Date post: | 20-Dec-2015 |
Category: |
Documents |
View: | 214 times |
Download: | 0 times |
The Metabolic Network
• From Palsson’s group• 1075 reactions and 7
62 compounds
Reaction type Number of reactions
The BIOMASS reaction (biomass)
1
Exchange reaction (ex_rct)
143
Metabolic reaction (meta_rct)
802
Single-compound transport (trans_1)
16
Facilitated (mixed) transport (trans_n)
113
The Mostly Connected Nodes
Node Degree
co2[c] 60
Nadh[c] 71
ppi[c] 74
nad[c] 76
h[e] 115
adp[c] 142
pi[c] 148
atp[c] 175
h2o[c] 292
h[c] 496
Using the objective function proposed by Palsson’s group: H[c] is the only compound whose free drainage increases biomass production significantly.
Compounds removed are: Atp, adp, nad, nadh, nadp, nadph, ppi, co2, fe2, h, h2o, k, na, nh4, pi, so4, and all other external compounds which have single-transport reaction.
Loop-Finding Algorithm
• Breadth-first search in Matlab
• A 2-compound loop is composed of two metabolites and two reactions, in the form of C1R1C2R2C1.
• A loop has directionality. C1R1C2R2C1 and C1R1C2R2C1 are considered to be two distinct loop.
Loops of Different SizesLoop type Number of this type
2R2C 820
3R3C 340
4R4C 1587
5R5C 5905
6R6C 30281
7R7C 163290
Loop type Number of this type
3R3C 24
4R4C 35
5R5C 29
6R6C 36
7R7C 29
Count of loops increases sharply as more compounds are allowed to be included.
If all connections which make up 2-compound loops are removed, the number of larger loops reduces dramatically.
Most Frequently Observed 2-Compound Pairs
• Many of the 2R2C loops have exactly the same set of 2C. For the 820 2R2C loops, 128 unique compound pairs are identified.
1st compound
2nd compound
Freq Diff
Glu-L[c] Akg[c] 215 H4N1O-1
Coa[c] Accoa[c] 177 C-2H-2O-1
Mqn8[c] Mql8[c] 60 H-2
Q8h2[c] Q8[c] 55 H2
2dmmq8[c]
2dmmql8[c]
25 H-2
Succ[c] Succ[e] 18
Pyr[c] Pep[c] 15 H1O-3P-1
Glu-L[c] Gln-L[c] 12 H-2N-1O1
Gtp[c] Gdp[c] 10 O3P1
Trodx[c] Trdrd[c] 9 H-2
Co-activation of Reactions in 2R2C Loop
• The conditions tested are Glc_aer, ac_aer, akg_aer, glyc_aer, lac-D_aer, lac-L_aer, mal-L_aer, pyr_aer, succ_aer, and glc_ana, where aer stands for aerobic and ana for anaerobic.
Type (by reactions activated)
Number of loops
All-0 216
All-2 153
Some 2 and some 0 8
Some 1 443
Classification of Connectivities of 2R2C Elements
• Order all the loop in the format of CRCR. 1connected; 0not connected to other components in the network.
• The majority (624 out of 820) have all component nodes connected.
Type Number of loops
0101 1 (1)
1000 / 0010 3 (3)
1001 / 0110 2 (2)
1010 39 (34)
1011 / 1110 142 (31)
1100 / 0011 1 (1)
1101 / 0111 8 (8)
1111 624 (65)