28 Genes with Significantly Altered Expression Patterns in Rat Liver
Treated with RDX Perturbation


**Data Mining and Knowledge Discovery in Toxicogenomics Datasets**

Gene Number Gene Symbol and Name Low Dose High Dose Possible Relavent Function More Information on Role or Phenotype
1 Scd1,
(Stearoyl-Coenzyme A desaturase 1)
Up Down Essential for epidermal integrity and Notch-mediated signaling.
2 Marveld1,
(MARVEL domain containing 1)
Down Down
  • Proteins are expected to localize in various compartments (nucleus, integral to membrane). testis, kidney bladder and liver.
  • The reduced expression is owing to DNA methylation and could be reversed by pharmacologic demethylation.
No known phenotype yet in human, but down-regulated in primary multiple tumors derived from ovary, vulva, uterus, cervix, breast, testis, kidney bladder and liver.

Check NCBI on MARVEL1
3 Pir, pirin
(iron-binding nuclear protein).
Down Down Pirin functions as a co-factor for NFI/CTF1 and Bcl-3, implicating it in DNA replication, transcriptional activation, and apoptosis.

Check GeneCards for Detail
4 Usp2,
(ubiquitin specific peptidase 2).
Up Up Involved in the regulation of intracellular protein breakdown, cell cycle regulation, and stress response.

USP2 in wikigenes.
5 Hamp,
(hepcidin antimicrobial peptide).
Up Up The HAMP gene provides instructions for the production of a protein called hepcidin, hepcidin plays a major role in maintaining iron balance in the body.

Hamp Wiki
6 Por,
(P450 (cytochrome) oxidoreductase).

We like this gene !
Up Up The electron donor protein for several oxygenase enzymes found on the endoplasmic reticulum of most eukaryotic cells.
NCBI GeneReview on Por
7 Aldh1a1,
(aldehyde dehydrogenase family 1, subfamily A1).
Up Up
  • Oxidoreductase activity.
  • GO:0042493 --- Response to drug.
  • GO:0006979 --- Response to oxidative stress.
Aldehyde dehydrogenase is the second enzyme of the major oxidative pathway of alcohol metabolism. Two major liver isoforms of this enzyme, cytosolic and mitochondrial, can be distinguished by their electrophoretic mobilities, kinetic properties, and subcellular localizations.

Aldh1a1 Wiki
8 Polg2 polymerase (DNA directed),gamma 2, accessory subunit. Up Up This gene encodes the processivity subunit of the mitochondrial DNA polymerase gamma. The encoded protein forms a heterotrimer containing one catalytic subunit and two processivity subunits.

Polg2 Wiki
9 Coq10b,
(coenzyme Q-binding protein).

We like this gene !
Up Up Most coenzyme Q (CoQ) exists freely in the mitochondrial membrane as a CoQ pool. Required for the function of coenzyme Q in the respiratory chain.

Coq10b in Wiki Gene
10 Mfsd2,
(major facilitator superfamily domain containing 2).
Up Up The encoded protein likely functions in efflux of organic anions, including the non-steroidal anti-inflammatory drugs indomethacin and diclofenac.

NCBI Human Mfsd2.
11 Edem1,
(ER degradation enhancer, mannosidase alpha-like 1).
Up Up Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER.

Deficiency of suppressor enhancer Lin12 1 like (SEL1L) in mice leads to systemic endoplasmic reticulum stress and embryonic lethality.
12 Cyp2b1,
(cytochrome P450, family 2, subfamily b, polypeptide 1).

We like this gene !
Up Up Cyp2b1 oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics.
13 Acsm2,
(acyl-CoA synthetase medium-chain family member 2).
Up Up Constitutes the rate-determining step in the pathway for the conjugation of most xenobiotics and therefore plays a role in detoxification, and is important for the intermediary metabolism of short- and medium-chain fatty acids.

NCBI AceView
14 Slc38a2,
(solute carrier family 38, member 2).
Up Up
  • Ion transport.
  • GO:0006814 --- Sodium ion transport.
  • GO:0015179 --- Amino acid transmembrane transporter activity.
  • GO:0016021 --- Integral to membrane.
Functions as a sodium-dependent amino acid transporter. Mediates the saturable, pH-sensitive and electrogenic cotransport of neutral amino acids and sodium ions with a stoichiometry of 1:1. May function in the transport of amino acids at the blood-brain barrier and in the supply of maternal nutrients to the fetus through the placenta.
15 Sds,
(serine dehydratase).
Up Up Sds is the serine dehydratase structural gene. Albino region deletions profoundly affect development and expression of some gluconeogenic enzymes, including Sds. In these deletion mice, Sds is expressed normally on the constitutive level, but fails to develop hormone-inducible expression.

