NEW YORK — Gannett Co., the biggest newspaper publisher in the U.S., increased its CEO's pay package by nearly 41 percent last year, according to an Associated Press analysis of a regulatory filing yesterday.

Gannett — which owns USA Today and The Honolulu Advertiser — gave CEO Craig Dubow compensation valued at $4.4 million. That was up from $3.1 million the year before. However, it was far below the $7.4 million he got in 2007.

Gannett has weathered the advertising slump at its newspapers and television stations by cutting costs, eliminating more than 11,000 jobs in the past two years and streamlining its operations.

Gannett announced last month that it was selling The Advertiser to the owner of the Honolulu Star-Bulletin, a deal that could lead to hundreds of layoffs. In a conference call with investors yesterday, Gannett said the sale of The Advertiser will result in a gain. Gannett described the deal as "very attractive to us."

Last year, Dubow's base pay fell 19 percent to about $942,000, reflecting a voluntary cut he took starting in 2008 and a companywide program of furloughs and pay cuts Gannett put in place last year.

But Dubow, 55, got a bonus of about $1.5 million, up 66 percent from 2008. Among other factors, Gannett said, it took into account its earnings last year in setting the bonus.

Despite a 17 percent drop in revenue, Gannett earned $355.3 million in 2009. That followed a loss of $6.65 billion the year before, a figure that included write-downs to account for the falling value of its assets and charges for consolidating facilities such as printing plants.

Dubow also got stock and options valued at $1.8 million when they were granted, almost double what he got the year before. Other perks, including life insurance and 401(k) contributions, amounted to $173,850.

The Associated Press formula is designed to isolate the value the company's board placed on the executive's total compensation package during the last fiscal year. It includes salary, bonus, performance-related bonuses, perks, above-market returns on deferred compensation and the estimated value of stock options and awards granted during the year. The calculations don't include chang-es in the present value of pension benefits. And they sometimes differ from the totals companies list in the summary compensation table of proxy statements filed with the Securities and Exchange Commission, which reflect the size of the accounting charge taken for the executive's compensation in the previous fiscal year.

Dubow also is on the AP's board of directors.