Table 3

Significant probe sets identified by comparison of reciprocal congenic strains

Ratio of expression (iP vs P.NP and NP.P vs iNP)^a

Amygdala

Nucleus accumbens

Frontal cortex

Hippocampus

Caudate putamen

Combined regions

Probe set

Symbol

Gene title

vs. P.NP

NP.P vs. iNP

vs. P.NP

NP.P vs. iNP

vs. P.NP

NP.P vs. iNP

vs. P.NP

NP.P vs. iNP

vs. P.NP

NP.P vs. iNP

vs. P.NP

NP.P vs. iNP

1399134_at

LOC500054

similar to POT1-like telomere end-binding protein

-1.13

-1.11

-1.13

-1.11

-1.07

-1.18

-1.13

-1.22

-1.06

-1.07

-1.10

-1.14

1386777_at

LOC500054

similar to POT1-like telomere end-binding protein

-1.04

-1.13

-1.10

-1.35

-1.10

-1.21

-1.19

-1.29

-1.05

-1.11

-1.10

-1.21

1382865_at

Tsga14

testis specific gene A14

-1.06

-1.09

-1.13

-1.06

-1.05

-1.06

-1.11

-1.10

-1.00

-1.14

-1.07

-1.09

1382409_at

Tsga14

testis specific gene A14

-1.06

-1.12

-1.06

-1.16

-1.09

-1.02

-1.04

-1.08

-1.09

-1.01

-1.07

-1.08

1383828_at

Tsga13

EST-testis specific gene A13 (predicted)

-1.25

-1.32

-1.45

-1.25

-1.19

-1.26

-1.57

-1.21

-1.26

-1.13

-1.34

-1.23

1369895_s_at

Podxl

podocalyxin-like

1.04

-1.01

1.00

1.15

1.05

1.01

1.04

1.08

1.03

1.06

1.03

1.06

1378956_at

---

EST-similar to plexin A4

1.55

2.16

1.73

1.55

1.95

1.39

2.28

1.91

1.41

1389291_at

Chchd3

coiled-coil-helix-coiled-coil-helix domain containing 3

-1.09

-1.10

-1.06

-1.13

-1.06

-1.15

-1.11

-1.10

-1.05

-1.16

-1.08

-1.13

1378824_at

---

EST-4.8 Kb at 3' side of similar to solute carrier family 35, member B4

1.06

1.08

1.09

1.10

1.08

1.03

1.04

1.09

1.07

1.10

1367734_at

Akr1b1

aldo-keto reductase family 1, member B1

1.12

1.22

1.13

1.27

1.29

1.16

1.11

1.25

1.24

1.20

1.18

1395190_at

Akr1b10

aldo-keto reductase family 1, member B10

1.28

1.12

1.55

1.27

1.21

1.34

1.05

1.23

1.38

1.32

1.20

1382034_at

Akr1b10

aldo-keto reductase family 1, member B10

1.19

-1.02

-1.41

-1.08

1.09

-1.16

-1.17

-1.05

1.12

-1.02

-1.04

1383551_at

Bpgm

2,3-bisphosphoglycerate mutase

1.12

1.10

1.14

-1.07

1.13

1.16

1.14

1.15

1.10

1.13

1.09

1388544_at

Bpgm

2,3-bisphosphoglycerate mutase

1.09

1.08

1.10

1.11

1.14

1.10

1.13

1.08

1.06

1.10

1390042_at

Tmem140

transmembrane protein 140

1.21

1.32

1.38

1.24

1.14

1.13

1.11

1.14

1.27

1.06

1.22

1.18

1383598_at

Wdr91

WD repeat domain 91 (Wdr91)

