Supplemental Table 1

Dentate gyrus enriched/lowest

MGI Gene Name / Molecular Function / Genbank Number / Category and Rank Order / Average Affymetrix AD Value
DG
CA3
CA1 / Median Fold Change
DG/CA3
DG/CA1
CA3/CA1 / Described in Literature? / Tested
by In Situ Hybridiz-
ation? /

CA1

/ CA2 / CA3 / DG Granule Cells / Hilus / Subiculum / Fimbria (Oligodend-
rocytes) / Choroid Plexus / Reason for DG Enriched/ Lowest Classification / Final Classification with Respect to Hippocampus

EST

(No MGI entry) / Unknown / AA087715
(also AA616577) / DGH.01
(also DGH.61) / 1846
885
921 / 2.18
1.96
-1.15 / - / Yes
(Supp.Fig. 8C, Supp.Fig. 12B) / + / ++ / - / ++++ / - / - / - / - / High in DG / DG+CA2
enriched

Dsp

desmoplakin / Structural constituent of cytoskeleton / AA690887 (also AA600542) / DGH.02 (also DGH.05) / 2854
906
678 / 3.34
5.58
1.48 / - / Yes
(Fig. 2A, Supp.Fig. 2A, Supp.Fig. 12A) / - / - / - / ++++ / - / - / - / + / High in DG / DG
restricted

Ntf3

neurotrophin 3 / Growth factor / X53257 / DGH.04 / 1665
554
471 / 3.04
2.94
1.07 / (Friedman et al., 1991) / Yes
(Supp.Fig. 8A) / - / +++ / - / ++++ / - / - / - / - / High in DG / DG+CA2
restricted

Calb2

calbindin 2
calretinin / Calcium ion binding protein / X73985 / DGH.06 / 17342
10025
8518 / 1.71
2.27
-1.02 / (Fujise et al., 1998) / Yes
(Fig. 2C, Supp.Fig. 2T) / - / - / - / - / +++ / - / - / - / High in DG / Dentate hilus
restricted

Tiam1

T-cell lymphoma invasion and metastasis 1 / Guanyl-nucleotide exchange factor / U05245 / DGH.07 / 8423
3247
4393 / 2.77
1.74
-1.36 / (Ehler et al., 1997) / Yes
(Fig. 3R, Supp.Fig. 8B) / - / ++ / - / ++++ / + / ++ / - / - / High in DG / DG+CA2
restricted

Pde1b

phosphodiesterase 1B, Ca2+-calmodulin dependent / 3',5'-cyclic-nucleotide phospho-diesterase / L01695 / DGH.08 / 7839
3560
4240 / 2.17
1.74
-1.20 / (Polli and Kincaid, 1994) / No / ++ / + / + / ++++ / - / + / - / - / High In DG / DG
enriched

Btg1

B-cell translocation gene 1, anti-proliferative / Negative regulation of cell proliferation / L16846 / DGH.09 / 3487
1619
1897 / 2.59
1.97
-1.31 / - / Yes
(Supp.Fig. 5C) / ++ / - / - / ++++ / - / - / - / - / High in DG / DG+CA1
restricted

Ermelin

endoplasmic reticulum membrane protein / Metal ion transporter / AA217411 / DGH.10 / 4358
2146
1862 / 2.13
2.14
1.20 / - / Yes
(data not shown) / + / + / + / ++++ / + / - / - / - / High in DG / DG
enriched

Calb1

calbindin-28K / Calcium ion binding protein / M21531 / DGH.11 / 7663
2721
4909 / 2.90
1.70
-1.71 / (Sequier et al., 1988) / Yes
(Fig. 2X, Supp.Fig. 5A) / +++ / - / - / ++++ / - / - / - / - / High in DG / DG+CA1
restricted

Ehd1

EH-domain containing 1 / Endosome transport / W40735 / DGH.12 / 9370
5424
4229 / 1.89
2.47
1.11 / - / Yes
(Supp.Fig. 2S) / +++ / ++ / ++ / ++++ / + / + / - / - / High in DG / DG
enriched

Cebpd

CCAAT/enhancer binding protein (C/EBP), delta / Transcription Factor / X61800 / DGH.13 / 6047
2572
2885 / 1.73
1.59
-1.06 / - / Yes
(data not shown) / ++ / ++ / ++ / ++++ / + / - / - / + / High in DG / DG
enriched

Mapk3

mitogen activated protein kinase 3
erk-1
/ Protein kinase / Z14249 / DGH.14 / 29227
15419
15961 / 1.91
1.77
-1.14 / (Hyman et al., 1994) / No / + / ++ / + / ++++ / N/A / N/A / N/A / N/A / High in DG / DG+CA2
enriched

Net1

neuroepithelial cell transforming gene 1 / Guanyl-nucleotide exchange factor / AA691232 / DGH.16 / 1292
466
618 / 2.62
1.96
-1.41 / - / Yes
(data not shown) / ++ / + / + / ++++ / + / + / - / - / High in DG / DG+CA1
enriched
Nsep1
nuclease sensitive element binding protein 1
mYB-1b / Transcription factor / AA073584 / DGH.17 / 7357
3978
4786 / 1.75
1.56
-1.12 / - / Yes
(data not shown) / ++ / + / + / ++++ / + / + / - / ++ / High in DG / DG+CA1
enriched

Mbp

myelin basic protein / Structural molecule / X67319 / DGH.18 / 5196
2360
2756 / 2.05
1.80
-1.27 / - / Yes
(data not shown) / + / + / + / +++ / - / - / ++++ / - / High in DG / DG
enriched

EST

(No MGI entry) / Unknown / AA223007 / DGH.20 / 437
106
134 / 3.64
2.09
1.31 / - / Yes
(data not shown) / + / + / + / ++++ / + / + / - / +++ / High in DG / DG
enriched

