Table 2.
Genes with significantly different renal expression in wild-type and RST knockout mice
| Locus | Description | Expression in WT, arbitrary units |
Ratio of Expression: KO/WT |
P | GO Molecular Function | GO Biological Process |
|---|---|---|---|---|---|---|
| Genes with decreased renal expression in KO compared with WT | ||||||
| Nr4a1 | Nuclear receptor subfamily 4, group A, member 1 | 7,585 | 0.23 | 4.60E-30 | Transcription factor | Apoptosis |
| Axud1 | AXIN1 upregulated 1 | 1,825 | 0.29 | 1.08E-09 | Apoptosis | |
| Gadd45g | Growth arrest and DNA-damage-inducible 45 gamma | 8,867 | 0.30 | 8.84E-26 | Protein binding | Apoptosis, development/differentiation |
| Gpaa1 | GPI anchor attachment protein 1 | 5,175 | 0.38 | 6.71E-17 | GPI anchor transamidase | Biosynthesis, GPI anchor |
| Ext1 | Exostoses (multiple) 1 | 2,235 | 0.45 | 8.58E-08 | Glycosyl transferase | Biosynthesis, proteoglycan |
| Gcnt1 | Glucosaminyl (N-acetyl) transferase 1, core 2 | 41,379 | 0.45 | 1.43E-16 | Glycosyl transferase | Biosynthesis, proteoglycan |
| Pkmyt1 | Protein kinase, membrane-associated tyrosine/threonine 1 | 1,651 | 0.37 | 5.27E-07 | Protein kinase | Cell cycle |
| Junb | Jun-B oncogene | 4,877 | 0.41 | 6.21E-15 | Transcription factor | Cell cycle |
| Fos | FBJ osteosarcoma oncogene | 5,386 | 0.13 | 1.33E-34 | Transcription factor | Cell cycle, development/differentiation |
| Jun | Jun oncogene | 10,829 | 0.38 | 2.97E-20 | Transcription factor | Cell cycle, development/differentiation |
| Per1 | Period homolog 1 (Drosophila) | 3,089 | 0.49 | 6.01E-09 | Transcription factor | Circadian rhythm |
| Plk3 | Polo-like kinase 3 (Drosophila) | 2,538 | 0.43 | 2.78E-09 | Protein kinase | Development/differentiation |
| Egr1 | Early growth response 1 | 4,0112 | 0.05 | 4.22E-53 | Transcription factor | Development/differentiation |
| Jarid2 | Jumonji, AT-rich interactive domain 2 | 2,749 | 0.49 | 4.62E-08 | Transcriptional repressor | Development/differentiation |
| Hbegf | Heparin-binding EGF-like growth factor | 3,615 | 0.45 | 2.89E-11 | Growth factor | Growth factor/cytokine signaling pathway |
| Tnfrsf9 | Tumor necrosis factor receptor superfamily, member 9 | 1,532 | 0.20 | 1.16E-09 | Receptor | Immune response |
| Pdk4 | Pyruvate dehydrogenase kinase, isoenzyme 4 | 4,895 | 0.49 | 4.34E-11 | Protein kinase | Metabolism, glucose |
| Zfp36 | Zinc finger protein 36 | 14,023 | 0.36 | 1.91E-22 | mRNA binding | mRNA catabolism |
| Sf1 | Splicing factor 1 | 2,165 | 0.45 | 1.53E-07 | mRNA binding | mRNA splicing |
| Fkbp5 | FK506 binding protein 5 | 2,563 | 0.25 | 2.83E-15 | Unfolded protein binding | Protein folding |
| Rabgap1 | RAB GTPase activating protein 1 | 2,136 | 0.31 | 6.96E-11 | GPCR activity | Signal transduction |
| Nrxn2 | Neurexin II | 2,680 | 0.34 | 9.24E-13 | Calcium channel regulator | Synaptic transmission |
| Slc22a12 | Solute carrier family 22 member 12 | 35,720 | 0.01 | 1.89E-57 | Transporter | Transport, organic anion |
| Atp4a | ATPase, H+/K+ exchanging, gastric, alpha polypeptide | 2,741 | 0.30 | 2.43E-14 | Transporter | Transport, inorganic cation transport |
| Nudt19 | Nudix-type motif 19 | 62,499 | 0.50 | 1.14E-13 | Hydrolase | |
| Ier2 | Immediate-early response 2 | 4,983 | 0.44 | 1.12E-13 | ||
| Malat 1 | Metastasis-associated lung adenocarcinoma transcript 1 | 5,497 | 0.49 | 1.57E-11 | ||
| Genes with increased renal expression in KO compared with WT | ||||||
| BC016495 | cDNA sequence BC016495 | 1,109 | 3.54 | 9.88E-21 | Protein kinase | Biosynthesis, pyrimidine nucleotide |
| Ccrk | Cell cycle-related kinase | 483 | 3.98 | 1.85E-11 | Protein kinase | Cell cycle |
| Rad9 | RAD9 homolog (S.pombe) | 1,130 | 2.09 | 1.61E-07 | Cell cycle | |
| Sema4b | Semaphorin 4B | 1,646 | 2.26 | 4.70E-12 | Receptor | Development/differentiation |
| Fen1 | Flap structure specific endonuclease 1 | 926 | 2.92 | 5.23E-13 | Endonuclease | DNA replication/repair |
| Cfd | Complement factor D (adipsin) | 940 | 5.99 | 2.67E-34 | Peptidase | Immune response |
| Ifi27 | Interferon, alpha-inducible protein 27 | 1,491 | 2.20 | 1.16E-10 | Immune response | |
| Car3 | Carbonic anhydrase 3 | 8,334 | 2.15 | 5.39E-16 | Carbonate dehydratase | Metabolism |
| Aldh1a7 | Aldehyde dehydrogenase family 1, subfamily A7 | 4,044 | 5.60 | 1.32E-41 | Oxidoreductase | Metabolism |
| Aldh1a1 | Aldehyde dehydrogenase family 1, subfamily A1 | 1,824 | 8.56 | 9.78E-48 | Oxidoreductase | Metabolism |
| Trf | Transferring | 727 | 2.59 | 6.47E-08 | Iron binding | Transport, iron |
| Pom121 | Nuclear pore membrane protein 121 | 4,845 | 2.06 | 4.49E-14 | Transporter | Transport, nucleocytoplasmic |
| Zdhhc12 | Zinc finger, DHHC domain containing 12 | 503 | 6.69 | 4.52E-26 | Acyltransferase | |
| Sdc4 | Syndecan 4 | 2,232 | 2.10 | 4.65E-12 | Cytoskeletal protein binding | |
| Col6a2 | Procollagen, type VI, alpha 2 | 1,419 | 2.05 | 1.26E-08 | Structural molecule | |
| Thrsp | Thyroid hormone responsive SPOT14 homolog | 660 | 3.59 | 1.60E-13 | ||
| cDNA sequence A230084D06 | 173 | 6.57 | 4.16E-07 | |||
A global comparison of renal gene expression in 3 each of wild-type (WT) and RST knockout (KO) mice was performed with high-density microarrays containing probes representing ~39,000 transcripts (Affymetrix MG 430 2.0 arrays). Genes with significantly different expression in WT and KO mice (as determined by Vampire; http://genome.ucsd.edu/microarray) and that were at least 2-fold increased or decreased are listed, along with their presumptive biological and molecular functions as annotated in the Gene Ontology (GO) database (www.geneontology.org). Genes with decreased expression in KO mice are presented first, followed by those with increased expression; within each group the lists are sorted by the GO biological process annotation.