Table 2.

Genes that showed significant alterations (q ≤ 5%) in brains of scrapie-infected mice at 104 dpi

Scan	Clone ID	Name	SAM Score(d)	q-value (%)	Ave. FC
L	AI848245	beta-2 microglobulin*	2.0	4.2	1.3
L	AI836786	complement component 1 q alpha*	2.1	4.2	1.3
L	AI835314	cyclin-dependent kinase 5, regulatory subunit (p35)	1.9	4.2	1.3
L	AI851280	docking protein 4	1.8	4.2	1.2
L	AI854785	endogenous retrovirus, Intracisternal A particles	1.8	4.2	1.2
L	SSHI-2f6	endogenous retrovirus truncated gag	1.8	4.2	1.4
L	AI841933	eukaryotic translation initiation factor 3, subunit 2 (beta)	1.8	4.2	1.2
L	AI836096	glial fibrillary acidic protein	3.7	4.2	1.9
L	AI854206	hexosaminidase B*	2.0	4.2	1.3
L	AI848012	kinesin family member 3A	1.9	4.2	1.3
L	AI842053	lectin, galactoside-binding, soluble, 3 binding protein*	1.9	4.2	1.2
L	AI849127	unknown EST	2.0	4.2	1.3
L	AI854905	unknown EST	1.9	4.2	1.3
L	AI853719	unknown EST	1.8	4.2	1.3
L	SSHII-1h12	not sequenced	1.8	4.2	1.2
L	AI840066	Immunoglobulin superfamily, member 4B*	1.9	4.2	1.3
L	AI849299	Protein tyrosine phosphatase, receptor type Z, polypeptide 1	1.8	4.2	1.2
L	AI851594	RIKEN cDNA 1300010M03 gene	1.8	4.2	1.2
L	AI850724	RIKEN cDNA 2400003C14 gene	2.3	4.2	1.3
L	AI843193	RIKEN cDNA E130114P18 gene	2.2	4.2	1.3
L	AI840441	secretogranin III*	1.9	4.2	1.2
L	AI846048	RIKEN cDNA 2900073H19 gene	1.8	4.2	1.3

* Genes with an asterisk encode proteins that localize to extracellular space

Clone ID is GenBank # for BMAP clones. Clone IDs that begin with SSHI are from Rashmi Korke's mouse cDNA library

L stands for low scan

FC stands for fold change