Jun

jun oncogene / Transcription factor / X12761 / DGH.21 / 15659
10244
7253 / 1.43
1.93
1.46 /
(Haas et al., 1997)
/ Yes
(data not shown) / + / - / ++ / ++++ / + / ++ / - / - / High in DG / DG
enriched

Nmyc1

neuroblastoma myc-related oncogene 1 / Transcription factor / X03919 / DGH.22 / 1098
487
415 / 2.00
2.70
1.32 / - / Yes
(Supp.Fig. 7D) / - / + / ++ / ++++ / + / ++ / - / - / High in DG / DG+CA2+CA3
enriched

Tle1

transducin-like enhancer of split 1, homolog of Drosophila E(spl)
groucho-related gene 1 / Transcription factor / U61362 / DGH.23 / 1525
872
912 / 2.03
1.88
-1.14 / - / Yes
(data not shown) / +++ / ++ / ++ / ++++ / ++ / N/A / - / + / High in DG / DG+CA1
enriched

Sstr2

somatostatin receptor 2 / G-protein coupled receptor / X68951 / DGH.24 / 3591
1728
2488 / 1.93
1.50
-1.34 / (Senaris et al., 1994) / No / + / +/- / +/- / +++ / - / N/A / N/A / N/A / High in DG / DG
enriched

Pcp4

Purkinje cell protein 4 / Calcium ion binding protein / X17320 / DGH.25 / 23342
16650
12043 / 1.42
1.98
1.40 / (Utal et al., 1998; Zhao et al., 2001) / Yes
(Fig. 3Q, Supp.Fig. 8D) / - / ++++ / - / ++++ / +++ / ++ / - / - / High in DG / DG+CA2
restricted

Ryr1

ryanodine receptor 1, skeletal muscle / Cation channel / X83932 / DGH.26 / 692
254
192 / 2.24
3.15
-1.10 / (Mori et al., 2000) / No / +++ / ++ / ++ / ++++ / N/A / + / N/A / N/A / High in DG / DG
enriched

Camk2g

calcium/calmodulin -dependent protein kinase II gamma / Protein kinase / W12204
(also AA068735) / DGH.30
(also DGH.41) / 1455
590
774 / 2.65
2.36
-1.13 / - / Yes
(data not shown) / ++ / ++ / ++ / ++++ / ++ / ++ / - / - / High in DG / DG
enriched

Ppp1r1a

protein phosphatase 1, regulatory (inhibitor) subunit 1A / Protein phosphatase inhibitor / AA116737 / DGH.31 / 24762
14144
16573 / 1.70
1.45
-1.30 /
(Gustafson et al., 1991)
/ No / - / - / - / ++++ / N/A / - / - / - / High in DG / DG
restricted

Lrrn1

leucine rich repeat protein 1, neuronal / Integral membrane protein / D45913 / DGH.33 / 2708
1682
2264 / 1.60
1.26
-1.32 /
(Taguchi et al., 1996)
/ No / ++ / - / - / ++++ / + / + / - / - / High in DG / DG+CA1
restricted

Dgat2

diacylglycerol O-acyltransferase 2 / Acyltransferase / W15862 / DGH.34 / 10888
5767
5839 / 1.94
2.06
-1.09 / - / Yes
(Supp.Fig. 2Q) / + / + / + / ++++ / + / + / - / - / High in DG / DG
enriched

Atp1a1

ATPase, Na+/K+ transporting, alpha 1 polypeptide / Sodium/ potassium-exchanging ATPase / AA063844
(also W12919) / DGH.38
(also DGH.46) / 2447
1586
1241 / 1.59
1.97
1.09 /
(Hieber et al., 1991)
/ Yes
(data not shown) / ++ / ++ / ++ / ++++ / + / + / - / ++ / High in DG / DG
enriched

EST

RIKEN cDNA 2810442O16 gene / Unknown / AA673970 / DGH.42 / 3219
1524
1259 / 2.38
3.07
1.22 / - / Yes
(data not shown) / ++ / ++ / ++ / ++++ / + / - / - / - / High in DG / DG
enriched

Ptpro

protein tyrosine phosphatase, receptor type, O
PTPphi
/ Protein tyrosine phosphatase / U37465 / DGH.43 / 2044
1353
1232 / 1.65
1.69
1.03 / - / Yes
(Supp.Fig. 2R) / ++ / ++ / ++ / ++++ / ++++ / - / - / - / High in DG / DG
enriched
Mcmd6
mini chromosome maintenance deficient 6 / DNA dependent ATPase / AA689977 / DGH.44 / 710
428
465 / 2.37
1.74
-1.04 / - / Yes
(Fig. 2B, Supp.Fig. 2D) / -
+++ in inter-
neurons / -
+++ in inter-
neurons / -
+++ in
inter-
neurons / +++ / ++++ / +++ / - / - / High in DG / DG
Restricted
(among
excitatory cell types)

Igfbp5

insulin-like growth factor binding protein 5 / Growth factor binding activity / L12447 / DGH.48 / 5687
3514
4874 / 1.72
1.33
-1.41 /
(Bondy and Lee, 1993)
/ Yes
(Supp.Fig. 2B) / - / - / - / ++++ / - / - / - / + / High in DG / DG
restricted

Pkia

protein kinase inhibitor, alpha / Protein kinase inhibitor / M63554 / DGH.52 / 1669
963
977 / 1.49
1.54
1.12 /
(Seasholtz et al., 1995)
/ Yes
(data not shown) / +/- / ++ / ++ / ++++ / + / ++ / - / - / High in DG / DG+CA2+CA3
enriched
Gabrd
gamma-aminobutyric acid (GABA-A) receptor, subunit delta / Chloride ion channel / M60596 / DGH.53 / 1373
146
659 / 12.43
2.70
-2.97 /
(Wisden et al., 1992)
/ Yes
(data not shown) / + / - / - / ++++ / - / ++ / - / - / High in DG / DG+CA1
restricted

