USD/JPY is the amount of JPY exchanged for one USD. The US dollar is issued by the United States; Federal Reserve policy, US economic conditions and its role in global trade and finance shape demand.
Comparing charts on this board
A rising USD/JPY line means more yen are required for one dollar: dollar strength and yen weakness. The same chart color as a stock gain does not mean the yen is appreciating. Yen appreciation corresponds to a lower USD/JPY quote; establishing that direction prevents mistakes when currencies and equities share a board.
A yen-based valuation of a US stock has two components: its dollar price and the dollar-to-yen exchange rate. Approximately, multiply the stock-price factor by the exchange-rate factor. A stock gain can therefore be reduced in yen terms by yen appreciation. Keep those layers separate, and do not attribute a Japanese company's share-price move to exchange rates alone.
Related charts: S&P 500 · Nikkei 225 · S&P 500 ETF JPY
Official references: Exchange-rate conventions