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Table 1 Classification of contributions to the inconsistency vector ( bottleneck; BN, invisible path; IP, chain disruptor; CD, close to input layer; CIL, close to output layer; COL, SIaa; Additional file 2 , SIcarb; Additional file 3 , SIlip; Additional file 4 , SIvit; Additional file 5 )

From: A network perspective on metabolic inconsistency

Contributor Category Topological class Biological interpretation Reference
AATAi** unspecific BN; IP 2-Aminoadipate transaminase;one out of two 2-oxoadipate producing reactions; missing GPR assoc. in all precursors. SIaa, B1
PROD2* unspecific CD; CIL Proline dehydrogenase; participates in a cycle that converts nadh to fadh2 (Figure 6); not expressed (Figure S5b). SIaa, D3
DPMVDx unspecific CD Diphosphomevalonate decarboxylase; essential step in the cholesterol biosynthesis pathway; not expressed; wrong or missing GPR assoc. (Figure S5c). SIlip, B5
GLYK unspecific CIL Glycerol kinase; not expressed in control and LIG, indicating that glycerol (provided in the in silico medium) might not be available as a in vivo medium component; slightly elevated expression levels in LIG (see Figure S5i). SIlip, E5
PHETHPTOX2 unspecific CIL Phenylalanine 4-monooxygenase; converts phenylalanine (provided in the in silico medium) into tyrosine (not provided in the in silico medium); the high unspecific contribution strength indicates that tyrosine might be available as an in vivo medium component. SIaa, A5
34HPPOR*** unspecific CD; CIL 4-Hydroxyphenylpyruvate dioxygenase; involed in tryosine to fumarate and acetoacetate conversion; not expressed (see Figure S5m). SIaa, B5
FUMtm unspecific — Fumarate transport (cytosol/mitochondria); expression just below threshold (see Figure S5o). no map
GLUTCOADHm** specific CD Glutaryl-CoA dehydrogenase; involved in the 2-oxoadipate pathway (see Figure S5); elevated expression levels in LIG (see Figure S6a). SIaa, A2
PDHm specific BN Pyruvate dehydrogenase; entry point to the TCA cycle; elevated expression levels in LIG (see Figure S6c). SIcarb, C3
MMEm specific CD Methylmalonyl-CoA epimerase; involved in isoleucine degradation; slightly elevated expression levels in LIG (see Figure S6d). SIaa, D1–E1
MEVK1x specific CD Mevalonate kinase; an essential step in cholesterol biosynthesis; decreased expression levels in LIG and HIG (see Figure S6e). SIlip, B5
G6PDH(1,2)rer specific – Glucose-6-phosphate dehydrogenase; slightly elevated expression levels in LIG (see Figure S6f). SIcarb, C4–D4
DHCR71r specific CD; COL 7-Dehydrocholesterol reductase; involved in cholesterol biosynthesis; slightly elevated expression levels in LIG (see Figure S6g). SIlip, A4
HEX1 specific CD; CIL Hexokinase; first step in glycolysis; slightly elevated expression levels in LIG (see Figure S6h). SIcarb, C4–C5
SQLEr specific CD Squalene epoxidase; decreased expression levels in LIG and HIG (see Figure S6i). SIlip, A5
  1. *Proline cycle issue; see Figure6.
  2. **2-Oxoadipate issue; see Figure7.
  3. ***Tyrosine path to fumarate and acetoacetate issue; see Figure S4 and Text S1.
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BMC Systems Biology

ISSN: 1752-0509

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