1.33

1.34

1.30

1.47

1.27

1.50

1.23

1.46

1.26

1.41

1.25

1378125_at

---

EST-0.5 Kb at 3' side of similar to HSPC049 protein

1.32

1.28

1.46

1.22

1.35

1.32

1.42

1.24

1.42

1.31

1.40

1.27

1373746_at

Wdr91

WD repeat domain 91

-1.21

-1.09

-1.30

-1.14

-1.20

-1.13

-1.26

-1.14

-1.18

-1.23

-1.14

1373190_at

Cnot4

CCR4-NOT transcription complex, subunit 4

1.00

1.09

1.02

1.16

1.02

1.01

1.07

1.14

1.03

1.00

1.03

1.08

1388441_at

LOC689574

hypothetical protein LOC689574

-1.10

-1.03

1.02

-1.06

-1.05

-1.13

-1.08

-1.10

-1.04

-1.09

-1.05

-1.08

1377890_at

---

EST-4.9 Kb at 3' side of solute carrier family 13, member 4

1.17

1.50

1.22

1.34

1.16

1.30

1.14

1.23

1.19

1.18

1.31

1392510_at

Fam180a

family with sequence similarity 180, member A

1.22

1.49

1.78

1.43

1.13

1.08

1.15

1.24

1.08

1.11

1.25

1.26

1391721_at

---

EST-2.5 Kb at 5' side of cholinergic receptor, muscarinic 2

-1.55

-2.91

-1.82

-2.10

-1.71

-1.63

-1.88

-1.92

-1.67

1379480_at

Dgki

diacylglycerol kinase, iota

1.13

1.14

1.23

1.22

1.17

1.24

1.26

1.09

1.25

1.27

1.21

1.19

1395107_at

Dgki

EST-similar to diacylglycerol kinase iota

-1.02

1.04

-1.15

1.06

1.01

-1.01

1.10

1.16

-1.01

1.02

-1.01

1.05

1393410_at

---

EST-0.79 Kb at 5' side of similar to contactin associated protein-like 2 isoform a

1.00

-1.18

1.09

1.15

-1.09

-1.11

1.02

-1.06

1.03

1.00

1.01

-1.04

1390393_at

---

EST-5 Kb at 5' side of similar to contactin associated protein-like 2 isoform a

-1.08

-1.15

-1.01

1.01

-1.16

-1.21

-1.03

-1.12

-1.03

-1.07

-1.06

-1.11

1370007_at

Pdia4

protein disulfide isomerase associated 4

1.34

1.24

1.24

1.10

1.14

1.19

1.06

1.12

1.36

1.14

1.22

1.16

1397447_at

Zfp398

zinc finger protein 398

-1.04

-1.13

-1.08

-1.04

1.01

-1.04

-1.02

-1.06

1.01

-1.05

-1.04

1380094_a_at

Zfp212

zinc finger protein 212

1.22

1.30

1.21

1.28

1.15

1.43

1.29

1.16

1390625_at

RGD1304879

similar to zinc finger protein 398 (zinc finger DNA binding protein p52/p71)

1.43

1.40

1.27

1.39

1.33

1.20

1.30

1.36

1.46

1.22

1.36

1.31

1377600_at

Znf777

zinc finger protein 777

1.08

1.10

1.07

-1.00

1.09

1.12

1.13

1.08

1.03

1.10

1.08

1375914_at

Krba1

KRAB-A domain containing 1

-1.04

-1.07

1.04

-1.07

-1.02

-1.05

-1.14

-1.06

-1.12

-1.06

1371691_at

Rarres2

retinoic acid receptor responder (tazarotene induced) 2

-1.14

-1.01

1.12

-1.09

-1.16

-1.22

-1.23

-1.19

-1.01

-1.08

-1.08

-1.11

1376401_at

RGD1561107

EST-replication initiator 1

1.12

1.10

1.16

1.13

1.19

1.12

1.13

1.18

1.14

1.15

1.12

1382755_at

Tra2a

rranscribed locus

1.11

1.16

-1.13

-1.12

1.07

1.20

1.13

1.32

1.11

1.43

1.06

1.19

1387154_at

Npy

neuropeptide Y

-1.04

-1.19

-1.06

1.12

-1.11

-1.09

-1.14

-1.08

-1.05

-1.08

-1.07

1380062_at

Mpp6

membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)

1.02

1.00

1.03

-1.09

1.07

1.04

1.13

1.19

1.06

1.02

1.06

1.03

1383324_at

Mpp6

membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)

