Table 2 of Tröße, Mol Vis 2009; 15:1332-1350.

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).

Tröße, Mol Vis 2009; 15:1332-1350. http://www.molvis.org/molvis/v15/a141

©2009 Molecular Vision http://www.molvis.org/molvis/

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