How to access the parentNode of a selection to raise an element?

A D3 selection is just a double-array wrapped around the element(s) selected. As you found with p3, you can dereference the arrays to find your first node, if you want. However, a better method does exist:

From the docs for selection.node():

Returns the first non-null element in the current selection. If the selection is empty, returns null.

In your case:

var dad = current_gene_pcp.node().parentNode;

However, if you don't need the line other than the DOM handle, you might as well just get that directly:

// Search document-wide...
var dad = document.querySelector(".line[name=" + current_gene_name + "]");

// ...or only as a child of the current DOM element
var dad = this.querySelector(".line[name=" + current_gene_name + "]");

Here's a quick way to move the mouseover element to the front:

selection.on("mouseover", function() { this.parentNode.appendChild(this); });

See also a related thread in the d3-js group.