SAM (Significance Analysis of Microarray) Results

Description of the problem:

Number of classes: 2
Number of genes that passed filtering criteria: 9984
Type of test used: SAM – Significance analysis of Microarray
Column of the Experiment Descriptors sheet that defines class variable : AFP_100
Target proportion of false discoveries : 0.1
Number of permutations : 100
Percentile for determining called genes that are false : 80

Genes which discriminate among classes:

Table 1
Class 1: 0; Class 2: 1.
There are 92 genes significant by SAM
The estimated false discovery rate among the 92 significant genes is 0.08236 .
The delta value used to identify the significant genes is 0.73681 .
The fudge factor for standard deviation is computed as 0.01517 .
d(i) is the observed relative difference for two-class problem. Click the HELP link at the top of the page for more information.

Order d(i) Geom mean of ratios in class 1 Geom mean of ratios in class 2 Fold-change Unique ID Annotations Clone ID Accession Symbol Entrez ID Defined Gene list
1 4.177 0.92 0.64 1.45 161146 161146 Info Incyte PD:2799664 U89281 HSD17B6 8630
2 4.144 0.95 0.69 1.36 168187 168187 Info Incyte PD:2099420 AI310515 ACSM2B 348158
3 3.892 0.85 0.59 1.43 161801 161801 Info Incyte PD:5034123 L21893 SLC10A1 6554
4 3.719 0.78 0.56 1.38 166007 166007 Info Incyte PD:606122 NM_000353 TAT 6898 Alkaloid biosynthesis I, Novobiocin biosynthesis,
Phenylalanine metabolism, Phenylalanine, tyrosine and
tryptophan biosynthesis, Tyrosine metabolism, immunology
5 3.64 0.94 0.66 1.42 167207 167207 Info Incyte PD:2590673 U39967 FMO3 2328 immunology
6 3.573 0.91 0.71 1.28 168452 168452 Info Incyte PD:1297179 NM_005956 MTHFD1 4522 Glyoxylate and dicarboxylate metabolism, One carbon pool
by folate
7 3.515 0.64 0.47 1.37 169374 169374 Info Incyte PD:2513602 NM_002150 HPD 3242 Phenylalanine metabolism, Tyrosine metabolism
8 3.485 0.78 0.62 1.26 168756 168756 Info Incyte PD:1794046 M93405 ALDH6A1 4329 Inositol metabolism, Propanoate metabolism, Valine,
leucine and isoleucine degradation
9 3.459 1.08 0.86 1.25 169717 169717 Info Incyte PD:1846226 AA970835 PGRMC1 10857
10 3.431 0.93 0.65 1.43 167792 167792 Info Incyte PD:1308102 D00230 OTC 5009 Arginine and proline metabolism, Urea cycle and
metabolism of amino groups, immunology, metabolism
11 3.385 0.8 0.56 1.42 164998 164998 Info Incyte PD:1633340 Y15793 CPS1 1373 Arginine and proline metabolism, Glutamate metabolism,
Nitrogen metabolism, Urea cycle and metabolism of amino
groups, immunology
12 3.351 0.86 0.71 1.22 165794 165794 Info Incyte PD:234123 AI301066 EPHX2 2053 Eicosanoid Metabolism, Arachidonic acid metabolism,
Tetrachloroethene degradation, immunology, metabolism,
pharmacology
13 3.348 1.13 0.92 1.23 160308 160308 Info Incyte PD:1445238 NM_014333 CADM1 23705 Cell adhesion molecules (CAMs)
14 3.346 0.83 0.57 1.47 161478 161478 Info Incyte PD:3752047 AB008775 AQP9 366
15 3.323 0.95 0.76 1.25 165324 165324 Info Incyte PD:1833801 BE393339 PXMP2 5827
16 3.307 0.99 0.83 1.2 168366 168366 Info Incyte PD:1287840 AI675901 SCP2 6342 PPAR signaling pathway
17 3.303 0.81 0.59 1.38 166095 166095 Info Incyte PD:1311471 AA113231 CPS1 1373 Arginine and proline metabolism, Glutamate metabolism,
Nitrogen metabolism, Urea cycle and metabolism of amino
groups, immunology
18 3.291 0.73 0.57 1.28 165233 165233 Info Incyte PD:1427681 H94887 GLYAT 10249
19 3.258 1.01 0.86 1.17 165777 165777 Info Incyte PD:685416 M36429 GNB2 2783
20 3.252 1 0.89 1.13 161491 161491 Info Incyte PD:2554470 X83441 LIG4 3981 DNA_adducts, DNA_damage