Sds in iHOP
16 Tat,
(tyrosine aminotransferase).
Up Up This enzyme helps break down the amino acid tyrosine, a protein building block found in many foods. Tyrosine aminotransferase is the first in a series of five enzymes that converts tyrosine to smaller molecules, which are excreted by the kidneys or used in reactions that produce energy.

Tyrosine aminotransferase Wiki.
17 Zfp354a,
(zinc finger protein 354A).

We like this gene!
Up Up Amino acid sequence contains Kruppel-associated box (KRAB) A and B domains in the N terminus and Kruppel-type zinc finger motifs in the C terminus.

Zfp354a in WikiGenes.
18 Ubd,
(ubiquitin D).
Up Up
  • GO:0043123 --- Positive regulation of I-kappaB kinase/NF-kappaB cascade.
  • GO:0016567 --- Protein ubiquitination.
  • GO:0006511 --- Ubiquitin-dependent protein catabolic process.
Ubiquitin-like protein modifier which can be covalently attached to target protein and subsequently leads to their degradation by the 26S proteasome.

Ubd in WikiGenes
19 Aldh1a7,
(aldehyde dehydrogenase family 1, subfamily A7).
Up Up
  • GO:0018479 --- Benzaldehyde dehydrogenase (NAD+) activity.
  • GO:0016491 --- Oxidoreductase activity.
Aldh1a7 Protein type: Oxidoreductase Cellular Component: cytoplasm
Molecular Function: identical protein binding; aldehyde dehydrogenase (NAD) activity; 3-chloroallyl aldehyde dehydrogenase activity; benzaldehyde dehydrogenase (NAD+) activity; oxidoreductase activity
Biological Process: metabolic process; retinoic acid metabolic process; protein homotetramerization
Alt. Names/Synonyms: Ahd2-like; AI987940; AL1A7; Aldehyde dehydrogenase 1 (phenobarbitol inducible); Aldehyde dehydrogenase family 1 member A7; aldehyde dehydrogenase family 1, subfamily A4; aldehyde dehydrogenase family 1, subfamily A7; Aldehyde dehydrogenase phenobarbital-inducible; Aldehyde dehydrogenase, cytosolic 1; ALDH class 1; ALDH-E1; Aldh-pb; Aldh1a4; Aldh1a7; Aldhpb; ALHDII
Gene Symbols: Aldh1a7
Molecular weight: 54,588 Da.

Aldh1a7 in NCBI AceView
20 Nr0b2 (transcription factor),
(nuclear receptor subfamily 0, group B, member 2).
Up Up Acts as a negative regulator of receptor-dependent signaling pathways. Specifically inhibits transactivation of the nuclear receptor with whom it interacts.

NR0B2 is an orphan nuclear receptor.

We like this gene!
21 Igfbp1,
(insulin-like growth factor binding protein 1).
Up Up The protein binds both insulin-like growth factors (IGFs) I and II and circulates in the plasma. Binding of this protein prolongs the half-life of the IGFs and alters their interaction with cell surface receptors.
22 Tsku,
(tsukushin).
Up Up Tsukushi (TSK), a member of the secreted small leucine rich repeat proteoglycan family, functions as a key coordinator of multiple pathways outside of cells through the regulation of an extracellular signaling network.
23 Fmo5,
(flavin containing monooxygenase 5).
Up Up Flavin-containing monooxygenases are NADPH-dependent flavoenzymes that catalyzes the oxidation of soft nucleophilic heteroatom centers in drugs,pesticides, and xenobiotics.
24 LOC683460, (hypothetical protein). Up Up N/A N/A
25 LOC684871, (similar to Protein C8orf4 (Thyroid cancer protein 1) (TC-1)). Up Up N/A N/A

** Notes:***

(1) Genes with expression of at least 2 fold changes with confidence P-value < 0.05 are selected for further data mining.
(2) Three probe sets with no known annotation (13781811_at, 1372524_at, and 1380306_at) are also up regulated as well in RDX perturbation.



First setup on May 11, 2011, last updated by Dr. Jeff Chen on May 27, 2011.