Skip to main content

Table 1 Functional categorization of Daphnia magna genes responding to acute ibuprofen exposure

From: Systems biology meets stress ecology: linking molecular and organismal stress responses in Daphnia magna

Process

Functional category

Induced

Suppressed

1 Metabolism

1.1 Carbohydrate metabolism

  
 

   Glycolysis/Gluconeogenesis (PATH:00010)

Eno

 
 

   Fructose and mannose metabolism (PATH:00051)

MANA

 
 

   Starch and sucrose metabolism (PATH:00500)

AmyA, GlyPa

 
 

1.2 Energy metabolism

  
 

   Oxidative phosphorylation (PATH:000190)

atpBb, CYTB, RISP

ANT, CO1c, CO2c, ND4d

 

1.3 Lipid metabolism

GM2AP

 
 

   Glycerolipid metabolism (PATH:00561)

Lip

 
 

   Eicosanoid metabolism (PATH:00590)

Ltb4dh

GPX e

 

1.4 Amino acid metabolism

  
 

   Cysteine metabolism (PATH:00272)

Sult1C

 
 

1.5 Metabolisms of co-factors and vitamins

  
 

   Nicotinate and nicotinamide metabolism (PATH:000760)

 

Nt5 f

 

1.6 Polypeptide metabolism (proteolysis)

BPTI

Spint

 

   Peptidases

CATL1, CPA2, Ctrb2, SC1, Try

ASTL, SP

2 Genetic information processing

2.1 Transcription

 

Ubn, H4

 

2.2 Translation

DEADc, Sep15

 
 

   Ribosome (PATH:03010)

16S rRNA, 28S rRNA, RpL6, RpL14, RpL15, RpL28, RpL30, RpL38, RpS2, RpS3A, RpS4, RpS12, RpS20, RpS25, RpS30

RpL9, RpL22, RpL27, RpS10, RpS13, RpS17

 

2.3 Chaperones and folding catalysts

HSP20, UBQ

PDI

3 Environmental information processing

3.1 Membrane transport

Inx2

 
 

3.2 Signal transduction

Ptn, Reep5

 
 

   MAPK signaling pathway (PATH:04010)

HSP70 g

 
 

   Calcium signaling pathway (PATH:04020)

VDAC2

 
 

   Wnt signaling pathway (PATH:04310)

RhoA h

CTBPi, Skp1j

 

3.3 Signaling molecules and interaction

 

CNTN1

 

3.4 Sensory system

A10

 

4 Cellular processes

4.1 Cell motility

MRLC2, Tm1

 
 

4.2 Cell communication (PATH:01430)

Reln k

Act h

 

4.3 Endocrine system

  
 

   PPAR signaling pathway (PATH:03320)

FABP3

ACS l

 

   Oogenesis (vitellogenesis and oocyte maturation) maturation)

DmagVTG1

JHE, LPD_N, VMO1

 

   Moulting

Chtm, ChtBD2, Gasp, LPCP29, Peritrophin-A

cap-2, ChtBD4, CP7, DD5, PCP16.7

 

4.4 Immune system

 

CLECT, CUB, GNBP

 

4.5 Inorganic ion transport and metabolism

AT1A, CRIP, Fer, Fer1HCH, dmHb2, VGCa

dmHb1, Sfat, Znf_AN1

  1. Genes presented in bold are directly linked to a Kyoto Encyclopedia of Genes and Genomes pathway, whereas other genes are listed with their functional category or subcategory based on Gene Ontology (see Additional data file 2). aGlyP is also associated with the insulin signaling pathway (PATH:04910). batpB is also associated with the type III secretion system (PATH:03070), flagellar assembly (PATH:02040), and epithelial cell signaling in Helicobacter pylori infection (PATH:05120). cCO1 and CO2 are also associated with the vascular endothelial growth factor signaling pathway (PATH:04370). dND4 is also associated with ubiquinone biosynthesis (PATH:00130). eGPX is also associated with glutathione metabolism (PATH:00480). fNt5 is also associated with purine metabolism (PATH:00230) and pyrimidine metabolism (PATH:00240). gHSP70 is also associated with antigen processing and presentation (PATH:004612) related to the immune system. hAct and RhoA are involved in eight and nine different pathways, respectively. Here they have been associated with one that is already represented, but because of this multi-alignment they have not been considered any further. iCTBP is also associated with the notch signaling pathway (PATH:04330). jSkp1 is also associated with the cell cycle (PATH:04110), ubiquitin-mediated proteolysis (PATH:04120), and transforming growth factor-β signaling pathway (PATH:04350), which all interlink through the Wnt signaling pathway. kReln is also associated with focal adhesion (PATH:04510) and extracellular matrix receptor interaction (PATH:04512). lACS is also associated with the adipocytokine signaling pathway (PATH:04920) and fatty acid metabolism (PATH:00071). mAlthough related to aminosugars metabolism (PATH:00530), Cht has been categorized with moulting because of the key role of the encoded enzyme (chitinase) in this process among arthropods. Full gene names are available in Additional data file 1. PPAR, peroxisome proliferator-activated receptor.
Back to article page

Genome Biology

ISSN: 1474-760X

Contact us