  New physics in neutrino sector can reveal itself via non-standard neutrino
interactions which can result in modification of the standard picture of
neutrino propagation in matter. Experiments with atmospheric neutrinos has been
used to probe this scenario. Using publicly available three-year low energy
data in IceCube DeepCore we place bounds on the parameters
$\epsilon_{\alpha\beta}$ of non-standard neutrino interactions in propagation.
We obtain restrictive constraints not only for $\mu\tau$ sector but also for
flavor changing interactions involving electron neutrinos.
