There is currently a debate over the existence of claimed statistical anomalies in the cosmic microwave background (CMB), recently confirmed in Planck data. Recent work has focussed on methods for measuring statistical significance, on masks and on secondary anisotropies as potential causes of the anomalies. We investigate simultaneously the method for accounting for masked regions and the foreground integrated Sachs-Wolfe (ISW) signal. We search for trends in different years of WMAP CMB data with different mask treatments. We reconstruct the ISW field due to the 2 Micron All-Sky Survey (2MASS) and the NRAO VLA Sky Survey (NVSS) up to l=5, and we focus on the Axis of Evil (AoE) statistic and even/odd mirror parity, both of which search for preferred axes in the Universe. We find that removing the ISW reduces the significance of these anomalies in WMAP data, though this does not exclude the possibility of exotic physics. In the spirit of reproducible research, all reconstructed maps and codes will be made available for download at http://www.cosmostat.org/anomaliesCMB.html .