21 3.222 0.9 0.7 1.28 166778 166778 Info Incyte PD:1631511 X92720 PCK2 5106 Adipocytokine signaling pathway, Citrate cycle (TCA
cycle), Insulin signaling pathway, PPAR signaling pathway,
Pyruvate metabolism
22 3.198 0.95 0.74 1.29 162315 162315 Info Incyte PD:489032 D43704 CACNB3 784 MAPK signaling pathway
23 3.168 0.96 0.81 1.18 166910 166910 Info Incyte PD:2058620 AI309555 ADI1 55256
24 3.138 0.93 0.77 1.22 167281 167281 Info Incyte PD:546754 NM_003718 CDK13 8621
25 3.137 0.91 0.77 1.18 164136 164136 Info Incyte PD:1300469 M74096 ACADL 33 beta-Alanine metabolism, Fatty acid metabolism, PPAR
signaling pathway, Propanoate metabolism, Valine, leucine
and isoleucine degradation, immunology
26 3.11 0.88 0.69 1.27 160425 160425 Info Incyte PD:666190 S52784 CTH 1491 Cysteine metabolism, Glycine, serine and threonine
metabolism, Methionine metabolism, Nitrogen metabolism,
Selenoamino acid metabolism, misc
27 3.108 0.91 0.68 1.33 165825 165825 Info Incyte PD:1902152 AW627651 SDS 10993 Cysteine metabolism, Glycine, serine and threonine
metabolism
28 3.092 0.74 0.5 1.49 161296 161296 Info Incyte PD:1669534 K01763 HP 3240 immunology, misc
29 3.088 0.95 0.82 1.15 161511 161511 Info Incyte PD:3271263 X12910 ATP1A3 478
30 3.084 0.82 0.66 1.25 166057 166057 Info Incyte PD:400429 NM_000306 POU1F1 5449 transcription
31 3.064 0.94 0.72 1.31 164992 164992 Info Incyte PD:4244645 AI791352 DAO 1610 Arginine and proline metabolism, D-Arginine and
D-ornithine metabolism, Glycine, serine and threonine
metabolism, immunology
32 3.06 0.86 0.66 1.29 169679 169679 Info Incyte PD:87242
33 2.989 0.92 0.81 1.14 163485 163485 Info Incyte PD:3561805 NM_001942 DSG1 1828 Cell Communication, immunology
34 2.984 0.89 0.72 1.23 160233 160233 Info Incyte PD:614679 Y12735 DYRK3 8444 signal_transduction
35 2.975 0.99 0.86 1.15 166974 166974 Info Incyte PD:1702350 AW025439 GADD45A 1647 ATM Signaling Pathway, Cell Cycle: G2/M Checkpoint,
Hypoxia and p53 in the Cardiovascular system, p53
Signaling Pathway, Cell cycle, MAPK signaling pathway
36 2.925 1 0.82 1.21 167196 167196 Info Incyte PD:1922001 AW246790 BDH1 622 Butanoate metabolism, Synthesis and degradation of
ketone bodies
37 2.922 1 0.9 1.12 163580 163580 Info Incyte PD:3200341 M15169 ADRB2 154 Corticosteroids and cardioprotection, Cystic fibrosis
transmembrane conductance regulator (CFTR) and beta 2
adrenergic receptor (b2AR) pathway, Phospholipase
C-epsilon pathway, Calcium signaling pathway, Neuroactive
ligand-receptor interaction, behavior, immunology
38 2.918 0.92 0.75 1.22 160471 160471 Info Incyte PD:532254 X95384 HRSP12 10247
39 2.916 0.87 0.68 1.28 169589 169589 Info Incyte PD:911015 U63008 HGD 3081 Styrene degradation, Tyrosine metabolism
40 2.913 0.92 0.75 1.23 159780 159780 Info Incyte PD:1601609 AJ001319 MPDZ 8777 Tight junction
41 2.912 0.7 0.51 1.37 161003 161003 Info Incyte PD:2373085 M24317 ADH1B 125 1- and 2-Methylnaphthalene degradation, Bile acid
biosynthesis, Fatty acid metabolism, Glycerolipid
metabolism, Glycolysis / Gluconeogenesis, Metabolism of
xenobiotics by cytochrome P450, Tyrosine metabolism
42 2.909 0.89 0.73 1.23 164412 164412 Info Incyte PD:1804662 NM_003869 CES2 8824
43 2.908 0.7 0.52 1.34 161259 161259 Info Incyte PD:2516815 X98332 SLC22A1 6580
44 2.896 0.74 0.55 1.34 160174 160174 Info Incyte PD:166909 J05064 C6 729 Alternative Complement Pathway, Cells and Molecules
involved in local acute inflammatory response, Classical
Complement Pathway, Complement Pathway, Lectin Induced
Complement Pathway, Complement and coagulation cascades,
