salmonella.json

{
  "salmonella": {
    "mass spectrometry": {
      "30": {
        "P": {
          "file": "data/salmonella/phosphorylation/Supplementary_Table_01.xlsx",
          "sheet": "Supplementary1",
          "accession column": "Protein",
          "position column": "Positions.within.proteins",
          "replicate columns": [
            "Ratio.H.L.normalized.E1",
            "Ratio.H.L.normalized.E2",
            "Ratio.H.L.normalized.E3",
            "Ratio.H.L.normalized.E4"
          ],
          "replicates": 2,
          "logarithm": 2
        },
        "U": {
          "file": "data/salmonella/ubiquitination/20151119_HeLa_HCT116_05h_2h_all.xlsx",
          "sheet": "20151119_HeLa_HCT116_05h_2h_all",
          "accession column": "Protein",
          "position column": "Positions within proteins",
          "position format": "(?=(?:^|;)([0-9]+)(?:;|$))",
          "replicate columns": [
            "Ratio H/L normalized HCT116_05_R1",
            "Ratio H/L normalized HCT116_05_R2",
            "Ratio H/L normalized HCT116_05_R3",
            "Ratio H/L normalized HCT116_05_R4"
          ],
          "replicates": 2,
          "logarithm": 2
        }
      },
      "120": {
        "P": {
          "file": "data/salmonella/phosphorylation/Supplementary_Table_01.xlsx",
          "sheet": "Supplementary1",
          "accession column": "Protein",
          "position column": "Positions.within.proteins",
          "replicate columns": [
            "Ratio.M.L.normalized.E1",
            "Ratio.M.L.normalized.E2",
            "Ratio.M.L.normalized.E3",
            "Ratio.M.L.normalized.E4"
          ],
          "replicates": 2,
          "logarithm": 2
        },
        "U": {
          "file": "data/salmonella/ubiquitination/20151119_HeLa_HCT116_05h_2h_all.xlsx",
          "sheet": "20151119_HeLa_HCT116_05h_2h_all",
          "accession column": "Protein",
          "position column": "Positions within proteins",
          "position format": "(?=(?:^|;)([0-9]+)(?:;|$))",
          "replicate columns": [
            "Ratio H/L normalized HCT116_2_R1",
            "Ratio H/L normalized HCT116_2_R2",
            "Ratio H/L normalized HCT116_2_R3",
            "Ratio H/L normalized HCT116_2_R4"
          ],
          "replicates": 2,
          "logarithm": 2
        }
      }
    },
    "protein-protein interactions": {
      "BioGRID": {
        "experimental system": [
          "Affinity Capture-Luminescence",
          "Affinity Capture-MS",
          "Affinity Capture-RNA",
          "Affinity Capture-Western",
          "Biochemical Activity",
          "Co-crystal Structure",
          "Co-purification",
          "FRET",
          "PCA",
          "Two-hybrid"
        ]
      },
      "CORUM": {
      },
      "IntAct": {
        "score": 0.27
      },
      "MINT": {
        "score": 0.27
      },
      "Reactome": {
      },
      "STRING": {
        "experiments score": 0.7,
        "combined score": 0.7
      }
    },
    "Cytoscape": {
      "bar chart": {
        "post-translational modifications": ["P", "U"]
      },
      "node color": {
        "post-translational modifications": ["P", "U"]
      },
      "node shape": {
        "post-translational modifications": ["P", "U"]
      }
    },
    "Gene Ontology enrichment": {
      "p": 0.05
    },
    "Reactome enrichment": {
      "p": 0.05
    },
    "Gene Ontology network": {
      "post-translational modifications": ["P", "U"]
    },
    "Reactome network": {
      "post-translational modifications": ["P", "U"]
    },
    "community detection": {
      "Gene Ontology enrichment": {
        "p": 0.05
      },
      "Reactome enrichment": {
        "p": 0.05
      },
      "measurement enrichment": {
        "p": 0.05
      },
      "measurement location": {
        "p": 0.05
      }
    }
  }
}