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Title:          The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer
Subject:        Nature Communications, doi:10.1038/s41467-023-43767-1
Keywords:       
Author:         Alexandros Armaos
Creator:        Springer
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     Item: 
      Title: The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate’cancer
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      Children: 
       Item: 
        Title: Results
        Destination: A1
        Children: 
         Item: 
          Title: The PENGUIN framework
          Destination: B1
         Item: 
          Title: EPIN composition and properties
          Destination: B2
         Item: 
          Title: Characterization of PrCa clusters identified by PENGUIN
          Destination: B3
         Item: 
          Title: Assessment of PENGUIN specificity
          Destination: B4
         Item: 
          Title: Involvement of E-P protein interactomes in tumor-related functional processes
          Destination: B5
         Item: 
          Title: SNPs path analysis in the E-P protein interactomes
          Destination: B6
         Item: 
          Title: Network paths with PrCa SNPs in enhancer binding’motifs
          Destination: B7
         Item: 
          Title: Network paths with PrCa SNPs in the genes coding for EPIN’nodes
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         Item: 
          Title: Examples: SNPs path analysis of MYC, CASC11 and GATA2 promoters
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       Item: 
        Title: Discussion
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       Item: 
        Title: Methods
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        Children: 
         Item: 
          Title: Experimental methods
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         Item: 
          Title: HICHIP
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         Item: 
          Title: ChIP
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         Item: 
          Title: RNA’seq
          Destination: B13
         Item: 
          Title: Conformation capture and E-P interactions
          Destination: B14
         Item: 
          Title: E-P HiChIP prioritization
          Destination: B15
         Item: 
          Title: DNA binding’motifs
          Destination: B16
         Item: 
          Title: Gene expression’data
          Destination: B17
         Item: 
          Title: Protein-protein interaction network
          Destination: B18
         Item: 
          Title: The PENGUIN pipeline
          Destination: B19
         Item: 
          Title: Node centrality measures
          Destination: B20
         Item: 
          Title: Clustering’EPINs
          Destination: B21
         Item: 
          Title: Identifying enriched functional annotations in EPIN clusters
          Destination: B22
         Item: 
          Title: Druggability information
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         Item: 
          Title: CTCF ChiP-Seq’peaks
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         Item: 
          Title: PrCa’SNPs
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         Item: 
          Title: Annotations of PENGUIN prioritized signals using ABC and cS2G’scores
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         Item: 
          Title: SNP paths (PrCa SNPs in enhancer binding motifs)
          Destination: B27
         Item: 
          Title: SNP paths (PrCa SNPs in intermediate proteins)
          Destination: B28
         Item: 
          Title: PrCa enrichment using GWAS Catalog and comparison with other diseases
          Destination: B29
         Item: 
          Title: Trans-eQTL hotspots
          Destination: B30
         Item: 
          Title: Super-enhancer-like regions
          Destination: B31
         Item: 
          Title: Oncogenes Gene’list
          Destination: B32
         Item: 
          Title: Enriched edges within each cluster
          Destination: B33
         Item: 
          Title: Significantly central intermediate nodes within each cluster
          Destination: B34
         Item: 
          Title: Functional gene set enrichment analysis
          Destination: B35
         Item: 
          Title: Differential gene expression
          Destination: B36
         Item: 
          Title: pQTL look-up
          Destination: B37
         Item: 
          Title: Gene dependency and gene effect metrics
          Destination: B38
         Item: 
          Title: Reporting summary
          Destination: B39
       Item: 
        Title: Data availability
        Destination: M1
       Item: 
        Title: Code availability
        Destination: M2
       Item: 
        Title: References
        Destination: A4
       Item: 
        Title: Acknowledgements
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       Item: 
        Title: Author contributions
        Destination: A6
       Item: 
        Title: Competing interests
        Destination: A7
       Item: 
        Title: Additional information
        Destination: M3
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