PCIe signal frequencies: 

Gen 1: 2.5GT/s (8/10 encoding) 80% efficient. Clock rate is 1/2 of datarate, so 1.25GHz

Gen 2: 5.0GT/s (8/10 encoding) 80% efficient. Clock rate is 1/2 of datarate, so 2.5GH

Gen 3: 8.0GT/s (128/130b encoding) (98% efficient). Clock rate is 1/2 of datarate, so 4.0GHz