1.01

1.09

1.10

-1.01

1.11

1.12

1.10

1.20

1.06

1.09

1.07

1.10

1397419_at

Mpp6

membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)

-1.02

1.12

1.01

1.18

1.13

1.14

1.22

1.07

1.10

1.09

1.11

1397949_at

---

EST-similar to MAGUK p55 subfamily member 6

-1.00

1.13

1.16

1.06

1.15

1.18

1.15

1.20

1.07

1.12

1.10

1.14

1398627_at

---

EST- similar to MAGUK p55 subfamily member 6

-1.01

1.04

1.05

1.10

1.09

1.07

1.16

1.04

1.02

1.05

1.08

1384136_at

Osbpl3

oxysterol binding protein-like 3

-1.06

-1.03

-1.09

1.07

-1.15

-1.03

-1.12

-1.16

-1.15

-1.06

-1.11

-1.04

1378543_at

Hnrnpa2b1

EST-heterogeneous nuclear ribonucleoprotein A2/B1 (predicted)

-1.31

-1.23

-1.26

-1.18

-1.17

-1.35

-1.16

-1.19

-1.25

-1.22

-1.23

1371395_at

Cbx3

chromobox homolog 3 (HP1 gamma homolog, Drosophila)

-1.07

-1.04

-1.00

-1.04

-1.02

-1.03

-1.05

-1.10

-1.04

1379275_at

Snx10

sorting nexin 10

2.18

1.40

1.67

-1.05

1.94

1.58

1.69

1.58

2.02

1.55

1.89

1.39

1383585_s_at

Snx10

EST-sorting nexin 10

-1.10

-1.17

-1.08

-1.05

-1.12

-1.09

-1.06

-1.03

-1.08

-1.26

-1.09

-1.12

1377198_at

---

EST-2 Kb at 3' side of src family associated phosphoprotein 2

-1.23

-1.33

-1.16

-1.09

-1.10

-1.09

-1.10

-1.19

-1.03

-1.15

-1.12

-1.17

1369979_at

Skap2

src family associated phosphoprotein 2

-1.20

-1.22

-1.11

-1.04

-1.03

-1.16

-1.05

-1.07

1.01

-1.12

-1.07

-1.12

1388118_at

Hibadh

3-hydroxyisobutyrate dehydrogenase

-1.07

-1.01

-1.04

-1.05

-1.09

-1.05

-1.03

-1.06

-1.05

-1.05

-1.04

1378742_at

LOC682099

EST-similar to juxtaposed with another zinc finger protein 1

2.05

1.64

1.92

1.80

2.11

1.71

1.85

1.76

1.83

1.43

1.95

1.66

1379629_at

---

EST-4.7 kb at 5' side of similar to cAMP responsive element binding protein 5 isoform alpha

-1.38

-1.35

-1.40

-1.37

-1.34

-1.27

-1.42

-1.20

-1.41

-1.34

-1.39

-1.30

1394833_at

---

EST-0.6 Kb at 5' side of beta chimerin

-1.12

-1.15

-1.04

-1.19

-1.08

1.02

-1.06

-1.10

1.08

-1.03

-1.04

-1.09

1370648_a_at

Wipf3

WAS/WASL interacting protein family, member 3

1.01

1.18

-1.01

1.00

-1.01

1.09

1.00

-1.10

1.11

1.12

1.02

1.06

1392541_at

Ggct

gamma-glutamyl cyclotransferase

-1.34

-1.19

-1.28

-1.06

-1.26

-1.18

-1.08

-1.33

-1.26

-1.28

-1.16

1398107_at

Ggct

gamma-glutamyl cyclotransferase

-1.10

-1.15

-1.02

1.14

-1.17

-1.06

-1.07

-1.15

-1.00

-1.10

-1.03

1394973_at

Pde1c

EST-cyclic nucleotide phosphodiesterase 1 C

1.14

-1.01

1.08

1.09

1.02

-1.02

-1.01

1.37

1.16

1.11

1.05

1375640_at

Fkbp9

FK506 binding protein 9

-1.05

1.28

1.23

1.01

1.15

1.04

1.02

1.01

1.07

1.05

1.08

1.07

1388493_at

Ecop

EGFR-coamplified and overexpressed protein

-1.05

-1.10

-1.04

-1.00

-1.10

-1.09

-1.05

-1.11

-1.09

-1.07

-1.06

1396215_at

---

EST-similar to RIKEN cDNA 2610022G08

1.01

-1.07

-1.10

-1.03

-1.07

-1.08

-1.07

-1.14

-1.20

-1.06

-1.10

1394939_at

Ppm1k

protein phosphatase 1 K (PP2C domain containing)

