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Table 1 Genes with known function altered at 146 dpi with q ≤ 5% and ≥ 1.5 fold change

From: Gene expression alterations in brains of mice infected with three strains of scrapie

Scan

ID

Name

SAM

q

ME7

22L

RML

Ave

Citations

  

Endocytosis or Lysosomal function

       

L H A

AI838658

cathepsin B*

4

1

1.4

1.7

1.3

1.5

9 13

L H A

AI845967

cathepsin S*

15

1

2.6

3.0

2.4

2.7

9 12 11 14 18

L H A

AI838302

Cd63 antigen

5

1

1.3

1.7

1.4

1.4

 

L

AI854206

hexosaminidase B*

4

1

1.9

1.8

1.4

1.7

9 11

H

AI841188

legumain

2

3

1.0

1.5

1.3

1.3

 

H A

AI850263

lysosomal membrane glycoprotein 2

2

3

1.0

1.6

1.2

1.2

9

L A

AI845968

protective protein for beta-galactosidase

5

1

1.2

1.5

1.5

1.4

9

H A

AI852375

sortilin 1*

-3

1

-1.2

-1.5

-1.1

-1.3

 

L H A

AI841326

transferrin*

4

1

1.1

1.6

1.6

1.4

9 22 20 23

  

Other proteases/protease inhibitors

       

L

SSHI-1h6

cathepsin Z

2

4

1.5

1.1

1.5

1.4

12 11

L H A

AI835498

cystatin C*

7

1

1.6

1.7

1.6

1.6

9 8

H A

AI842540

transmem. Pr. with EGF-like and 2 follistatin-like domains 1

-3

1

-1.5

-1.1

-1.3

-1.3

 
  

Protein folding

       

L H A

AI848744

heat shock protein 1, beta

-3

1

-1.0

-1.2

-1.5

-1.2

 

L A

AI844835

peptidylprolyl isomerase B

3

1

-1.1

1.6

1.6

1.3

 
  

Immunity

       

L H A

AI848245

beta-2 microglobulin*

10

1

2.6

2.9

2.2

2.6

10 9 20 12 11

L H A

AI836786

complement component 1 q alpha*

6

1

1.4

1.8

1.9

1.7

1 8 12 11

L H A

AI854126

complement component 1, q beta*

4

1

2.2

1.6

1.6

1.8

1 8 12 11

H

AI853826

Fms interacting protein

-2

5

-1.2

-1.7

-1.4

-1.4

 

H A

AI841111

lymphocyte antigen 6 complex, locus E*

2

3

1.0

1.6

1.2

1.3

 
  

Calcium regulation

       

L

AI834839

calcium channel voltage-dependent T alpha1H

3

1

1.3

1.4

1.6

1.4

 

L H A

AI835341

calmodulin 1

-4

1

-1.2

-1.3

-1.5

-1.3

 

L H A

AI835663

calponin 3, acidic

3

1

1.7

1.4

1.1

1.4

9 11

L H A

AI853527

copine VIII

3

1

1.4

1.2

1.6

1.4

 

H A

AI847702

inositol 1,4,5-triphosphate receptor 1

-3

1

-1.2

-1.5

-1.2

-1.3

 

H A

AI839585

visinin-like 1

-3

2

-1.5

-1.2

-1.3

-1.3

 
  

Cytoskeleton

       

L

AI841156

actin related protein 2/3 complex, subunit 1A

3

1

1.0

1.4

1.6

1.3

 

H A

AI846176

capping protein (actin filament) muscle Z-line, beta

3

1

1.3

2.3

1.1

1.5

 

L H A

AI836096

glial fibrillary acidic protein

6

1

4.9

12

4.3

6.3

11 8 41 25 26 27 19 17

L A

AI849905

neurofilament 3, medium

-3

1

-1.3

-1.6

-1.3

-1.4

10

L H A

AI845192

peripherin 1

4

1

1.2

1.6

1.2

1.3

 

H

AI845991

RIKEN cDNA 4930488L10 gene

-2

4

-1.6

1.0

-1.2

-1.2

 

L H A

AI845820

vimentin

6

1

2.2

2.6

1.4

2.0

10 9 8 19 11

  

Pumps or channels

       

L H A

AI841308

ATPase, Na+/K+ transporting, beta 1 polypeptide

-3

1

-1.6

-1.3

-1.2

-1.4

 

L H A

AI836767

potassium inwardly-rectifying channel J 4

7

1

1.6

1.8

2.1

1.8

 

L H A

AI839063

solute carrier family 25 (mitochondrial carrier), member 18

5

1

1.4

1.5

1.2

1.4

9

  

Lipid processing

       

L H A

AI840024

apolipoprotein D*

8

1

1.5

2.6

2.3

2.1

9 12 17

L H A

AI848248

apolipoprotein E*

8

1

1.9

1.8

2.0

1.9

9 18

  

Phosphatase or Kinase

       

H

AI852186

ectonucleotide pyrophosphatase/phosphodiesterase 5*

-2

5

-1.1

-1.6

-1.4

-1.4

 

H A

AI841245

ethanolamine kinase 1

-2

5

-1.5

-1.1

-1.1

-1.2

 

