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         </style>
         </style>


         <h1 id="firstHeading" class="firstHeading">FF:10563-108A5</h1>
         <h1 id="firstHeading" class="firstHeading">FF:10717-109I6, TF to Motif to TF network</h1>


<p>TF to TF network. Mouseover nodes and edges to see attributes.  Motif is an attribute of the source TF nodes (shown in green).  Promoter and z-score are attributes of the TF to TF edge.</p>
<p>Mouseover nodes and edges to see attributes.  Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow).  TF to Motif edges are shown in orange.</p>
<p>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).
</p>


         <div id="cytoscapeweb" style="width:800px;height:600px">
         <div id="cytoscapeweb" style="width:800px;height:600px">
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<script type="text/javascript">
<script type="text/javascript">
var request = new XMLHttpRequest();
var request = new XMLHttpRequest();
request.open("GET", "https://fantom5-collaboration.gsc.riken.jp/resource_browser/nwfiles/10563-108A5.gml", false);
request.open("GET", "https://fantom5-collaboration.gsc.riken.jp/resource_browser/nwfiles/10717-109I6_2.graphml", false);
request.send(null);
request.send(null);
xml = request.responseText;
xml = request.responseText;
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var target = event.target;
var target = event.target;
 
 
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["id"];
var lurl = "https://fantom5-collaboration.gsc.riken.jp/resource_browser/RB_SearchResults?sq="+target.data["label"];
//window.location = lurl;
window.location = lurl;
alert(lurl);
//alert(lurl);
}
}
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var colorMapper = {
var colorMapper = {
attrName: "motif",
attrName: "type",
entries: [ { attrValue: "", value: "#0099ff" } ]
entries: [ { attrValue: "motif", value: "#ff9900" },
  { attrValue: "tf", value: "#0099ff" } ]
};
};
 
var tooltipMapper = {
var shapeMapper = {
attrName: "motif",
attrName: "type",
entries: [ { attrValue: "", value: "<b>TF: ${id}</b>" } ]
entries: [ { attrValue: "motif", value: "rectangle" },
  { attrValue: "tf", value: "ELLIPSE" } ]
};
var edgeColorMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "#ff9900" }, { attrValue: "promotes", value: "#0099ff" } ]
};
var edgeArrowMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "arrow" }, { attrValue: "promotes", value: "delta" } ]
};
var edgeTooltipMapper = {
attrName: "type",
entries: [ { attrValue: "has_motif", value: "" }, { attrValue: "promotes", value: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}" } ]
};
};
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},
},
nodes: {
nodes: {
label: { passthroughMapper: { attrName: "id" } },
//label: { passthroughMapper: { attrName: "id" } },
//tooltipText: "<b>TF: ${id}</b><br />Motif: ${motif}",
tooltipText: "<b>${type}: ${label}</b>",
tooltipText: { defaultValue: "<b>TF: ${id}</b><br />Motif: ${motif}", discreteMapper: tooltipMapper },
shape: { defaultValue: "ellipse", discreteMapper: shapeMapper },
shape: "ellipse",
borderWidth: 1,
borderWidth: 1,
borderColor: "#000000",
borderColor: "#000000",
size: 30,
size: 30,
color: "#ff9900",
//color: "#ff9900",
color: { defaultValue: "#ff9900", discreteMapper: colorMapper },
color: { defaultValue: "#ff9900", discreteMapper: colorMapper },
//opacity: 0.8,
//opacity: 0.8,
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},
},
edges: {
edges: {
width: { passthroughMapper: { attrName: "zscore" } },
width: { defaultValue: 5, passthroughMapper: { attrName: "zscore" } },
label: { passthroughMapper: { attrName: "id" } },
label: { passthroughMapper: { attrName: "promoter" } },
tooltipText: "<b>Promoter: ${id}</b><br />Z-Score: ${zscore}",
//tooltipText: "<b>Promoter: ${promoter}</b><br />Z-Score: ${zscore}",
color: "#011e59",
tooltipText: { defaultValue: "", discreteMapper: edgeTooltipMapper },
//color: { defaultValue: "#011e59", discreteMapper: edgeColorMapper },
//color: "#011e59",
//targetArrowShape: { defaultValue: "delta", discreteMapper: edgeArrowMapper },
color: { defaultValue: "#011e59", discreteMapper: edgeColorMapper },
targetArrowShape: { defaultValue: "delta", discreteMapper: edgeArrowMapper },
sourceArrowShape: "",
sourceArrowShape: "",
labelGlowOpacity: 0.8,
labelGlowOpacity: 0.8,

Latest revision as of 12:57, 8 May 2012

FF:10717-109I6, TF to Motif to TF network

Mouseover nodes and edges to see attributes. Motifs are shown in orange, TFs are shown in blue. Promoter and z-score are attributes of the Motif to TF edges (blue arrow). TF to Motif edges are shown in orange.

Motifs shown are the top (maximum 30) motifs in the sample. TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample. Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).

Cytoscape Web will replace the contents of this div with your graph.

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