Visualization Community | St. Jude Cloud

Tau PTM sites

St. Jude Children's Research Hospital

Apr 15, 2022

< 1k

Mass Spec.

Here we demonstrate NetAD data integrated with ProteinPaint. Phosphorylation sites common in Alzheimer's Disease (AD) are displayed on the peptide sequence of MAPT, also known as the Tau protein. The log2 ratio of phosphoryation in AD cases versus references samples is displayed per site and phosphosites are colored coded by amino acid.

Loading Visualization

runproteinpaint({
    host: "https://proteinpaint.stjude.org",
    holder: visualizationContainer[0],
    parseurl: true,
    noheader: true,
    nobox:1,
    genome: "hg38",
    gene: "NM_001203252",
    tracks: [
        {
            type: "mds3",
            name:"Tau Phosphosites",
            skewerModes: [
                {
                    type: "numeric",
                    byAttribute: "logValue",
                    label: "Log2FC AD vs Control",
                    inuse: true,
                    axisheight: 100
                }
            ],
            custom_variants:[
                
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45962452,mname:"T39",class:"M",dt:1, logValue: 1.32},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971861,mname:"S46",class:"I",dt:1, logValue: -0.06},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971873,mname:"T50",class:"M",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971879,mname:"T52",class:"M",dt:1, logValue: -0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971891,mname:"S56",class:"I",dt:1, logValue: 0.16},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971906,mname:"S61",class:"I",dt:1, logValue: -0.03},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971912,mname:"T63",class:"M",dt:1, logValue: -0.05},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971915,mname:"S64",class:"I",dt:1, logValue: -0.02},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971927,mname:"S68",class:"I",dt:1, logValue: -0.03},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971930,mname:"T69",class:"M",dt:1, logValue: -0.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971936,mname:"T71",class:"M",dt:1, logValue: 0.08},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45974390,mname:"T76",class:"M",dt:1, logValue: -0.12},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45978398,mname:"T111",class:"M",dt:1, logValue: 0.65},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45978404,mname:"S113",class:"I",dt:1, logValue: 0.56},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991553,mname:"T175",class:"M",dt:1, logValue: 1.74},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991571,mname:"T181",class:"M",dt:1, logValue: 0.82},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991580,mname:"S184",class:"I",dt:1, logValue: 1.44},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991583,mname:"S185",class:"I",dt:1, logValue: 0.49},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996413,mname:"S191",class:"I",dt:1, logValue: 0.73},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996425,mname:"S195",class:"I",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996431,mname:"Y197",class:"F",dt:1, logValue: 0.44},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996434,mname:"S198",class:"I",dt:1, logValue: 1.01},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996437,mname:"S199",class:"I",dt:1, logValue: 1.59},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996446,mname:"S202",class:"I",dt:1, logValue: 1.69},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996455,mname:"T205",class:"M",dt:1, logValue: 1.53},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996464,mname:"S208",class:"I",dt:1, logValue: -0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996470,mname:"S210",class:"I",dt:1, logValue: 0.04},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996476,mname:"S212",class:"I",dt:1, logValue: 1.94},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996482,mname:"S214",class:"I",dt:1, logValue: 0.01},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996492,mname:"T217",class:"M",dt:1, logValue: 2.35},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996502,mname:"T220",class:"M",dt:1, logValue: 1.82},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996533,mname:"T231",class:"M",dt:1, logValue: 4.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996545,mname:"S235",class:"I",dt:1, logValue: 4.31},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996551,mname:"S237",class:"I",dt:1, logValue: 2.77},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996554,mname:"S238",class:"I",dt:1, logValue: 4.36},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996563,mname:"S241",class:"I",dt:1, logValue: 1.52},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996626,mname:"S262",class:"I",dt:1, logValue: 2.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996629,mname:"T263",class:"M",dt:1, logValue: 2.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010340,mname:"S285",class:"I",dt:1, logValue: 3.22},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010352,mname:"S289",class:"I",dt:1, logValue: 2.83},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010400,mname:"S305",class:"I",dt:1, logValue: 5.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46014297,mname:"S324",class:"I",dt:1, logValue: 2.20},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46018686,mname:"S356",class:"I",dt:1, logValue: 0.65},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46018701,mname:"T361",class:"M",dt:1, logValue: 0.85},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024001,mname:"T386",class:"M",dt:1, logValue: 1.76},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024025,mname:"Y394",class:"F",dt:1, logValue: 1.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024031,mname:"S396",class:"I",dt:1, logValue: 2.02},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024043,mname:"S400",class:"I",dt:1, logValue: 2.06},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024052,mname:"T403",class:"M",dt:1, logValue: 1.72},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024055,mname:"S404",class:"I",dt:1, logValue: 0.61},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024070,mname:"S409",class:"I",dt:1, logValue: 0.95},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024085,mname:"T414",class:"M",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024091,mname:"S416",class:"I",dt:1, logValue: 0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024109,mname:"S422",class:"I",dt:1, logValue: 0.53},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024143,mname:"S433",class:"I",dt:1, logValue: 0.32},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024149,mname:"S435",class:"I",dt:1, logValue: 0.51}

            ],
        }
    ],
    mclassOverride: {
        className: "Amino Acid Phosphosite",
        classes:{
            M: {
                label: "Threonine",
                color: "#2874A6",
                desc: "phosphorylated amino acid"
            },
            I: {
                label: "Serine",
                color: "#E74C3C",
                desc: "phosphorylated amino acid"
            }, 
            F: {
                label: "Tyrosine",
                color: "#00A86B",
                desc: "phosphorylated amino acid"
            }
        }
    }
})