Fbln1

fibulin 1
BM-90
/ Extracellular matrix protein / X70854 / DGH.55 / 676
127
84 / 5.86
6.33
-1.03 / - / Yes
(data not shown) / +/- / +/- / +/- / ++
(++++ at ventral tip) / - / ++ / - / - / High in DG / DG
enriched

Trpc6

transient receptor potential cation channel, subfamily C, member 6 / Cation channel / U49069 / DGH.60 / 655
28
71 / 9.96
4.37
-1.10 /
(Mizuno et al., 1999)
/ No / - / - / - / ++++ / - / - / - / - / High in DG / DG
restricted

Siat8e

sialyltransferase 8 (alpha-2, 8-sialyltransferase) E / Protein amino acid glycosylation / X98014 / DGL.02 / 2577
4243
5623 / -1.74
-1.84
-1.29 / - / Yes
(Supp.Fig. 3B) / ++++ / ++++ / ++++ / - / ++ / ++ / - / - / Lowest in DG / CA1-CA3
restricted
CA3 enriched/lowest
MGI Gene Name / Molecular Function / Genbank Number / Category and Rank Order / Average Affymetrix AD Value
CA3
DG
CA1 / Median Fold Change

CA3/DG

CA3/CA1
DG/CA1 / Described in Literature? / Tested
by In Situ Hybridiz-
ation? /

CA1

/ CA2 / CA3 / DG Granule Cells / Hilus / Subiculum / Fimbria (Oligodend-
rocytes) / Choroid Plexus / Reason for DG Enriched/ Lowest Classification / Final Classification with Respect to Hippocampus

Prkcd

protein kinase C, delta / Protein kinase / X60304 / CA3H.01 / 3718
1495
857 / 2.60
3.98
1.68 / (Zhao et al., 2001) / Yes
(Supp.Fig. 4B) /

-

/ - / +++ / - / ++ / + / - / - / High in CA3 / CA3
restricted

Spock1

sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1
testican / Extracellular matrix protein / X92864 / CA3H.02 / 3425
201
32 / 29.30
55.67
1.00 /
(Bonnet et al., 1996)
/ Yes
(Supp.Fig. 4Q) /

-

/ ++++ / ++++ / - / - / - / - / - / High in CA3 / CA2+CA3
restricted

Npy2r

neuropeptide Y receptor Y2 / G-protein coupled receptor / D86238 / CA3H.04 / 1560
880
235 / 1.64
7.46
3.30 /
(Gustafson et al., 1997)
/ No /

-

/ +++ / ++++ / + / N/A / N/A / - / - / High in CA3 / CA2+CA3
enriched

Tgfb2

transforming growth factor, beta 2 / Growth factor / X57413 / CA3H.05 / 2637
1387
844 / 1.80
3.22
1.80 / - / Yes
(Fig. 3C, Supp.Fig. 7A) /

+

/ ++++ / ++++ / ++ / + / - / - / +++ / High in CA3 / DG+CA2+CA3
enriched

Frzb

frizzled-related protein / Negative regulation of Wnt receptor signaling / U68058 / CA3H.06 / 2324
1459
219 / 1.94
12.96
7.98 / - / Yes
(Fig. 3D, Supp.Fig. 7B) /

-

/ ++++ / ++++ / ++ / - / + / - / - / High in CA3 / DG+CA2+CA3
restricted

Myo5b

myosin Vb / Cytoskeletal protein / M55253 / CA3H.08 / 2932
1875
986 / 1.33
2.83
1.89 / - / Yes
(data not shown) /

++

/ ++ / ++++ / +++ / - / + / - / ++ / High in CA3 / CA3
enriched

Chgb

chromogranin B / Secretory granule protein / X53028 / CA3H.09 / 37726
22479
20032 / 1.97
2.24
1.11 /
(Mahata et al., 1993)
/ No /

++

/ ++++ / ++++ / ++ / N/A / + / - / - / High in CA3 / CA2+CA3
enriched

Sh3gl2

SH3-domain GRB2-like 2
endophilin I
/ Clathrin-mediated vesicle endocytosis / U58886 / CA3H.10 / 8690
5266
5422 / 1.74
1.67
-1.05 / - / Yes
(data not shown) /

++

/ + / ++++ / + / + / + / - / - / High in CA3 / CA3
enriched

Golph2

golgi phosphoprotein 2 / Unknown / AA030688 / CA3H.11 / 6663
4685
1568 / 1.40
4.05
2.79 / - / Yes
(Supp.Fig. 7C) /

+

/ ++++ / ++++ / +++ / ++ / + / - / - / High in CA3 / DG+CA2+CA3
enriched

Gtpat12

gene trap PAT 12 / Unknown / AA444426 / CA3H.12 / 2325
1405
893 / 1.13
2.36
1.53 / - / Yes
(data not shown) /

+++

/ ++++ / ++++ / +++ / - / + / - / ++ / High in CA3 / CA2+CA3
enriched

EST

(No MGI entry) / Unknown / AA611744 / CA3H.14 / 1847
816
866 / 2.15
2.27
1.03 / - / Yes
(Supp.Fig. 3C) /

+++

/ ++++ / ++++ / - / +++ / - / - / + / High in CA3 / CA1-CA3
restricted

Ap2a2

adaptor protein complex AP-2, alpha 2 subunit
alpha-adaptin (C) / Vesicle-mediated transport / X14972 / CA3H.15 / 2529
1724
1404 / 1.37
1.69
1.32 /
(Robinson, 1989)
/ No /

+

/ ++++ / ++++ / ++ / + / N/A / N/A / N/A / High in CA3 / CA2+CA3
enriched

Lbp

lipopolysaccharide binding protein / Lipid transport / AA212971 / CA3H.16 / 2166
1204
1348 / 1.97
1.42
-1.23 / - / Yes
(Supp.Fig. 10M) /

-

/ - / - / - / - / - / - / ++++ / High in choroid plexus / Not expressed in hippocampus

