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Table 4 Data resources and models for translational PCa informatics

From: Data-driven translational prostate cancer research: from biomarker discovery to clinical decision

Name Description PMID
Databases and knowledge bases
 DDPC Dragon Database of Genes associated with Prostate Cancer: an integrated knowledge base of genes experimentally supported for PCa
http://cbrc.kaust.edu.sa/ddpc/
20880996
 PCP Prostate cancer proteomics: a database created by the results from proteomic studies of human PCa
http://ef.inbi.ras.ru/
22649669
 Pancanmet Pan-cancer metabolites: A web resource for metabolites and associated clinical significance across cancers
http://www.sanderlab.org/pancanmet/
29396322
 TCIA The Cancer Imaging Archive: a data platform for advanced medical imaging of cancers
https://www.cancerimagingarchive.net/
23884657
 PCaLiStDB Prostate Cancer Lifestyle Database: a database for lifestyle-wide association studies of PCa
http://www.sysbio.org.cn/pcalistdb/
31950190
 CaPSURE Cancer of the Prostate Strategic Urologic Research Endeavor: documenting the impact of PCa, including resource utilization, clinical outcomes, health-related quality of life, etc. 8911524
 PCaO Prostate Cancer Ontology: a data resource for providing the standardized concepts and knowledge for PCa precision study
http://pcaontology.net/
N/A
Computational models and tools
 PPI-based network model miRNAs regulating hub genes in PPI network are identified for predicting high-grade PCa 30367364
 PCa-specific PPI network model Identifying module biomarkers for PCa progression based on gene expression and PPI data
http://www.ibio-cn.org/HPC-PPIN/
25080090
 Network vulnerability-based model miRNAs with stronger single-line regulatory power are identified for predicting PCa metastasis
http://sysbio.suda.edu.cn/MiRNA-BD/
29784056
 WGCNA-based model Identifying lincRNA module biomarkers for PCa diagnosis and prognosis 26100580
 RF-based classification model Predicting aggressive behavior of PCa based on DNA methylation data and RF modeling 31640781
 CCI-reinforced SVM and RF models Predicting the recurrence-associated death from localized PCa 31428684
 CNN-based model A computer-aided diagnosis system for automatically detecting PCa using MRI data 29772101
 Deep learning model Dividing patients with PCa into clinically meaningful groups 31238766
 Integrated network and SVM model Prioritizing PCa-associated miRNAs based on miRNA target-dysregulated network analysis and SVM classification 21768329
  1. PCa prostate cancer, RF random forest, SVM support vector machine, CCI Charlson comorbidity index, CNN convolutional neural network, MRI magnetic resonance imaging, PPI protein–protein interaction, WGCNA weighted gene co-expression network analysis, N/A not applicable, URL uniform resource locator, PMID PubMed ID