(Adds details, analyst comments; updates shares)

May 22 (Reuters) - Isis Pharmaceuticals Inc said its experimental blood thinner was more effective than a commonly prescribed anticoagulant in patients undergoing total knee replacement surgery.

The company's shares rose as much as 5 percent in early trading on the Nasdaq.

Isis said patients treated with a 300 mg dose of the drug, ISIS-FXIRx, experienced a significantly lower incidence of blood clots in their veins, compared with patients given the approved anticoagulant, enoxaparin, in a mid-stage trial.

Patients receiving Isis's treatment also experienced lower rates of bleeding, the biotechnology company said on Thursday.

The reduced bleeding rate could offer an advantage over existing therapies, Deutsche Bank analysts wrote in a note.

The treatment was developed using Isis's "antisense" technology, which helps a compound bind to a specific gene to interrupt the production of disease-causing proteins.

ISIS-FXIRx targets Factor XI, a clotting factor produced in the liver. High levels of Factor XI raises the risk of thrombosis, a condition where abnormal blood clot formation could lead to heart attacks and strokes.

The trial was evaluating 200 mg and 300 mg doses of Isis's treatment against enoxaparin in 300 patients. The smaller dose failed to show any significant benefit over enoxaparin.

"Due to the potential breadth of use as an anticoagulant, we expect Isis will partner this program within the next year," Deutsche Bank analysts wrote.

Isis is developing 32 other drugs to treat a number of diseases. The company's cholesterol drug, Kynamro, is sold by partner Genzyme Corp, a unit of French drugmaker Sanofi SA .

Carlsbad, California-based Isis's shares were up 4 percent at $24.14.

(Reporting by Natalie Grover in Bangalore; Editing by Savio D'Souza and Kirti Pandey)