immunology
45 2.89 0.99 0.89 1.11 161323 161323 Info Incyte PD:3419068 AF071542 SEMA7A 8482 Axon guidance
46 2.887 0.91 0.77 1.18 163533 163533 Info Incyte PD:1930954 AA805411 ECHDC2 55268
47 2.886 0.93 0.81 1.15 162878 162878 Info Incyte PD:1805089 AI192537 TMEM56 148534
48 2.858 0.77 0.65 1.17 163887 163887 Info Incyte PD:1595081 M59979 PTGS1 5742 Aspirin Blocks Signaling Pathway Involved in Platelet
Activation, Eicosanoid Metabolism, Mechanism of
Acetaminophen Activity and Toxicity, Arachidonic acid
metabolism, immunology
49 2.857 0.75 0.6 1.24 159969 159969 Info Incyte PD:1664320 M14058 C1R 715 Classical Complement Pathway, Complement Pathway,
Complement and coagulation cascades, immunology
50 2.838 0.91 0.74 1.23 161484 161484 Info Incyte PD:2515733 AF054821 CYP4F3 4051 Arachidonic acid metabolism, pharmacology
51 2.829 1.04 0.87 1.2 165274 165274 Info Incyte PD:1740924 AA203542 SLC6A1 6529
52 2.828 0.78 0.54 1.44 162599 162599 Info Incyte PD:1740889 M69197 HPR 3250///3240 immunology
53 2.813 1 0.88 1.13 164597 164597 Info Incyte PD:1923117 AI269221 C8orf40 114926
54 2.807 0.83 0.64 1.28 169027 169027 Info Incyte PD:2516665 U32576 APOC4 346
55 2.795 1.03 0.9 1.15 160100 160100 Info Incyte PD:1811220 NM_001182 ALDH7A1 501 Arginine and proline metabolism, Ascorbate and aldarate
metabolism, beta-Alanine metabolism, Bile acid
biosynthesis, Butanoate metabolism, Fatty acid metabolism,
Glycerolipid metabolism, Glycolysis / Gluconeogenesis,
Histidine metabolism, Limonene and pinene degradation,
Lysine degradation, Propanoate metabolism, Pyruvate
metabolism, Tryptophan metabolism, Valine, leucine and
isoleucine degradation
56 2.794 0.97 0.84 1.16 164495 164495 Info Incyte PD:1968776 AW275347 ACACB 32 Adipocytokine signaling pathway, Fatty acid
biosynthesis, Insulin signaling pathway, Propanoate
metabolism, Pyruvate metabolism
57 2.793 0.84 0.7 1.2 165554 165554 Info Incyte PD:943569 AA707391 ALAS1 211 Hemoglobin\’s Chaperone, Glycine, serine and threonine
metabolism
58 2.792 0.79 0.59 1.33 164296 164296 Info Incyte PD:2514507 NM_000040 APOC3 345 PPAR signaling pathway, immunology
59 2.758 1.05 0.91 1.15 166966 166966 Info Incyte PD:1638850 NM_004493 HSD17B10 3028 Butanoate metabolism, Caprolactam degradation, Fatty
acid elongation in mitochondria, Fatty acid metabolism,
Lysine degradation, Tryptophan metabolism, Valine, leucine
and isoleucine degradation
60 2.741 0.99 0.85 1.16 169282 169282 Info Incyte PD:88935
61 2.739 0.81 0.61 1.32 162415 162415 Info Incyte PD:139449 NM_001713 BHMT 635 Glycine, serine and threonine metabolism, Methionine
metabolism, misc
62 2.732 0.97 0.87 1.12 168483 168483 Info Incyte PD:1938951 AI536745 FAM134B 54463
63 2.731 0.97 0.85 1.15 167750 167750 Info Incyte PD:2840195 NM_001123 ADK 132 Purine metabolism, cell_cycle, cell_signaling,
immunology, signal_transduction
64 2.722 0.97 0.85 1.13 165041 165041 Info Incyte PD:259054 AL034562 LOC727993 727993///140885///5173
65 2.713 0.77 0.64 1.21 160017 160017 Info Incyte PD:1664796 D85510 MMP15 4324 immunology
66 2.711 0.94 0.82 1.14 161416 161416 Info Incyte PD:1957615 X52638 PFKFB1 5207 Fructose and mannose metabolism
67 2.686 0.9 0.63 1.43 162311 162311 Info Incyte PD:480059 NM_000488 SERPINC1 462 Acute Myocardial Infarction, Extrinsic Prothrombin
Activation Pathway, Intrinsic Prothrombin Activation
Pathway, Complement and coagulation cascades
68 2.686 0.68 0.55 1.24 164943 164943 Info Incyte PD:168865 M17398 CYP2C8 1558 Arachidonic acid metabolism, Linoleic acid metabolism,