Ly6e

lymphocyte antigen 6 complex, locus E
Stem cell antigen 2 (Sca2) / Signal transduction / U04268 / CA3H.17 / 41066
28593
23950 / 1.25
1.43
1.18 / - / Yes
(Supp.Fig. 4R) /

+

/ ++++ / ++++ / + / ++ / - / - / - / High in CA3 / CA2+CA3
enriched

Ywhah

tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide
14-3-3 eta / Signal transduction / D87661 / CA3H.20 / 15044
11112
8734 / 1.29
1.83
1.16 /
(Toyooka et al., 2002)
/ No /

++

/ ++++ / ++++ / ++ / ++ / + / - / - / High in CA3 / CA2+CA3
enriched

Enpp2

ectonucleotide pyrophosphatase/phosphodiesterase 2 / Nucleotide pyrophosphatase / AA178190 / CA3H.21 / 23324
8202
14844 / 2.58
1.81
-1.40 / - / Yes
(Supp.Fig. 10C) /

+/-

/ +/- / +/- / +/- / - / - / +++ / ++++ / High in choroid plexus and fimbrial oligodend-rocytes / Low uniform expression in primary excitatory hippocampal neurons

Neurod6

neurogenic differentiation 6 / Transcription factor / U29086 / CA3H.22 / 5078
2802
3644 / 1.93
1.40
-1.16 /
(Bartholoma and Nave, 1994)
/ No /

++++

/ ++++ / ++++ / - / +++ / N/A / - / - / High in CA3 / CA1-CA3
restricted

Gpc1

glypican 1 / Extracellular matrix protein / AA009160 / CA3H.23 / 16902
10334
8839 / 1.50
1.77
1.29 /
(Litwack et al., 1994)
/ No /

+++

/ ++++ / ++++ / ++ / +++ / + / - / - / High in CA3 / CA2+CA3
enriched

Bok

bcl-2-related ovarian killer protein / Apoptosis activator activity / AA537500 / CA3H.25 / 11437
7290
2353 / 1.88
5.14
3.33 / - / Yes
(Fig. 2U, Supp.Fig. 4A) /

-

/ - / ++++ / - / ++ / - / - / - / High in CA3 / CA3
restricted

Kit

kit oncogene / Protein tyrosine kinase / Y00864 / CA3H.26 / 7416
4080
5704 / 1.97
1.12
-1.44 /
(Hirota et al., 1992)
/ No /

++

/ ++++ / ++++ / ++ / + / N/A / - / - / High in CA3 / CA2+CA3
enriched

Prss19

protease, serine, 19
neuropsin / Serine-type endopeptidase / D30785 / CA3H.27 / 3926
2131
2392 / 1.92
1.49
-1.24 /

(Suzuki et al., 1995)

/ Yes
(Fig. 3T, Supp.Fig. 9C) /

++++

/ - / ++++ / - / - / - / - / - / High in CA3 / CA1+CA3
restricted

Car4

carbonic anhydrase 4 / Carbonate dehydratase / U37091 / CA3H.28 / 6100
4860
3466 / 1.21
1.70
1.37 / - / Yes
(data not shown) /

+++

/ ++ / ++++ / ++ / + / + / - / - / High in CA3 / CA1+CA3
enriched

Cpne6

copine VI / Vesicle-mediated transport / R74842 / CA3H.29 / 27413
22269
16942 / 1.22
1.58
1.21 /

(Nakayama et al., 1999)

/ No /

++

/ ++ / ++++ / ++ / +++ / N/A / - / - / High in CA3 / CA3
enriched

Msx1

homeo box, msh-like 1
Hox-7
/ Transcription factor / X59251 / CA3H.31 / 1786
925
1271 / 2.03
1.36
-1.46 / - / Yes
(Fig. 4C, Supp.Fig. 10N) /

-

/ - / - / - / - / - / - / ++++ / High in choroid plexus / Not expressed in hippocampus

Kl

klotho / O-glycosyl compound hydrolase / AB005141 / CA3H.32 / 5036
1466
3051 / 3.60
1.47
-1.53 / - / Yes
(data not shown) /

+++

/ ++ / ++ / ++ / - / - / - / ++++ / High in choroid plexus / CA1
enriched

Lpl

lipoprotein lipase / Lipid catabolism / AA683731 / CA3H.33 / 4328
2813
2444 / 1.51
1.89
1.08 /

(Bessesen et al., 1993)

/ Yes
(Fig. 2D, Supp.Fig. 3O) /

+++

/ ++ / +++ / - / + / ++ / - / - / High in CA3 / CA1-CA3
restricted

Snap91

synaptosomal-associated protein 91 / Coated pit protein / M83985 / CA3H.34 / 10060
7288
6756 / 1.19
1.44
-1.06 /

(Sousa et al., 1992)

/ Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / ++ / ++ / - / - / High in CA3 / CA2+CA3
enriched

Prkca

protein kinase C, alpha / Protein kinase / M25811 / CA3H.38 / 894
275
270 / 2.93
2.83
1.16 /

(McGinty et al., 1991)

/ No /

+++

/ ++++ / ++++ / + / +++ / N/A / N/A / N/A / High in CA3 / CA2+CA3
enriched

Elavl2

ELAV (embryonic lethal, abnormal vision, Drosophila)-like 2 (Hu antigen B)
Mel-N1
/ RNA binding protein / U29088 / CA3H.39 / 1545
751
1100 / 2.17
1.75
-1.49 / - / Yes
(data not shown) /

-

/ ++++ / ++++ / - / +++ / ++ / - / - / High in CA3 / CA2+CA3
restricted
Mobp
myelin-associated oligodendrocytic basic protein / Structural constituent of myelin sheath / R75491 / CA3H.40 / 11683
3229
8512 / 3.87
1.43
-2.80 / - / Yes
(Fig. 4A, Supp.Fig. 10A) /

