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Table 6 Upstream candidates of a list of metabolites participating in glycolysis a

From: Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism

Upstream regulatory candidatesb

Official symbol

Full name

Main GO process

 

Enzymes

TPI

Triose-phosphate isomerase 1

Carbohydrate metabolic process

PC

Pyruvate carboxylase

Carbohydrate metabolic process

GCK

Glucokinase (hexokinase)

Carbohydrate metabolic process

G6PC

Glucose-6-phosphatase

Carbohydrate metabolic process

GPI

Glucose-6 phosphate isomerase

Carbohydrate metabolic process

AKR1B1

Aldose reductase

Carbohydrate metabolic process

SDS

Serine dehydratase

Gluconeogenesis

GBA

Glucosidase

Carbohydrate metabolic process

GNPDA1

Glucosamine-6-phosphate deaminase

Carbohydrate metabolic process

AK1

Adenylate kinase

ATP metabolic process

CAT

Catalase

Cellular response to growth factor stimulus

 

Protein binding

SLC2A2

Facilitated glucose transporter member 2 (GLUT2)

Carbohydrate metabolic process

SLC2A4

Facilitated glucose transporter member 4 (GLUT4)

Carbohydrate metabolic process

HSPA5

heat shock 70 kDa protein 5 (glucose-regulated protein)

activation of signaling protein activity involved in unfolded protein response

GRIN1

Glutamate receptor

Calcium ion transport

WSF1

Wolfram syndrome 1

Calcium ion homeostasis, glucose homeostasis

BCL2

B-cell CLL/lymphoma 2

B-cell homeostasis

 

Integration points

MAPK8

Mitogen-activated protein kinase 8 (JNK1)

JNK cascade

MAP3K7

Mitogen-activated protein kinase kinase kinase 7

Activation of MAPK activity; JNK cascade

 

Transcription factor binding

DDIT3

DNA damage inducible transcript 3

Negative regulation of transcription, DNA-dependent; activation of signaling protein activity involved in unfolded protein response

XBP1

X-box binding protein

Activation of signaling protein activity involved in unfolded protein response

  1. aThe input target list included the 7 metabolites in the successive steps of the glycolytic pathway in mammalian cells[32]: Glucose; Glucose-6-phosphate; D-fructose-6-phosphate; Fructose-1,6-biphosphate-1; D-glyceraldehyde-3-phosphate; Phosphoenol-pyruvate and Pyruvate. They were supposed to have an increased abundance (i.e., a positive sign) in the situation tested.
  2. bThe regulatory candidates were proposed from the confrontation of the target list to encyclopedic information within a causality graph. Gene ontology (GO) terms for biological process and function were then associated.
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BMC Systems Biology

ISSN: 1752-0509

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