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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.