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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.