Metabolism of xenobiotics by cytochrome P450
69 2.682 0.79 0.64 1.24 161326 161326 Info Incyte PD:3146420 AF057034 RDH16 8608
70 2.68 0.67 0.5 1.33 163931 163931 Info Incyte PD:1583076 M12272 ADH1C 126 1- and 2-Methylnaphthalene degradation, Bile acid
biosynthesis, Fatty acid metabolism, Glycerolipid
metabolism, Glycolysis / Gluconeogenesis, Metabolism of
xenobiotics by cytochrome P450, Tyrosine metabolism
71 2.679 0.76 0.54 1.42 162099 162099 Info Incyte PD:763477 U50929 BHMT 635 Glycine, serine and threonine metabolism, Methionine
metabolism, misc
72 2.669 0.78 0.63 1.25 160366 160366 Info Incyte PD:260090 AL162049 USP10 9100
73 2.659 0.99 0.85 1.17 169315 169315 Info Incyte PD:2591494 NM_003944 SELENBP1 8991
74 2.628 1.2 1.07 1.12 169441 169441 Info Incyte PD:2058949 W24219 NDUFA1 4694 Electron Transport Reaction in Mitochondria, Oxidative
phosphorylation
75 2.61 1.15 0.99 1.16 169675 169675 Info Incyte PD:1215248 NM_000154 GALK1 2584 Leloir pathway of galactose metabolism, Galactose
metabolism, immunology
76 2.576 0.9 0.77 1.17 165440 165440 Info Incyte PD:1812030 AI866254 PBLD 64081
77 2.57 0.74 0.6 1.24 162162 162162 Info Incyte PD:5035985 M16974 C8A 731 Alternative Complement Pathway, Classical Complement
Pathway, Complement Pathway, Lectin Induced Complement
Pathway, Complement and coagulation cascades, immunology
78 2.549 0.82 0.68 1.19 160741 160741 Info Incyte PD:2043488 AI051566 ALDH8A1 64577
79 2.544 1.09 0.91 1.2 163597 163597 Info Incyte PD:1755193 AK000373 SYBU 55638
80 2.544 0.99 0.81 1.22 167287 167287 Info Incyte PD:2103752 AI064915 CYB5A 1528
81 2.54 0.96 0.85 1.13 162192 162192 Info Incyte PD:1988940 AA505399 ACADM 34 beta-Alanine metabolism, Fatty acid metabolism, PPAR
signaling pathway, Propanoate metabolism, Valine, leucine
and isoleucine degradation, immunology
82 2.505 1 0.83 1.21 168791 168791 Info Incyte PD:1965695 AF104913 EIF4G1 1981 Eukaryotic protein translation, Internal Ribosome entry
pathway, mTOR Signaling Pathway, Regulation of eIF4e and
p70 S6 Kinase, immunology
83 2.473 0.81 0.65 1.26 166785 166785 Info Incyte PD:778212 AW204828 SLC38A4 55089
84 2.469 0.95 0.83 1.14 167390 167390 Info Incyte PD:1217904 U60873 NEAT1 283131
85 -4.418 0.86 1.58 0.55 165127 165127 Info Incyte PD:29365 AA334619 AFP 174 immunology
86 -3.559 1.01 1.24 0.81 167243 167243 Info Incyte PD:387863 NM_003097 SNRPN 6638 immunology
87 -3.384 1.48 2.12 0.7 162373 162373 Info Incyte PD:645584 U50410 GPC3 2719
88 -3.353 1 1.14 0.88 161147 161147 Info Incyte PD:2416415 NM_004760 STK17A 9263 apoptosis, signal_transduction
89 -3.233 1.08 1.34 0.8 163304 163304 Info Incyte PD:1420380 U76705 IGF2BP3 10643
90 -3.212 0.99 1.12 0.88 166900 166900 Info Incyte PD:429577 AA417813 STEAP4 79689
91 -3.147 1.08 1.52 0.71 162399 162399 Info Incyte PD:2060823 AI151190 S100P 6286
92 -3.093 0.84 1.01 0.83 160418 160418 Info Incyte PD:444957 AB013382 DUSP6 1848 Regulation of MAP Kinase Pathways Through Dual
Specificity Phosphatases, MAPK signaling pathway

SAM

CCD

Filtering parameters:

R version 2.13.2 (2011-09-30)
Name of the project file: HCCProject.xls
Time of the analysis: Mon Jan 07 13:07:20 2013
BRB – Array Tools Version: 4.2.1 – Stable Release (January 2012)
Project annotated by SOURCE (source stanford.edu), searched by gene identifier: Symbol, on 4/30/2011 5:52:48 PM

  • Apply Background adjustment: OFF
  • Spot Filters: OFF
  • Average the replicate spots within an array: OFF
  • Use a common reference design: OFF
  • Normalization: OFF
  • Gene Filters: OFF
  • Gene Subsets: OFF