Table 2. SAM ranked gene list.

Rank	Accession Number	Transcript name	d[i]	de[i]	Fold Change	q-value	Regulation category*
1	CK990996	Metallothionein B	−7.557	−2.868	1.757	0	L
2	CA062118	PREDICTED: similar to POMT2 [Danio rerio]	5.977	2.89	−1.907	0	L
3	CA051877	UNKNOWN	5.144	2.66	−1.855	0	E
4	CB507722	Metallothionein B	−5.119	−2.649	1.58	0	E
5	CB493454	Lipocalin precursor	4.976	2.521	−1.666	0	E
6	CB498358	Fatty acid-binding protein. intestinal	4.875	2.439	−2.403	0	L
7	CA054659	Fatty acid-binding protein. intestinal	4.766	2.382	−2.539	0	L
8	CB492836	Lipocalin precursor	4.564	2.33	−1.639	0	L
9	CA064204	Protein S100-B	4.539	2.293	−1.579	0	L
10	CN442545	Cytochrome c oxidase subunit 3	−4.529	−2.528	1.504	0	L
11	CK990592	Metallothionein B	−4.493	−2.447	1.549	0	L
12	CB509992	Lipocalin precursor	4.439	2.256	−1.527	0	E
13	CB496407	Betaine aldehyde dehydrogenase	4.406	2.225	−1.824	0	L
14	CB515799	UNKNOWN	−4.403	−2.385	1.638	0	L
15	CA063208	UNKNOWN	4.387	2.194	−1.951	0	E
16	CA769320	Fatty acid-binding protein. intestinal	4.361	2.167	−2.247	0	L
17	CB498606	Fatty acid-binding protein. intestinal	4.328	2.142	−2.372	0	L
18	CB511332	Fatty acid-binding protein. intestinal	4.297	2.119	−2.156	0	L
19	CB492197	Metallothionein A	−4.276	−2.336	1.487	0	L
20	CB515213	B-cell linker protein	4.275	2.098	−1.604	0	L
21	CA046225	Metallothionein B	−4.218	−2.294	1.512	0	L
22	CA051958	Trafficking protein particle complex subunit 3	4.213	2.079	−1.6	0	L
23	CA051480	UNKNOWN	4.2	2.06	−2	0	L
24	CA044316	Excluded (Chimera)	4.196	2.044	−1.433	0	L
25	CB494699	Gamma crystallin M2	4.192	2.028	−1.544	0	L
26	CK990422	UNKNOWN	4.172	2.013	−1.669	0	L
27	CA059685	UNKNOWN	−4.163	−2.258	1.713	0	E
28	CB498630	Apolipoprotein Eb precursor	−4.161	−2.225	1.818	0	L
29	CA058895	Apolipoprotein Eb precursor	−4.07	−2.195	2.113	0	E
30	CA064247	CD9 antigen	4.068	1.998	−1.866	0	L
31	CA053993	UNKNOWN	4.062	1.985	−1.736	0	L
32	CB499689	Chromodomain-helicase-DNA-binding protein 2	4.059	1.971	−1.74	0	L
33	CA055129	UNKNOWN	4.045	1.958	−1.573	0	L
34	CA042615	SH3 domain-binding glutamic acid-rich-like protein	4.039	1.946	−1.528	0	L
35	CB510889	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 4	4.022	1.935	−1.461	0	L
36	CA061651	PREDICTED: similar to calmodulin-dependent phosphodiesterase [Danio rerio]	3.961	1.924	−1.81	0	L
37	CA041385	Proactivator polypeptide precursor	−3.888	−2.169	1.396	0	E
38	CA042089	Ependymin precursor	3.868	1.913	−1.684	0	E
39	CB510842	Calcium-regulated heat stable protein 1	3.867	1.902	−1.952	0	L
40	CB492748	pigment epithelium-derived factor [Paralichthys olivaceus] >gi|71063313|gb|AAZ22324.1| pigment epithelium-derived factor [Paralichthys olivaceus]	3.866	1.892	−1.625	0	L
41	CA058611	Clusterin precursor	−3.863	−2.145	1.698	0	L
42	CB510615	UNKNOWN	3.852	1.883	−1.47	0	L
43	CA063671	UNKNOWN	−3.841	−2.123	1.751	0	L
44	CA042930	UNKNOWN	3.832	1.875	−1.612	0	L
45	CA062117	Protein FAM44B	3.795	1.865	−1.72	0	L
46	CN442558	Cytochrome c oxidase subunit 3	−3.745	−2.103	1.433	0	L
47	CA043114	Meprin A subunit alpha precursor	3.744	1.855	−1.738	0	L
48	CA043730	Fructose-bisphosphate aldolase B	3.74	1.847	−1.674	0	L
49	CB494396	Glycylpeptide N-tetradecanoyltransferase 1	3.717	1.839	−1.719	0	E
50	CB494172	Keratin. type II cytoskeletal 8	−3.716	−2.086	1.533	0	L
