Table 1.

Genes regulated by CR across five or more tissue types. Genes were identified based upon comparative analysis of thirteen microarray experiments that collectively evaluated the effects of CR in ten different mouse tissues (liver, heart, muscle, white adipose tissue, hypothalamus, hippocampus, colon, lung, kidney and cochlea) (Swindell, 2008). Each CR-regulated gene was identified based upon experimental data linked to a specific Affymetrix Mouse Genome 430 2.0 probeset. The identifier associated with that probeset is listed in the table below along with a gene symbol and description generated from the NetAffyx database in January 2008 (Liu et al., 2003). Groups of co-expressed genes are identified in footnotes, with significantly overrepresented transcription factor binding sites listed below the table. Overrepresented binding sites were identified based upon sequence analysis of the 500 bp upstream promoter region using the CisView database (Sharov et al., 2006). Descriptions of each binding site are available online (see: http://lgsun.grc.nia.nih.gov/cisview/).

Gene Symbol	Affymetrix Identifier	Description
CR-Downregulated
H2-AaA	1452431_s_at	Histocompatibility 2, class II antigen A, alpha
Cd74A	1425519_a_at	CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated). Receptor for macrophage migration inhibitory factor (MIF) (Leng et al., 2003).
TgtpA	1449009_at	T-cell specific GTPase
Ifi27A	1426278_at	Interferon, alpha-inducible protein 27
Col3alB	1427884_at	Procollagen, type III, alpha 1
Col1a1B	1423669_at	Procollagen, type I, alpha 1
Serpinh1B	1450843_a_at	Serine (or cysteine) peptidase inhibitor, clade H, member 1
Ccl9	1417936_at	Chemokine (C-C motif) ligand 9
Ifitm3	1423754_at	Interferon induced transmembrane protein 3
Gng11	1448942_at	Guanine nucleotide binding protein (G protein), gamma 11
C1qb	1417063_at	Complement component 1, q subcomponent, beta polypeptide
Hsp110	1425993_a_at	Heat shock protein 110
CR-Upregulated
Mt1C	1422557_s_at	Metallothionein 1
Mt2C	1428942_at	Metallothionein 2
Per1	1449851_at	Period homolog 1 (Drosophila)
Per2	1417602_at	Period homolog 2 (Drosophila)
Ppara	1449051_at	Peroxisome proliferator activated receptor alpha
Peci	1431012_a_at	Peroxisomal delta3, delta2-enoyl-Coenzyme A isomerase
Sult1a1	1427345_a_at	Sulfotransferase family 1A, phenol-preferring, member 1
MGI: 1924575	1436316_at	RIKEN cDNA 9430029L20 gene
Ddit4	1428306_at	DNA-damage-inducible transcript 4
Nfkbia	1449731_s_at	Nuclear factor of kappa light chain gene enhancer in B-cells inhibitor, alpha. Inhibitor of NF-κB DNA binding (Arenzana-Seisdedos et al., 1995)
Fkpb5	1416125_at	FK506 binding protein 5
Rbm3simD	1422660_at	Similar to RNA binding motif protein 3
Pim3	1451069_at	Proviral integration site 3
Tspan4	1448276_at	Tetraspanin 4
Cdkn1a	1421679_a_at	Cyclin-dependent kinase inhibitor 1A (P21)
Pnpla2	1428143_a_at	Patatin-like phospholipase domain containing 2

^AImmunity Group. Note that H2-Aa is an updated annotation and was previously H2-Ea in Swindell (2008). Promoter anlaysis identified five significantly overrepresented transcription factor binding sites that were present in the promoter regions of H2-Aa, Cd74, Tgtp and Ift27 (ADD_PAX8, TF_NFY, TF_MAZR, TF_MZF, MIT_013LEF) (P < 0.05).

^BCollagen Group. For most analyses, since two transcripts were associated with Col3a1, expression values associated with both transcripts were averaged. Promoter anlaysis identified five significantly overrepresented transcription factor binding sites that were present in the promoter regions of genes in this module (TF_MAF, TF_MYB, TF_MEIS, TF_NFKB) (P < 0.004).

^CMetallothioneins. Promoter anlaysis identified twelve significantly overrepresented transcription factor binding sites that were present in the promoter regions of genes in this module (TF_MIF, TF_STAT, TF_ZIC, TF_HEN1, TF_HNF4, TF_SREBP, TF_OLF1, ADD_MTF1A, ADD_MTF1B, MIT_051TATA, TF_MYB, ADD_PAX8) (P < 0.04).

^DRbm3sim is an unofficial gene symbol for LOC100043257. Updated from Swindell (2008).