-1.74

-2.67

-2.05

-2.36

-2.79

-2.57

-1.86

-2.05

-2.39

-2.05

-2.13

-2.33

1392921_at

Ppm1k

Protein phosphatase 1 K (PP2C domain containing)

-1.07

-1.22

-1.21

-1.19

-1.12

-1.16

-1.14

-1.22

-1.15

-1.12

-1.14

-1.18

1388778_at

---

EST-3.6 Kb at 5' side of similar to protein phosphatase 1 K (PP2C domain containing)

-1.27

-1.27

-1.17

-1.18

-1.27

-1.22

-1.23

-1.22

-1.26

-1.23

-1.24

1367977_at

Snca

synuclein, alpha

1.03

-1.08

-1.04

-1.11

-1.10

-1.09

1.07

1.03

-1.12

-1.03

-1.07

1385271_at

RGD1565731

EST-similar to KIAA1680 protein (predicted)

-1.02

1.04

-1.05

-1.08

-1.03

-1.02

-1.20

-1.11

-1.09

-1.01

-1.08

-1.04

1391945_at

---

Transcribed locus

2.01

1.33

2.37

1.60

1.54

1.38

1.88

1.30

2.61

1.70

2.05

1.45

1393607_at

Grid2

EST-glutamate receptor, ionotropic, delta 2

-1.27

-1.34

-1.13

1.04

-1.17

-1.14

-1.12

-1.23

-1.02

-1.08

-1.14

1386869_at

Actg2

actin, gamma 2, smooth muscle, enteric

1.03

1.05

1.07

-1.11

1.03

-1.00

-1.06

-1.10

-1.01

-1.02

1.01

-1.03

1379610_at

---

EST

1.19

1.31

-1.00

1.14

1.03

1.24

1.07

-1.03

1.10

1.06

1376481_at

Adamts9

a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9

1.09

1.30

1.16

1.22

1.30

1.28

1.27

1.20

1.18

1376747_at

---

EST, strongly similar to membrane associated guanylate kinase, WW and PDZ domain containing 1 isoform b [Mus musculus]

-1.11

-1.22

1.00

1.05

-1.25

-1.12

1.06

1.02

-1.20

-1.13

-1.09

-1.08

1381871_at

Transcribed locus

1.21

1.20

-1.05

1.90

1.28

1.49

1.31

1.42

1.19

1.08

1.18

1.39

1384504_at

Magi1

membrane associated guanylate kinase, WW and PDZ domain containing 1

1.15

1.05

1.41

1.16

1.20

1.20

1.08

1.17

1.13

1.17

1397438_at

Magi1

membrane associated guanylate kinase, WW and PDZ domain containing 1

1.26

1.01

1.12

1.09

1.02

1.26

1.17

1.08

1.18

1.04

Comparison of iP versus P.NP (this paper) and NP.P versus iNP [47] data. Probe sets that were significant (at P ≤ 0.05) with consistent direction in at least one brain region or in the average of the brain regions were analyzed. ^aPositive number is the ratio of the expression level of iP/P.NP (this paper) or NP.P/iNP [47] (that is, in both cases expression is higher in the strain with the P alleles in the introgressed region); negative numbers indicate the ratio of expression level of P.NP/iP (this paper) or iNP/NP.P [47]. Bold numbers indicate significant ratio of expression. ND indicates not detectable. The probe sets were sorted by genomic location; all are on chromosome 4.

Liang et al. Genome Biology 2010 11:R11 doi:10.1186/gb-2010-11-2-r11