51	CA052024	UNKNOWN	3.709	1.83	−1.796	0	L
52	CB510653	Salvelinus alpinus metallothionein B gene. introns 1 and 2 and partial cds	−3.708	−2.068	1.376	0	L
53	CB506047	Thymosin beta-12	−3.674	−2.052	1.504	0	L
54	CA052938	UNKNOWN	3.663	1.822	−1.828	0	L
55	CA054630	Sodium/potassium-transporting ATPase subunit alpha-1 precursor	−3.66	−2.036	1.409	0	L
56	CB511371	Gamma crystallin M3	3.654	1.814	−1.584	0	L
57	CA063207	UNKNOWN	3.653	1.806	−1.776	0	L
58	CA055638	UNKNOWN	3.651	1.799	−1.497	0	L
59	CA044410	UNKNOWN	3.65	1.792	−1.561	0	L
60	CB498510	UNKNOWN	3.644	1.785	−1.652	0	L
61	CB510188	Gamma crystallin M2	3.643	1.778	−1.825	0	L
62	CB511962	Salmo salar TNF-alpha 2 gene. complete cds	3.613	1.77	−1.392	0	L
63	CN442525	ATP synthase a chain	−3.603	−2.02	1.298	0	L
64	CB512365	UNKNOWN	3.6	1.764	−1.451	0	E
65	CA047979	UNKNOWN	−3.599	−2.006	1.482	0	L
66	CB508872	GDP-L-fucose synthetase	−3.584	−1.992	1.388	0	L
67	CA056904	UNKNOWN	3.573	1.757	−1.75	0	L
68	CK990888	UNKNOWN	−3.567	−1.98	1.234	0	L
69	CA052962	Pentraxin fusion protein precursor	3.567	1.75	−1.639	0	L
70	CA062371	UNKNOWN	3.566	1.743	−1.622	0	L
71	CB517893	UNKNOWN	−3.559	−1.967	1.657	0	L
72	CB514528	Annexin A2-A	−3.543	−1.956	1.43	0	L
73	CB493750	Thymosin beta-12	−3.541	−1.944	1.53	0	L
74	CB505442	Calpain small subunit 1	−3.541	−1.932	1.395	0	L
75	CB502127	UNKNOWN	3.539	1.738	−1.836	0	L
76	CA039176	Gamma crystallin M2	3.538	1.732	−1.321	0	L
77	CB511903	Uncharacterized protein C1orf74 homolog	3.535	1.725	−1.682	0	L
78	CN442536	Cytochrome c oxidase subunit 3	−3.534	−1.921	1.3	0	L
79	CA063802	UNKNOWN	3.514	1.719	−1.455	0	L
80	CA047126	Glyceraldehyde-3-phosphate dehydrogenase	−3.499	−1.911	1.378	0	L
81	CA051479	UNKNOWN	3.47	1.714	−1.928	0	L
82	CA050751	Asparaginyl-tRNA synthetase. cytoplasmic	−3.47	−1.899	1.39	0	L
83	CA061252	Pleckstrin homology-like domain family A member 1	3.457	1.708	−1.62	0	L
84	CB502503	Cathepsin L precursor	3.453	1.702	−1.306	0	L
85	CB509531	Clusterin precursor	−3.447	−1.89	1.626	0	L
86	CA057824	Apolipoprotein Eb precursor	−3.436	−1.88	1.626	0	E
87	CA059732	Oncorhynchus mykiss SYPG1 (SYPG1). PHF1 (PHF1). and RGL2 (RGL2) genes. complete cds; DNaseII pseudogene. complete sequence; LGN-like. PBX2 (PBX2). NOTCH-like. TAP1 (TAP1). and BRD2 (BRD2) genes. complete cds; and MHCII-alpha and Raftlin-like pseudogenes. complete sequence	3.423	1.697	−1.716	0	L
88	CB513063	Perforin-1 precursor	3.417	1.692	−1.463	0	L
89	CA768741	UNKNOWN	−3.413	−1.871	1.357	0	L
90	CK990741	60S acidic ribosomal protein P1	3.398	1.687	−1.421	0	L
91	CB512134	Myosin light polypeptide 6	−3.388	−1.863	1.423	0	E
92	CB498494	Gamma crystallin M2	3.363	1.681	−1.345	0	L
93	CB502483	Fructose-bisphosphate aldolase B	3.358	1.676	−1.485	0	L
94	CA047466	UNKNOWN	3.344	1.671	−1.338	0	L
95	CB496999	UNKNOWN	−3.34	−1.854	1.273	0	L
96	CA060333	Hypoxanthine-guanine phosphoribosyltransferase	3.339	1.666	−1.267	0	L
97	CA062021	UNKNOWN	−3.323	−1.845	1.348	0	L
98	CA768027	Ubiquitin carboxyl-terminal hydrolase 32	3.321	1.661	−1.436	0	L
99	CA063261	Hexokinase-2	3.316	1.656	−1.633	0	L
100	CN442552	Cytochrome c oxidase subunit 3	−3.312	−1.837	1.334	0	L
101	CA042961	Eukaryotic peptide chain release factor subunit 1	−3.309	−1.829	1.345	0	L
102	CA057781	Nascent polypeptide-associated complex subunit alpha	3.308	1.651	−1.241	0	L
