Table 1.

List of Evidence for Putative Indirect Interactions Used for Simulation Tests

No.MutationResulting Changes
1Off (AGO10)Up (miR165), down (REV)
2On (AGO10)Up (REV)
3Off (AGO7)Unchanged (FIL), up (ARF4, ETT)
4Off (AS1)Unchanged (FIL), up (ETT)
5off( AS2)Up (ETT, FIL)
6On (AS2)Down (FIL)
7Off (AS2, AGO10)Up (miR165), down (REV)
8Off (AS1, AGO7)Up (FIL)
9Off (AS2, AGO7)Up (miR165, FIL), down (REV)
10Off (ANT, FIL)Down (REV)
11Off (TAS3siRNA)Up (ETT, ARF4)
12Off (AS1, TAS3siRNA)Down (REV), up (miR165)
13Off (AS2, TAS3siRNA)Down (REV), up (miR165, FIL)
14On (AUXIN)Down (CK), up (IPT5)
15Off (KAN1)Up (REV)
16On (KAN1)Down (REV)
17On (miR165)Down (AGO10), up (ETT, ARF4)
18On (REV)Down (FIL, KAN1), up (AS2)
19On (CK)Up (AS1)
20On (FIL)Down (AS2)
  • The 20 mutations tested are listed. “On” designates the ectopic expression of an element, whereas “off” designates the loss of function. The element(s) mutated is (are) given in parentheses after the type of mutation (on or off). The resulting changes are indicated: down when the element was downregulated, up when it was upregulated, and unchanged when it was unchanged following the mutation. Altogether, these tests summarize 37 indirect interactions since a mutation can affect the state of several genes (elements). A test is validated if, for at least one steady configuration of the mutated network, the genes at the right side of the evidence list are regulated as expected (i.e., as reported by experimental evidence).