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Functional categorization of Daphnia magna genes responding to acute ibuprofen exposure |
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| Process |
Functional category |
Induced |
Suppressed |
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| 1 Metabolism |
1.1 Carbohydrate metabolism |
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| Glycolysis/Gluconeogenesis (PATH:00010) |
Eno |
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| Fructose and mannose metabolism (PATH:00051) |
MANA |
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| Starch and sucrose metabolism (PATH:00500) |
AmyA, GlyPa |
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| 1.2 Energy metabolism |
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| Oxidative phosphorylation (PATH:000190) |
atpBb, CYTB, RISP |
ANT, CO1c, CO2c, ND4d |
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| 1.3 Lipid metabolism |
GM2AP |
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| Glycerolipid metabolism (PATH:00561) |
Lip |
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| Eicosanoid metabolism (PATH:00590) |
Ltb4dh |
GPXe |
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| 1.4 Amino acid metabolism |
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| Cysteine metabolism (PATH:00272) |
Sult1C |
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| 1.5 Metabolisms of co-factors and vitamins |
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| Nicotinate and nicotinamide metabolism (PATH:000760) |
Nt5f |
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| 1.6 Polypeptide metabolism (proteolysis) |
BPTI |
Spint |
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| Peptidases |
CATL1, CPA2, Ctrb2, SC1, Try |
ASTL, SP |
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| 2 Genetic information processing |
2.1 Transcription |
Ubn, H4 |
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| 2.2 Translation |
DEADc, Sep15 |
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| 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 |
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| 2.3 Chaperones and folding catalysts |
HSP20, UBQ |
PDI |
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| 3 Environmental information processing |
3.1 Membrane transport |
Inx2 |
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| 3.2 Signal transduction |
Ptn, Reep5 |
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| MAPK signaling pathway (PATH:04010) |
HSP70g |
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| Calcium signaling pathway (PATH:04020) |
VDAC2 |
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| Wnt signaling pathway (PATH:04310) |
RhoAh |
CTBPi, Skp1j |
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| 3.3 Signaling molecules and interaction |
CNTN1 |
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| 3.4 Sensory system |
A10 |
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| 4 Cellular processes |
4.1 Cell motility |
MRLC2, Tm1 |
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| 4.2 Cell communication (PATH:01430) |
Relnk |
Acth |
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| 4.3 Endocrine system |
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| PPAR signaling pathway (PATH:03320) |
FABP3 |
ACSl |
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| Oogenesis (vitellogenesis and oocyte maturation) maturation) |
DmagVTG1 |
JHE, LPD_N, VMO1 |
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| Moulting |
Chtm, ChtBD2, Gasp, LPCP29, Peritrophin-A |
cap-2, ChtBD4, CP7, DD5, PCP16.7 |
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| 4.4 Immune system |
CLECT, CUB, GNBP |
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| 4.5 Inorganic ion transport and metabolism |
AT1A, CRIP, Fer, Fer1HCH, dmHb2, VGCa |
dmHb1, Sfat, Znf_AN1 |
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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. | |||
Heckmann et al. Genome Biology 2008 9:R40 doi:10.1186/gb-2008-9-2-r40 |
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