-

/ - / - / - / - / - / ++++ / - / High in fimbrial oligodend-rocytes / Not expressed in primary hippocampal neurons

Ttr

transthyretin
prealbumin / Plasma carrier of thyroid hormones / D89076 / CA3H.42 / 9703
3477
6564 / 2.19
1.25
-1.88 /

(Kato et al., 1986)

/ No /

-

/ - / - / - / - / - / - / ++++ / High in choroid plexus / Not expressed in hippocampus

Dlat

dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) / Acetyl-transferase / W29756 / CA3H.43 / 3822
2628
2345 / 1.35
1.64
1.21 / - / Yes
(data not shown) /

+

/ ++++ / +++ / ++ / ++ / +++ / - / - / High in CA3 / CA2+CA3
enriched

Cadps

Ca2+dependent activator protein for secretion / Unknown / D86214 / CA3H.44 / 7033
4285
4760 / 1.57
1.45
-1.10 / - / Yes
(Fig. 2W, Supp.Fig. 4T) /

++

/ ++++ / ++++ / + / +++ / + / - / - / High in CA3 / CA2+CA3
enriched

Nell2

nel-like 2 homolog / Structural molecule / U59230 / CA3H.45 / 4335
3336
1931 / 1.32
2.40
1.33 /

(Kuroda et al., 1999)

/ No /

+++

/ ++++ / ++++ / +++ / N/A / N/A / - / - / High in CA3 / CA2+CA3
enriched

Atp2a2

ATPase, Ca++ transporting, cardiac muscle, slow twitch 2
SERCA2a
/ Calcium-transporting ATPase / AA153484 / CA3H.47 / 3397
1831
2352 / 1.63
1.48
-1.22 / - / Yes
(data not shown) /

+++

/ ++++ / ++++ / ++ / ++ / ++ / - / - / High in CA3 / CA2+CA3
enriched

Slc31a1

solute carrier family 31, member 1
High affinity copper uptake protein 1 / Copper ion transporter / AA190119 / CA3H.48 / 1636
944
947 / 1.92
2.06
1.06 / - / Yes
(Supp.Fig. 10O) /

+

/ + / + / + / - / - / - / ++++ / High in choroid plexus / Uniform expression in primary excitatory hippocampal neurons

Pfkp

phosphofructokinase, platelet / 6-phospho-fructokinase / AA072252 / CA3H.49 / 3506
2391
2282 / 1.54
1.52
1.08 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / + / ++ / ++ / - / - / High in CA3 / CA2+CA3
enriched

Ak4

adenylate kinase 4 / Phospho-transferase / C79612 / CA3H.52 / 3110
2421
2097 / 1.30
1.45
1.12 /

(Yoneda et al., 1998)

/ No /

++

/ +++ / +++ / + / + / N/A / - / - / High in CA3 / CA2+CA3
enriched

Dfy

Duffy blood group / G-protein coupled receptor / AF016697 / CA3H.53 / 4231
3187
2867 / 1.49
1.57
-1.11 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / ++ / - / - / - / High in CA3 / CA2+CA3
enriched
Sgk
serum/glucocorticoid regulated kinase / Protein kinase / AA217550 / CA3H.55 / 5013
3615
3195 / 1.67
1.59
1.05 /

(Lee et al., 2001)

/ Yes
(Supp.Fig. 4S) /

+

/ ++++ / ++++ / + / ++ / - / +++ / +++ / High in CA3 / CA2+CA3
enriched

Mod1

malic enzyme, supernatant / Malate dehydrog-enase / AA189662 / CA3H.56 / 4257
2499
2511 / 1.89
1.66
1.13 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / +/- / + / + / - / ++ / High in CA3 / CA2+CA3
enriched

Sms

spermine synthase / Spermine metabolism / AF031486 / CA3H.57 / 3095
1881
1482 / 1.73
2.11
1.18 / - / Yes
(data not shown) /

+

/ ++++ / ++++ / ++ / + / + / - / - / High in CA3 / CA2+CA3
enriched

Cldn11

claudin 11 / Component of tight junctions / U19582 / CA3H.59 / 12547
4206
9109 / 2.78
1.29
-2.08 / - / Yes
(Fig. 4B, Supp.Fig. 10B) /

-

/ - / - / - / - / - / ++++ / - / High in fimbrial oligodend-rocytes / Not expressed in primary excitatory hippocampal neurons

EST

RIKEN cDNA 1700016D08 gene / Unknown / AA273803 / CA3H.60 / 2881
1665
1858 / 1.92
1.43
-1.18 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / ++ / ++ / - / ++ / High in CA3 / CA2+CA3
enriched

Gdi1

guanosine diphosphate (GDP) dissociation inhibitor 1
rab GDP dissociation inhibitor alpha / GTPase activator / AA060905 / CA3H.62 / 11191
7736
7897 / 1.38
1.48
-1.16 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / + / ++ / - / - / High in CA3 / CA2+CA3
enriched

Nefl

neurofilament, light polypeptide / Cytoskeletal protein / M20480 / CA3H.63 / 9468
6051
4949 / 1.38
2.20
1.01 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / +++ / +++ / ++ / - / - / High in CA3 / CA2+CA3
enriched

EST

RIKEN cDNA 0610009A07 gene / Electron transfer flavoprotein / AA212774 / CA3H.64 / 305
64
29 / 2.44
4.78
1.16 / - / Yes
(Supp.Fig. 4C) /

-

/ - / ++++ / + / - / - / - / - / High in CA3 / CA3
enriched

Socs2

suppressor of cytokine signaling 2 / Negative regulator of the growth hormone/IGF1 signaling pathway / U88327 / CA3H.65 / 407
40
56 / 6.43
4.07
1.02 / - / Yes
(Fig. 2V, Supp.Fig. 4D) /