103	CA045638	Ubiquitin-conjugating enzyme E2 D4	3.304	1.646	−1.39	0	L
104	CA052800	THO complex subunit 1	3.285	1.641	−1.274	0	L
105	CB511609	Cathepsin L precursor	−3.279	−1.821	1.367	0	L
106	CB511219	Gamma crystallin M2	3.279	1.636	−1.504	0	E
107	CK990761	Cytochrome b	−3.275	−1.813	1.387	0	L
108	CA056981	UNKNOWN	3.274	1.631	−1.37	0	E
109	CA063526	Oncorhynchus mykiss G-protein (P-ras) mRNA. complete cds	3.263	1.627	−1.681	0	L
110	CN442497	Cytochrome c oxidase subunit 3	−3.259	−1.805	1.403	0	L
111	CA051104	Salmo salar TNF-alpha 2 gene. complete cds	3.247	1.622	−1.472	0	L
112	CA055845	UNKNOWN	3.244	1.618	−1.653	0	L
113	CA056167	Clusterin precursor	−3.209	−1.798	1.697	0	L
114	CA768207	Barrier-to-autointegration factor	3.206	1.613	−1.557	0	L
115	CA043681	UNKNOWN	−3.186	−1.791	1.25	0	L
116	CA047249	Excluded (Chimera)	−3.185	−1.784	1.63	0	L
117	CA052125	UNKNOWN	−3.185	−1.777	1.441	0	L
118	CB488101	Cold-inducible RNA-binding protein	−3.184	−1.77	1.35	0	L
119	CB515267	Integral membrane protein 2C	3.18	1.609	−1.436	0	L
120	CB499782	ADP-ribosylation factor 4	3.177	1.605	−1.585	0	L
121	CB492597	Ependymin precursor	3.17	1.6	−1.405	0	E
122	CK990775	UNKNOWN	−3.16	−1.763	1.291	0	L
123	CA051121	Homo sapiens calcium homeostasis endoplasmic reticulum protein (CHERP). mRNA	−3.157	−1.756	1.308	0	L
124	CB496460	hyperosmotic glycine rich protein [Salmo salar]	−3.147	−1.749	1.353	0	L
125	CB497026	Cathepsin L2 precursor	−3.146	−1.742	1.256	0	L
126	CA064587	UNKNOWN	3.146	1.596	−1.282	0	L
127	CA051534	UNKNOWN	−3.141	−1.736	1.391	0	L
128	CA052327	Mus musculus 10 days neonate skin cDNA. RIKEN full-length enriched library. clone:4732428C20 product:unclassifiable. full insert sequence	−3.138	−1.73	1.225	0	L
129	CB512146	B-cell linker protein	3.135	1.592	−1.468	0	L
130	CA041767	UNKNOWN	3.13	1.588	−1.399	0	L
131	CB497995	Eukaryotic translation initiation factor 4 gamma 1	3.127	1.584	−1.399	0	L
132	CA062835	Cold-inducible RNA-binding protein	−3.122	−1.725	1.297	0	L
133	CB514425	UNKNOWN	3.114	1.58	−1.383	0	L
134	CA037913	UNKNOWN	−3.096	−1.718	1.489	0	E
135	CB501344	Uncharacterized protein C8orf4 homolog	−3.095	−1.713	1.53	0	L
136	CA039269	UNKNOWN	3.094	1.576	−1.282	0	L
137	CK990381	Beta crystallin B3	3.092	1.572	−1.312	0	L
138	CK990533	Keratin. type II cytoskeletal 8	−3.077	−1.706	1.619	0	L
139	CA052374	UNKNOWN	3.071	1.568	−1.41	0	L
140	CA063499	UNKNOWN	3.055	1.564	−1.327	0	L
141	CA043660	Nuclear receptor 0B2	−3.044	−1.701	1.378	0	E
142	CA064148	UNKNOWN	−3.038	−1.696	1.271	0	L
143	CB494413	UNKNOWN	−3.009	−1.69	1.345	0	L
144	CB498981	RAB3A-interacting protein	3.003	1.561	−1.661	0	L
145	CA046217	UNKNOWN	−3.002	−1.685	1.357	0	L

The transcripts shown are those with a q-value of 0% with the most significantly differentially expressed transcripts on top of the list. The complete list is given in Appendix 1. Abbreviations used in the table header are: d[i], SAM score for a transcript i; de[i], expected SAM score for a transcript i. * The term "Regulation category" in the header of the last column refers to a categorization of the transcripts determined by appearance of the graphs resulting from correlation of expression levels to individual cataract scores (see Results section). The two categories are named E (“early” regulated transcripts), and L (“late” regulated transcripts).