Exhaustive Analysis of the Modular Structure of the Spliceosomal Assembly Network: A Petri Net Approach - Biological Petri Nets - page 267

Table 2
Maximal common transition sets (MCTS) as determined from the 71 T-invariants that cover the network

MCTS Transition IDs T-Invariant IDs Biological Interpretation

ID ID # % ID # %

1 t0, t1 2 1.24 i13-i18, i23-i26, i29-i32, i35-

i40, i44-i47, i50-i53, i56-i59,
i64-i71

40 56.34 Recognition of 3'ss by U2AF35

2 t3, t7, t11, t18-t21, t26,

t42, t44-t54, t68-t72,
t86, t87, t93, t96-t98,
t104-t106, t110, t111,
t113, t114, t118-t129,
t144, t145, t150, t151

54 33.54 i13-i40, i44-i71 56 78.87 Branch point definition, 15S U2

snRNP assembly, SF3a formation,
partial SF3b formation, U5-and
U6-maturation, CypH trimer for-
mation, ATP-in-ADP-efflux

3 t4-t6 3 1.86 i13-i18, i21-i26, i29-i32, i35-

i40, i44-i47, i50-i53, i56-i61,
i64-i71

44 61.97 U2AF dimerization

4 t8, t23, t57, t158, t159 5 3.11 i13-i18, i23-i26, i29-i32, i35-

i38, i44-i47, i50-i53, i56-i59,
i64-i69

36 50.70 Reactions of U2 snRNP remod-
eling variant 1, involving hPrp43
and UAP56

5 t9, t12, t141-t143 5 3.11 i15-i20, i62-i67 12 16.90 ASF phosphorylation and 5'ss def-

inition via ASF/U1 snRNP/TIA1
interactions

6 t10, t137-t139 4 2.48 i21-i26, i56-i61 12 16.90 5'Terminal 5'ss definition via U1

snRNP interactions with cap bind-
ing complex

7 t15, t24 2 1.24 i15-i18, i23-i26, i29-i32, i35-

i38, i44-i47, i50-i53, i56-i59,
i64-i67

32 45.07 FBP11 dependent U2 snRNP

binding to the branch point

8 t16, t31, t32 3 1.86 i13, i14, i68, i69 4 5.63 U1 snRNP independent 5'ss defi-

nition and A complex formation

9 t22, t109 2 1.24 i14, i16, i18, i20, i22, i24, i26,

i28, i30, i32, i34, i36, i38, i40,
i45, i47, i49, i51, i53, i55, i57,
i59, i61, i63, i65, i67, i69, i71

28 39.44 SF3b125 dependent 17S U2
snRNP maturation

10 t25, t27-t29, t55 5 3.11 i39, i40, i70, i71 4 5.63 U1/U2 snRNP bridging by Prp5

and simultaneous binding to 5'ss
and branch point

11 t33, t34, t133-t136 6 3.73 i15-i40, i44-i67, i70, i71 52 73.24 U1 snRNP maturation and

recycling

12 t35, t56, t152, t155 4 2.48 i19-i22, i27, i28, i33, i34, i48,

i49, i54, i55, i60-i63

16 22.54 U2AF independent A complex

formation

13 t36, t146, t147, t149 4 2.48 i7 1 1.41 U4 snRNP maturation and recycl-

ing

14 t58, t59 2 1.24 i15, i16, i25, i26, i31, i32, i37,

i38, i44, i45, i50, i51, i56, i57,
i66, i67

16 22.54 FBP11 supported U1 snRNP/SF1
binding and subsequent interac-
tion with U2AF bound PPT-3'ss

15 t60-t63 4 2.48 i3 1 1.41 PTB inhibitory pathway (without

t2.PPT in )

16 t65, t66 2 1.24 i41, i44-i71 29 40.85 NTC-complex formation and sta-

ble Prp19 integration

17 t76, t77, t81, t82, t84,

t85, t88-t92,

15 9.32 i13-i40 28 39.44 Prp16 dependent remodeling of

C-complex, 2nd catalytic step of
splicing, release of ligated exons
and disassembly of postspliceoso-
mal complex

t94, t95,

t101, t160