Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension

BMC Neuroscience

Table 4 Significant differentially expressed probesets from three mild ExpG eyes compared to eight control eyes by microarray.

PROBESET	Definition	Group Fold Change	Representative Public ID	Gene Title	Gene Symbol	RP	SAM	ONH Astrocyte	RGC
Hs.103291	HS, PT	2.19 ± 0.87	NM_016588	neuritin 1	NRN1	0.03	0.07	NA	Y
Hs.165636	HS, PT	2.21 ± 0.65	NM_017594	DIRAS family, GTP-binding RAS-like 2	DIRAS2	0.02	0.01	NA	NA
Hs.198760	HS, PT	4.67 ± 2.47	X15306	neurofilament, heavy polypeptide 200 kDa	NEFH	0.02	0.20	N	Y
Hs.369397	HS, PT	1.86 ± 0.46	NM_000358	transforming growth factor, beta-induced, 68 kDa	TGFBI	0.11	0.05	Y	NA
Hs.515369	HS	1.63 ± 0.23	NM_003332	TYRO protein tyrosine kinase binding protein	TYROBP	0.20	0.01	N	NA
Hs.529571	HS, PT	1.94 ± 0.48	NM_002899	retinol binding protein 1, cellular	RBP1	0.08	0.02	Y	Y
Hs.75318	HS, PT	1.57 ± 0.20	AL565074	tubulin, alpha 4a	TUBA4A	0.20	0.02	Y	NA
Hs.211914	PT	1.65 ± 0.22	BC005954	NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20 kDa (NADH-coenzyme Q reductase)	NDUFS7	0.23	0.01	Y	NA
Hs.512610	PT	1.76 ± 0.36	NM_016199	LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae)	LSM7	0.15	0.02	Y	NA

This comparison was performed to preferentially identify transcripts that changed during the mild stages of glaucomatous axonal damage. Samples 577, 578, and 579 had axonal losses ranging from 25%–32% (Table 2) and were tested separately. Results are shown here. Samples 566 and 529 had more severe axonal loss (74% and 59%, respectively; Table 2) and were excluded from this comparison. 'Definition' indicates the species definitions used; 'HS' indicates human; 'PT' indicates chimpanzee. For transcripts identified by both definitions (e.g. NRN1), the data shown in the table were produced using the human definition. Fold change (i.e. fold increase or fold decrease) and standard error of fold change were calculated as described in Methods. 'RP' indicates indicates p-values generated by Rank Products; 'SAM' indicates indicates p-values generated by significance analysis of microarrays. 'ONH Astrocyte' and 'RGC' indicate probable expression in optic nerve head astrocytes and retinal ganglion cells, respectively (see Methods); 'NA' indicates no data were available.

ISSN: 1471-2202