-

/ ++++ / ++++ / - / - / + / - / - / High in CA3 / CA2+CA3
restricted

Cacna1a

calcium channel, voltage-dependent, P/Q type, alpha 1A subunit / Voltage-gated calcium channel / U76716 / CA3H.66 / 634
324
126 / 2.02
3.89
1.28 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / + / + / - / - / High in CA3 / CA2+CA3
enriched

Ccnd2

cyclin D2 / Cyclin-dependent protein kinase / M83749 / CA3H.69 / 730
346
187 / 1.48
3.09
2.09 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++ / ++ / + / - / +++ / High in CA3 / CA2+CA3
enriched

D0H4S114

DNA segment, human D4S114
P311
/ Unknown / X70398 / CA3L.01
(also CA1H.40) / 4053
9063
9882 / -2.19
-2.34
-1.08 / - / Yes
(Supp.Fig. 2C) /

-

/ - / - / +++ / + / ++++
(pre-
subiculum) / - / + / Low in CA3 / DG
restricted

Ngef

neuronal guanine nucleotide exchange factor / Guanine nucleotide exchange factor / AA607353 / CA3L.02
(also CA1H.48) / 4290
11354
12772 / -2.54
-2.97
-1.12 / - / Yes
(Fig. 2Y, Supp.Fig. 5B) /

++++

/ - / - / +++ / - / ++ / - / - / Low in CA3 / DG+CA1
restricted

Marcks

myristoylated alanine rich protein kinase C substrate / Cytoskeletal protein / M60474 / CA3L.05 / 4991
7579
7991 / -1.61
-1.56
-1.05 /

(McNamara and Lenox, 1998)

/ No /

++

/ - / - / ++++ / - / ++ / - / - / Low in CA3 / DG+CA1
restricted

Rex3

reduced expression 3 / Unknown / AA473525 / CA3L.06 / 683
1596
1301 / -2.91
-2.11
1.21 / - / Yes
(data not shown) /

++++

/ ++ / ++ / ++++ / ++ / ++ / - / - / Low in CA3 / DG+CA1
enriched

Acta2

actin, alpha 2, smooth muscle, aorta / Cytoskeletal protein / X13297 / CA3L.13 / 2613
5519
4669 / -2.22
-2.04
1.34 / - / Yes
(data not shown) /

++++

/ +++ / +++ / ++++ / + / ++ / - / - / Low in CA3 / DG+CA1
enriched

Kcnj9

potassium inwardly-rectifying channel, subfamily J, member 9
GIRK3
/ Potassium ion channel / U11860 / CA3L.20 / 322
722
774 / -2.03
-2.41
-1.35 / - / Yes
(data not shown) /

+++

/ + / + / ++++ / - / +++ / - / - / Low in CA3 / DG+CA1
enriched

CA1 enriched/lowest

MGI Gene Name / Molecular Function / Genbank Number / Category and Rank Order / Average Affymetrix AD Value
CA1
DG
CA3 / Median Fold Change

CA1/DG

CA1/CA3
DG/CA3 / Described in Literature? / Tested
by In Situ Hybridiz-
ation? /

CA1

/ CA2 / CA3 / DG Granule Cells / Hilus / Subiculum / Fimbria (Oligodend-
rocytes) / Choroid Plexus / Reason for DG Enriched/ Lowest Classification / Final Classification with Respect to Hippocampus

Nov

nephroblastoma overexpressed gene / Growth factor / Y09257 / CA1H.01 / 24271
8493
5647 / 2.73
4.50
1.61 /

(Zhao et al., 2001)

/ Yes
(Fig. 3A, Supp.Fig. 6A) /

++++

/ - / - / - / - / ++++ / - / - / High in CA1
(and
subiculum) / CA1
restricted

Rbp4

retinol binding protein 4, plasma / Retinoid transporter / AA049662
(also W11658) / CA1H.02
(also CA1H.15) / 4507
1674
1349 / 2.67
3.56
1.35 / - / Yes
(Supp.Fig. 11C) /

-

/ - / - / - / - / ++++ / - / - / High in subiculum / Not expressed in hippocampus

Zfp312

zinc finger protein 312
fez-like / Transcription factor / W98265 / CA1H.03 / 9137
3650
3909 / 2.25
2.41
1.13 / - / Yes
(data not shown) /

+++

/ +++ / +++ / - / ++ / ++++ / - / - / High in CA1
(and subiculum) / CA1-CA3
restricted

Prss12

protease, serine, 12 neurotrypsin (motopsin) / Serine-type endopeptidase / AA063841
(also AA166254) / CA1H.04
(also CA1H.36) / 3120
1684
856 / 1.99
3.12
1.51 /

(Gschwend et al., 1997)

/ Yes
(Supp.Fig. 11D) /

+

/ + / + / ++ / + / ++++ / - / - / High in subiculum / DG
enriched

Mrg1

myeloid ecotropic viral integration site (meis)-related gene 1
Mrg1b
/ Transcription factor / AI323389 / CA1H.05 / 1709
492
723 / 3.03
2.52
-1.55 / - / Yes
(FIG. 2E, Supp.Fig. 3A) /

++++

/ ++++ / ++++ / - / - / - / - / - / High in CA1 / CA1-CA3
restricted

Fn1

fibronectin 1 / Extracellular matrix protein / M18194 / CA1H.07 / 3753
1903
1491 / 2.17
2.49
1.26 / - / Yes
(Fig. 4D, Supp.Fig. 11A) /

-

/ - / - / - / - / ++++ / - / - / High in subiculum / Not expressed in hippocampus

Tmsb10

thymosin, beta 10 / Cytoskeletal protein / AA230776 (also AA537404) / CA1H.08 (also CA1H.10) / 26180
12884
9683 / 1.97
2.67
1.34 /

(Carpintero et al., 1999)

