additional file 4 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 3: Table S2. Hub protein analysis.
DOI: 10.6084/m9.figshare.19311320
title: Additional file 5 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 4: Table S3. Downstream proteins of the Ras network.
DOI: 10.6084/m9.figshare.19311320.v1
title: Additional file 5 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 4: Table S3. Downstream proteins of the Ras network.
DOI: 10.6084/m9.figshare.19311317.v1
title: Additional file 4 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 3: Table S2. Hub protein analysis.
DOI: 10.6084/m9.figshare.19311323
title: Additional file 6 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 5: Table S4. Effector-related feedback analysis.
DOI: 10.6084/m9.figshare.19311329
title: Additional file 8 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 7: Table S6. Pathway enrichment analysis using PANTHER.
DOI: 10.6084/m9.figshare.19311323.v1
title: Additional file 6 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 5: Table S4. Effector-related feedback analysis.
DOI: 10.6084/m9.figshare.19311326
title: Additional file 7 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 6: Table S5. Functional analysis of the Ras network proteins using SysGO.
DOI: 10.6084/m9.figshare.19311326.v1
title: Additional file 7 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 6: Table S5. Functional analysis of the Ras network proteins using SysGO.
DOI: 10.6084/m9.figshare.19311329.v1
title: Additional file 8 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 7: Table S6. Pathway enrichment analysis using PANTHER.
DOI: 10.6084/m9.figshare.19311332.v1
title: Additional file 9 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 8: Network S1. CellDesigner diagram as zip.
DOI: 10.6084/m9.figshare.19311332
title: Additional file 9 of Reconstruction and analysis of a large-scale binary Ras-effector signaling network

description: Additional file 8: Network S1. CellDesigner diagram as zip.
DOI: 10.6084/m9.figshare.19311319
title: Additional file 2 of Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM

description: Additional file 2: Table S1. Summary of qualified sequencing throughputs and numbers of unique clonotypes.
DOI: 10.6084/m9.figshare.19311319.v1
title: Additional file 2 of Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM

description: Additional file 2: Table S1. Summary of qualified sequencing throughputs and numbers of unique clonotypes.
DOI: 10.25345/c58k74z35
title: MassIVE Reanalysis RMSV000000355.317 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, RDH16 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c5db7vr7x
title: MassIVE Reanalysis RMSV000000355.319 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PRKRA [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311337
title: Additional file 8 of Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM

description: Additional file 8: Table S2. Information of cross-individual clonal lineages and their nodes.
DOI: 10.6084/m9.figshare.19311337.v1
title: Additional file 8 of Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM

description: Additional file 8: Table S2. Information of cross-individual clonal lineages and their nodes.
DOI: 10.25345/c5125qb50
title: MassIVE Reanalysis RMSV000000355.318 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, TRPS1 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.25345/c54t6f49t
title: MassIVE Reanalysis RMSV000000355.320 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, PXK [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311353
title: Additional file 2 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 2. LINCS compound properties. Total list of compound properties used for the feature generation model and each value.
DOI: 10.25345/c5w950q00
title: MassIVE Reanalysis RMSV000000355.323 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, H2AFB2 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311353.v1
title: Additional file 2 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 2. LINCS compound properties. Total list of compound properties used for the feature generation model and each value.
DOI: 10.6084/m9.figshare.19311356.v1
title: Additional file 3 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 3. The number of positive and negative triplets for each side effect type. Detailed number of triplets for each side effect type in Case 1 dataset.
DOI: 10.25345/c5rj48w67
title: MassIVE Reanalysis RMSV000000355.325 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GOT1 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311356
title: Additional file 3 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 3. The number of positive and negative triplets for each side effect type. Detailed number of triplets for each side effect type in Case 1 dataset.
DOI: 10.25345/c5ms3k330
title: MassIVE Reanalysis RMSV000000355.326 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, OR4D6 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311359
title: Additional file 4 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 4. DDI prediction model performance for Case 1. Side effect specific performance of DDI model in Case 1 (unseen interactions).
DOI: 10.6084/m9.figshare.19311362
title: Additional file 5 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 5. DDI prediction model performance for Case 2. Side effect specific performance of DDI model in Case 2 (one-unseen drug).
DOI: 10.25345/c5h41jp10
title: MassIVE Reanalysis RMSV000000355.324 - CCMS MassIVE Knowledge Base (MassIVE-KB) MS-GF+ reanalysis of Bioplex AP-MS Dataset for Library Construction, GXYLT2 [launched by aea60c3352304ba6ab67140f655b6785]
title: Center for Computational Mass Spectrometry (CCMS) systematic reanalysis of public proteomics mass spectrometry (MS) datasets provides a public, large-scale and comparable set of dataset reanalyses results including detailed provenance records. To further facilitate the broad reusability of public proteomics MS data, these reanalyses were also used to build the MassIVE Knowledge Base (MassIVE-KB) spectral library, a community-wide resource derived from hundreds of millions of identified spectra from tens of terabytes of mass spectrometry data.
DOI: 10.6084/m9.figshare.19311362.v1
title: Additional file 5 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 5. DDI prediction model performance for Case 2. Side effect specific performance of DDI model in Case 2 (one-unseen drug).
DOI: 10.6084/m9.figshare.19311365
title: Additional file 6 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 6. DDI prediction model performance for Case 3. Side effect specific performance of DDI model in Case 3 (both unseen drugs).
DOI: 10.6084/m9.figshare.19311359.v1
title: Additional file 4 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 4. DDI prediction model performance for Case 1. Side effect specific performance of DDI model in Case 1 (unseen interactions).
DOI: 10.6084/m9.figshare.19311365.v1
title: Additional file 6 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 6. DDI prediction model performance for Case 3. Side effect specific performance of DDI model in Case 3 (both unseen drugs).
DOI: 10.6084/m9.figshare.19311368
title: Additional file 7 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 7. List of predicted DDIs. The list of positively predicted triplets in unseen interactions test set. The validation labels from DrugBank are annotated.
DOI: 10.6084/m9.figshare.19311368.v1
title: Additional file 7 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 7. List of predicted DDIs. The list of positively predicted triplets in unseen interactions test set. The validation labels from DrugBank are annotated.
DOI: 10.6084/m9.figshare.19311371
title: Additional file 8 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 8. The list of ATC codes of drugs in each cluster from dynamic drug features of cyclophosphamide. The second level of ATC codes was obtained which represents therapeutic subgroups. The list is sorted by the odds ratio of the number of drugs in the cluster over the total number of drugs with the code.
DOI: 10.6084/m9.figshare.19311371.v1
title: Additional file 8 of DeSIDE-DDI: interpretable prediction of drug-drug interactions using drug-induced gene expressions

description: Additional file 8. The list of ATC codes of drugs in each cluster from dynamic drug features of cyclophosphamide. The second level of ATC codes was obtained which represents therapeutic subgroups. The list is sorted by the odds ratio of the number of drugs in the cluster over the total number of drugs with the code.