H

AI849290

mitogen activated protein kinase kinase 5

-2

4

-1.3

-1.3

-1.6

-1.4

 

H A

AI842000

neurotrophic tyrosine kinase receptor type 2

3

2

1.1

1.9

1.3

1.4

9

H A

AI848471

protein tyrosine phosphatase, receptor type, F

-2

3

-1.1

-1.3

-1.5

-1.3

 

H

AI854349

serum/glucocorticoid regulated kinase

2

4

1.6

1.2

1.0

1.2

9 12

L H A

AI854038

sorbin and SH3 domain containing 1

3

1

1.6

1.3

1.0

1.3

 
  

Other enzymes

       

L H A

AI851848

aldehyde dehydrogenase family 1, subfamily A1

4

1

1.2

1.7

1.5

1.5

10 9

H A

AI838156

carbonic anhydrase 8

-2

3

-1.3

-1.7

1.0

-1.3

9

L H A

AI839962

malate dehydrogenase 1, NAD (soluble)

-3

1

-1.1

-1.5

-1.1

-1.2

9

  

Transcription or Translation

       

L

AI840211

A kinase (PRKA) anchor protein 8-like

2

4

1.6

1.3

1.1

1.3

 

H

AI835606

eukaryotic translation elongation factor 1 alpha 2

-2

3

-1.0

-1.1

-1.5

-1.2

 

H A

AI853820

eukaryotic translation initiation factor 5A

-3

1

-1.5

-1.3

-1.4

-1.4

 

L

AI845998

GLI-Kruppel family member HKR2

2

5

1.6

1.3

-1.0

1.3

 

L

AI847701

heterogeneous nuclear ribonucleoprotein D-like

-3

5

-1.1

-1.8

-1.2

-1.3

 

L A

AI845667

mitochondrial ribosomal protein L9

2

5

1.0

1.2

1.5

1.2

 

L A

AI838178

myotrophin

3

1

-1.1

1.4

2.1

1.4

 

A

AI842636

phenylalanine-tRNA synthetase 1 (mitochondrial)

-2

4

-1.5

-1.0

-1.2

-1.2

 

L A

AI851649

ribosomal protein L12

3

1

1.1

1.2

1.5

1.2

 

H A

AI854670

RIKEN cDNA A730098D12 gene

-2

4

-1.1

-1.1

-1.5

-1.2

 

L A

AI852411

SRY-box containing gene 9

3

1

-1.0

1.2

1.5

1.2

9

L A

AI838500

TSPY-like 2

3

1

1.0

1.5

1.7

1.4

 

L

AI854130

TSPY-like 4

-3

5

1.1

-1.3

-1.5

-1.2

 
  

Other

       

L H A

AI854515

CD9 antigen

5

1

1.3

1.9

1.5

1.6

12 11

L H A

AI836624

clusterin*

6

1

1.6

1.6

1.6

1.6

9 8 23 19 28

L H A

AI841459

diazepam binding inhibitor

5

1

1.2

1.5

1.7

1.5

9

L H A

AI854785

Endogenous retrovirus

3

1

2.0

1.2

1.9

1.6

21

H A

AI843767

endosulfine alpha

-2

5

-1.4

-1.3

-1.5

-1.4

 

L H A

AI839644

ferritin light chain 1

5

1

1.4

1.2

1.6

1.4

 

A

AI836826

glycoprotein 38*

2

4

1.2

1.6

1.4

1.4

 

L H A

AI842053

lectin galactoside-binding sol. 3 binding prot.*

7

1

1.7

2.4

1.8

1.9

12 11

L H A

AI841372

N-myc downstream regulated gene 4

-4

1

-1.1

-1.7

-1.3

-1.4

 

L

AI854649

oxysterol binding protein

2

4

1.5

1.5

1.1

1.4

 

L

AI837057

Septin 3 (Sept3), mRNA

-3

5

1.0

-1.7

-1.4

-1.3

 

L

AI845319

SPARC-like 1

3

1

1.0

1.3

1.5

1.3

 

L H A

AI838871

synaptosomal-associated protein 25

-4

1

-1.5

-1.2

-1.3

-1.3

10 16

L H A

AI854259

thyroid hormone receptor associated protein 2

-3

1

-1.1

-1.2

-1.5

-1.3

 

L H A

AI841166

Ywhah

-3

1

-1.2

-1.3

-1.5

-1.3

 

H

AI854309

WD repeat domain, X-linked 1

-2

4

-1.0

-1.1

-2.1

-1.3

 
  1. SAM Score (T-statistic), q (q-value %), Ave (average fold change for all three strains)
  2. Scan (Scan(s) that showed gene with significant alteration in scrapie brain)
  3. L, H, and A (Low, High, or Average of Low and High powered scans)
  4. Expression values shown for scan and clone that showed the highest SAM score.
  5. ID (GenBank # for BMAP clones. IDs that begin with SSHI are from Rashmi Korke's mouse cDNA library)
  6. Struckthrough BMAP accession numbers indicate that our sequencing results did not match the published sequence for that clone.
  7. IDs with struckthrough BMAP accession numbers are listed with the gene name that reflects our sequencing results.
  8. *Genes with an asterisk encode extracellular proteins.
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BMC Genomics

ISSN: 1471-2164

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