Visualization Code

runproteinpaint({
    host: "https://proteinpaint.stjude.org",
    holder: visualizationContainer[0],
    parseurl: true,
    noheader: true,
    nobox:1,
    genome: "hg38",
    gene: "NM_001203252",
    tracks: [
        {
            type: "mds3",
            name:"Tau Phosphosites",
            skewerModes: [
                {
                    type: "numeric",
                    byAttribute: "logValue",
                    label: "Log2FC AD vs Control",
                    inuse: true,
                    axisheight: 100
                }
            ],
            custom_variants:[
                
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45962452,mname:"T39",class:"M",dt:1, logValue: 1.32},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971861,mname:"S46",class:"I",dt:1, logValue: -0.06},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971873,mname:"T50",class:"M",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971879,mname:"T52",class:"M",dt:1, logValue: -0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971891,mname:"S56",class:"I",dt:1, logValue: 0.16},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971906,mname:"S61",class:"I",dt:1, logValue: -0.03},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971912,mname:"T63",class:"M",dt:1, logValue: -0.05},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971915,mname:"S64",class:"I",dt:1, logValue: -0.02},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971927,mname:"S68",class:"I",dt:1, logValue: -0.03},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971930,mname:"T69",class:"M",dt:1, logValue: -0.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45971936,mname:"T71",class:"M",dt:1, logValue: 0.08},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45974390,mname:"T76",class:"M",dt:1, logValue: -0.12},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45978398,mname:"T111",class:"M",dt:1, logValue: 0.65},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45978404,mname:"S113",class:"I",dt:1, logValue: 0.56},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991553,mname:"T175",class:"M",dt:1, logValue: 1.74},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991571,mname:"T181",class:"M",dt:1, logValue: 0.82},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991580,mname:"S184",class:"I",dt:1, logValue: 1.44},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45991583,mname:"S185",class:"I",dt:1, logValue: 0.49},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996413,mname:"S191",class:"I",dt:1, logValue: 0.73},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996425,mname:"S195",class:"I",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996431,mname:"Y197",class:"F",dt:1, logValue: 0.44},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996434,mname:"S198",class:"I",dt:1, logValue: 1.01},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996437,mname:"S199",class:"I",dt:1, logValue: 1.59},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996446,mname:"S202",class:"I",dt:1, logValue: 1.69},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996455,mname:"T205",class:"M",dt:1, logValue: 1.53},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996464,mname:"S208",class:"I",dt:1, logValue: -0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996470,mname:"S210",class:"I",dt:1, logValue: 0.04},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996476,mname:"S212",class:"I",dt:1, logValue: 1.94},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996482,mname:"S214",class:"I",dt:1, logValue: 0.01},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996492,mname:"T217",class:"M",dt:1, logValue: 2.35},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996502,mname:"T220",class:"M",dt:1, logValue: 1.82},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996533,mname:"T231",class:"M",dt:1, logValue: 4.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996545,mname:"S235",class:"I",dt:1, logValue: 4.31},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996551,mname:"S237",class:"I",dt:1, logValue: 2.77},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996554,mname:"S238",class:"I",dt:1, logValue: 4.36},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996563,mname:"S241",class:"I",dt:1, logValue: 1.52},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996626,mname:"S262",class:"I",dt:1, logValue: 2.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:45996629,mname:"T263",class:"M",dt:1, logValue: 2.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010340,mname:"S285",class:"I",dt:1, logValue: 3.22},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010352,mname:"S289",class:"I",dt:1, logValue: 2.83},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46010400,mname:"S305",class:"I",dt:1, logValue: 5.07},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46014297,mname:"S324",class:"I",dt:1, logValue: 2.20},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46018686,mname:"S356",class:"I",dt:1, logValue: 0.65},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46018701,mname:"T361",class:"M",dt:1, logValue: 0.85},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024001,mname:"T386",class:"M",dt:1, logValue: 1.76},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024025,mname:"Y394",class:"F",dt:1, logValue: 1.43},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024031,mname:"S396",class:"I",dt:1, logValue: 2.02},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024043,mname:"S400",class:"I",dt:1, logValue: 2.06},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024052,mname:"T403",class:"M",dt:1, logValue: 1.72},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024055,mname:"S404",class:"I",dt:1, logValue: 0.61},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024070,mname:"S409",class:"I",dt:1, logValue: 0.95},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024085,mname:"T414",class:"M",dt:1, logValue: -0.21},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024091,mname:"S416",class:"I",dt:1, logValue: 0.14},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024109,mname:"S422",class:"I",dt:1, logValue: 0.53},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024143,mname:"S433",class:"I",dt:1, logValue: 0.32},
                {gene:"MAPT",isoform:"NM_001203252",chr:"chr17",pos:46024149,mname:"S435",class:"I",dt:1, logValue: 0.51}

            ],
        }
    ],
    mclassOverride: {
        className: "Amino Acid Phosphosite",
        classes:{
            M: {
                label: "Threonine",
                color: "#2874A6",
                desc: "phosphorylated amino acid"
            },
            I: {
                label: "Serine",
                color: "#E74C3C",
                desc: "phosphorylated amino acid"
            }, 
            F: {
                label: "Tyrosine",
                color: "#00A86B",
                desc: "phosphorylated amino acid"
            }
        }
    }
})

Tau PTM sites

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Visualization Code