/ No /

+++

/ ++ / ++ / ++ / + / N/A / N/A / N/A / High in CA1 / CA1
enriched

Tyro3

TYRO3 protein tyrosine kinase 3 / Protein tyrosine kinase / U05683 / CA1H.09 / 3686
1554
1606 / 2.46
2.47
-1.08 /

(Prieto et al., 2000)

/ Yes
(Fig. 3S, Supp.Fig. 9A) /

++++

/ - / ++ / - / - / ++ / + / - / High in CA1 / CA1+CA3
restricted

EST

(No MGI entry) / Unknown / AA717225 / CA1H.11 / 726
221
308 / 3.23
3.19
-1.47 / - / Yes
(Supp.Fig. 3M) /

++++

/ ++++ / ++++ / - / - / +++ / - / ++++ / High in CA1
(and subiculum) / CA1-CA3
restricted

Etv1

ets variant gene 1
ets-related protein 81 (ER81) / Transcription factor / L10426 / CA1H.12 / 2210
775
995 / 3.00
2.37
-1.35 / - / Yes
(Fig. 3B, Supp.Fig. 6B) /

+++

/ ++ / ++ / + / - / ++++ / - / - / High in CA1
(and subiculum) / CA1
enriched

Man1a

mannosidase 1, alpha / N-linked glycosylation / U04299 / CA1H.14 / 2394
1197
1360 / 2.12
1.68
-1.06 / - / Yes
(Supp.Fig. 9D) /

++++

/ - / + / - / - / - / - / + / High in CA1 / CA1+CA3
restricted

Rab3b

RAB3B, member RAS oncogene family / Small monomeric GTPase / AA166533 / CA1H.16 / 3017
1640
1613 / 1.91
2.00
1.19 / - / Yes
(data not shown) / +
+++ in
inter-
neurons / +
+++ in
inter-
neurons / +
+++ in
inter-
neurons / + / +++ / ++++ / - / - / High in subiculum / Uniform expression in primary excitatory hippocampal neurons

Sez6

seizure related gene 6 / Integral membrane protein / D29763 / CA1H.17 / 3578
1589
1684 / 2.17
2.33
-1.13 /

(Herbst and Nicklin, 1997)

/ Yes
(Supp.Fig. 3N) /

++++

/ ++++ / +++ / + / +++ / +++ / - / - / High in CA1
(and subiculum) / CA1-CA3
enriched

Dcn

decorin / Extracellular matrix protein / X53929 / CA1H.18 / 5612
2939
2641 / 1.96
2.04
1.20 / - / Yes
(data not shown) /

+++

(caudal CA1 only) / - / - / - / - / ++++ / - / +++ / High in CA1
(and subiculum) / CA1
restricted

Satb1

special AT-rich sequence binding protein 1 / Transcription factor / U05252 / CA1H.19 / 3296
1846
1714 / 1.77
1.76
-1.09 / - / Yes
(data not shown) /

+

/ - / +++ / ++ / ++++ / ++++ / - / - / High in subiculum / CA3
enriched

Lxn

latexin / Carboxy-peptidase inhibitor / D88769 / CA1H.24 / 6375
3527
3583 / 1.76
1.71
1.00 / - / Yes
(data not shown) /

++

/ + / + / - / + / ++++ / - / - / High in subiculum / CA1-CA3
restricted
Stac
src homology three (SH3) and cysteine rich domain / Signal transduction / D86639 / CA1H.28 / 707
506
355 / 1.39
1.79
1.09 /

(Suzuki et al., 1996)

/ No /

+++

/ + / + / + / N/A / - / N/A / N/A / High in CA1 / CA1
enriched

Pva

parvalbumin / Calcium ion binding protein / X67141 / CA1H.31 / 6481
3008
4524 / 2.26
1.50
-1.35 /

(de Lecea et al., 1995)

/ Yes
(data not shown) /

-

+++ in
inter-
neurons / -
+++ in
inter-
neurons / -
+++ in
inter-
neurons / - / +++ / +++ / - / - / High in subiculum / Not expressed in primary excitatory hippocampal neurons

Dusp1

dual specificity phosphatase 1
mitogen-activated protein kinase phosphatase MKP-1 (3CH134) / Protein phosphatase / X61940 / CA1H.32 / 4797
3034
2968 / 1.53
1.55
-1.03 / - / Yes
(data not shown) /

++++

/ ++ / ++ / - / + / + / - / - / High in CA1 / CA1
enriched

Stmn1

stathmin 1 / Microtubule destabilizing protein / Z31235 (also AA117100) / CA1H.33 (also CA1H.34) / 18506
12443
11684 / 1.46
1.57
1.06 /

(Sugiura and Mori, 1995)

/ Yes
(data not shown) /

+

/ + / + / + / ++ / ++++ / - / - / High in subiculum / Uniform expression in primary excitatory hippocampal neurons

EST

expressed sequence AI480459 / Unknown / AA591428 / CA1H.35 / 6079
4492
3630 / 1.38
1.62
1.25 / - / Yes
(Supp.Fig. 6C) /

++++

/ ++ / ++ / ++ / ++ / - / - / - / High in CA1 / CA1
enriched

Egr1

early growth response 1
zif/268 / Transcription factor / M22326 / CA1H.37 / 9981
7079
7036 / 1.41
1.51
1.02 /

(Schlingensiepen et al., 1991)

/ No /

+++

/ + / + / + / N/A / ++ / - / - / High in CA1 / CA1
enriched

Sst

somatostatin / Neuropeptide / X51468 / CA1H.43 / 60649
38426
38569 / 1.64
1.43
1.01 /

(Bering and Johansen, 1993)

/ No /

-

+++ in
inter-neurons / -
+++ in
inter-
neurons / -
+++ in
inter-
neurons / - / +++ / N/A / - / - / High in CA1 / Not expressed in primary excitatory hippocampal neurons

Nr4a2

nuclear receptor subfamily 4, group A, member 2
Nurr1
/ Transcription factor / U86783 / CA1H.47 / 470
121
89 / 2.92
5.55
1.65 /

(Tseng et al., 2000)

/ No /

+

/ + / + / + / N/A / ++++ / N/A / N/A / High in subiculum / Uniform expression in primary excitatory hippocampal neurons

Man2a1

mannosidase 2, alpha 1 / N-linked glycosylation / X61172 / CA1H.49 / 1255
461
709 / 3.29
1.70
-1.56 / - / Yes
(Supp.Fig. 9B) /

++++

/ - / ++ / - / - / ++++ / - / - / High in CA1
(and subiculum) / CA1+CA3
restricted

Elavl4

ELAV (embryonic lethal, abnormal vision, Drosophila)-like 4
Hu antigen D
/ RNA binding protein / D31953 / CA1H.50 / 2853
962
1101 / 2.89
2.79
-1.46 /

(Clayton et al., 1998)

/ Yes
(data not shown) /

++

/ +++ / +++ / + / +++ / ++++ / - / - / High in subiculum / CA2+CA3
enriched

Itpr1

inositol 1,4,5-triphosphate receptor 1 / Calcium ion channel / X15373 / CA1H.55 / 7841
4854
3671 / 1.58
2.51
1.47 /

(Rodrigo et al., 1993)

/ Yes
(Supp.Fig. 5D) /

++++

/ + / + / +++ / - / ++ / - / ++++ / High in CA1
(and subiculum) / DG+CA1
enriched

Igfbp4

insulin-like growth factor binding protein 4 / Growth factor binding activity / X81582 / CA1H.56 / 3784
2138
1310 / 1.97
2.71
2.66 /

(Stenvers et al., 1994)

/ No /

+

/ ++++ / - / - / ++ / ++++ / - / - / High in subiculum
(and CA2) / CA2
enriched

Bhlhb2

basic helix-loop-helix domain containing, class B2
Stra13
/ Transcription factor / AF010305 / CA1H.58 / 892
582
380 / 1.40
2.23
1.53 /

(Rossner et al., 1997)

/ No /

+++

/ - / - / - / - / +++ / - / - / High in CA1
(and subiculum) / CA1
restricted

Pbx3

pre B-cell leukemia transcription factor 3 / Transcription factor / AF020200 / CA1H.65 / 290
28
28 / 4.54
4.21
-1.01 / - / Yes
(data not shown) /

++

/ + / + / + / - / + / - / - / High in CA1 / CA1
enriched

EST

expressed sequence R74641 / Unknown / R74641 / CA1H.66 / 2049
543
749 / 3.96
2.96
-1.34 / - / Yes
(Supp.Fig. 11B) /

-

/ - / - / - / - / +++ / - / - / High in subiculum / Not expressed in primary excitatory hippocampal neurons

Usp11

ubiquitin specific protease 11 / Cysteine-type peptidase / W87254 / CA1L.21 / 340
1040
1136 / -3.17
-2.32
-1.13 / - / Yes
(data not shown) /

+++

/ +++ / +++ / +++ / + / + / - / ++++ / Low in subiculum / Uniform expression in primary excitatory hippocampal neurons

Snca

synuclein, alpha / Unknown / W75614 / CA1L.22 / 616
5450
4534 / -4.77
-4.19
1.14 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / +++ / ++ / + / - / - / Low in CA1
(and subiculum) / DG+CA2+CA3
enriched

Hspa2

heat shock protein 2 / Chaperone protein / M20567 / CA1L.23 / 1490
2096
2156 / -1.59
-1.69
-1.01 / - / Yes
(data not shown) /

++

/ +++ / +++ / ++++ / +++ / - / - / + / Low in CA1
(and subiculum) / DG+CA2+CA3
enriched

Anxa11

annexin A11 / Calcium ion binding protein / U65986 / CA1L.24 / 847
2239
1758 / -2.88
-2.24
-1.04 / - / Yes
(data not shown) /

++

/ ++++ / ++++ / ++++ / - / - / - / ++ / Low in CA1
(and subiculum) / DG+CA2+CA3
enriched

Supplemental Table 1. Compilation of microarray and expression data. Standardized nomenclature from Mouse Genome Informatics (MGI) is used to describe each gene. In cases where a gene name in common usage in the literature differed from the MGI name, it has been included in italics. The corresponding Genbank accession numbers are included, as well as a functional annotation based on Gene Ontology (GO) listings (Ashburner et al., 2000) derived from MGI ( Blake et al., 2003), Affymetrix (Liu et al., 2003) and Swiss-Prot/TrEMBL ( Appel et al., 1994) databases. The entire list is ordered by the ranking from the initial data analysis (e.g., DGH.01 is the top-ranked candidate for enrichment in the dentate gyrus). In cases where a gene was represented more than once on the microarrays, the rank order and Genbank number for each instance are listed. DGH.53-60, CA3H.64-69, and CA1H.58-66 were obtained using a drawn gene template 40-fold higher in one hippocampal subregion than the others, as described in the Results section. The average expression value, or Affymetrix AD value, for each hippocampal region is expressed as the trimmed mean to remove outliers and give a more representative value, and the fold changes (FCs) between regions are expressed as the median values. FCs were calculated using Affymetrix criteria:

+1 if FC>0

–1 if FC<0,

where and are the noise levels associated with each microarray, and is a constant multiplier used for this particular microarray. For both AD values and FCs, chip noise levels were used in cases where the expression level was lower than the noise. In situ hybridization data are summarized for the primary neuronal populations within each hippocampal subregion as well as in surrounding structures. Relative expression levels observed by in situ hybridization were scored by visual inspection of the intensity of the in situ hybridization signal, and a four-point scale is used to describe labeling intensity in different cell populations, taking into account labeling intensity in other brain regions. A posthoc justification is made for the inclusion of each gene in its initial category, and a final classification of the expression pattern within hippocampal regions CA1, CA2, CA3 and the dentate gyrus is included in the last column.

References

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