Table 2. The genes classified as grain filling in Zhu et al. 2002 are grouped and ordered by node from hierarchical clustering. C is the node correlation value from Cluster. P is the percent of genes in a node that rank above the 80th percentile in a ranking based on the second singular vector. †Although node 439 was selected in its entirely, it is better described by two nodes, for which C and P values are shown. Genes ranked at the 80th percentile or higher in the ranking based on the second singular vector have their percentiles colored yellow. The second singular vector exhibits a grain-filling pattern and these genes are classified as grain filling. Genes not selected in this manner, but are above the 80th percentile in other rankings by singular vectors have their percentiles colored red. Three probe sets that were excluded in Zhu et al. from the set of 98 due to absent calls are indicated by italics: OS010689.1, OS003342, OS015423.
Percentile rankings based on Left Singular Vectors / Probe Set ID / AnnotationLSV 6 / LSV 5 / LSV 4 / LSV 3 / LSV 2
Node 439
C = † / P = 0.92
C = 0.37 / P = 0.93
67.8% / 31.2% / 48.5% / 58.0% / 65.6% / OS017582.1_r_at / gi|7267708| sucrose-phosphate synthase-like protein [Arabidopsis thaliana]
69.0% / 36.3% / 43.8% / 52.1% / 71.7% / OS019628.1_at / gi|7576210| palmitoyl-protein thioesterase precursor-like [Arabidopsis thaliana]
75.6% / 51.9% / 51.1% / 67.8% / 81.7% / OS010477_at / CIT1_KLEPN P16482 KLEBSIELLA PNEUMONIAE. CITRATE-PROTON SYMPORT
68.2% / 42.8% / 71.9% / 74.5% / 83.3% / OS007446_at / LPXK_FRANO Q47909 FRANCISELLA NOVICIDA.
PROBABLE TETRAACYLDISACCHARIDE 4 -KINASE
38.5% / 90.0% / 9.2% / 83.5% / 90.2% / OS000530_at / gi|5257102 granule bound starch synthase [Oryza sativa subsp. japonica]
83.1% / 93.3% / 11.6% / 88.0% / 91.2% / OS020623_i_at / ACSA_ALCEU P31638 ALCALIGENES EUTROPHUS.
ACETYL-COENZYME A SYNTHETASE
90.0% / 95.5% / 23.8% / 91.0% / 92.9% / OS001586.1_s_at / gi|22327| corn Hageman factor inhibitor [Zea mays]
93.3% / 64.2% / 17.3% / 79.6% / 89.6% / OS000904.1_at / gi|1620753 proteinase inhibitor [Oryza sativa]
55.8% / 58.9% / 7.9% / 79.2% / 92.5% / OS003023.1_at / gi|553108 UDP-glucose starch glycosyl transferase
40.1% / 63.3% / 8.1% / 70.7% / 90.4% / OS007380_at / UGS3_SOLTU Q43847 SOLANUM TUBEROSUM
14.3% / 75.4% / 3.3% / 54.0% / 93.3% / OS011873_s_at / gi|169759 ADP-glucose pyrophosphorylase 51kD subunit
19.8% / 81.9% / 5.5% / 53.2% / 92.1% / OS001827.1_s_at / GLGS_ORYSA P15280 ORYZA SATIVA
52.1% / 76.4% / 27.1% / 56.0% / 90.6% / OS001067_at / gi|5257290 unknown [Zea mays]
90.6% / 97.8% / 2.6% / 73.1% / 97.4% / OS015404_at / gi|1783306 starch debranching enzyme precursor [Oryza sativa]
89.2% / 85.1% / 15.1% / 85.5% / 93.1% / OS000274_r_at / gi|1398918 allergenic protein [Oryza sativa]
82.3% / 92.3% / 8.6% / 85.1% / 94.1% / OS003024_at / GL19_ORYSA P29835 ORYZA SATIVA
69.9% / 90.8% / 26.7% / 67.4% / 94.7% / OS_ORF005803_at / Open Reading Frame OS_ORF005803 ST(R) HTC034709-A01.26
FRAME: 3 ORF: 12 LEN: 840
67.2% / 88.8% / 18.1% / 43.2% / 90.8% / OS011173.1_at / gi|3252794 isoamylase [Oryza sativa]
83.3% / 86.6% / 6.5% / 42.4% / 91.9% / OS006427.1_at / gi|5825470 isoamylase 1 [Hordeum vulgare]
69.5% / 57.0% / 16.7% / 37.1% / 94.3% / OS_ORF006718_at / Open Reading Frame OS_ORF006718 HTC040339-A01.27
FRAME: 2 ORF: 29 LEN: 711
80.7% / 25.7% / 91.4% / 38.9% / 86.4% / OS014371.1_at / PTR2_YEAST P32901 SACCHAROMYCES CEREVISIAE
93.5% / 67.8% / 93.7% / 29.1% / 91.4% / OS009174_s_at / ACBP_GOSHI Q39779 GOSSYPIUM HIRSUTUM
87.2% / 58.2% / 97.6% / 36.3% / 91.0% / OS005956_f_at / gi|4455257| oleosin, 18.5K [Arabidopsis thaliana]
99.0% / 22.2% / 99.8% / 29.7% / 94.9% / OS006526_at / gi|944830| soybean 24 kDa oleosin isoform [Glycine max]
94.7% / 25.1% / 99.2% / 32.8% / 92.7% / OS009002_f_at / gi|1171354 18 kDa oleosin [Oryza sativa]
95.1% / 20.6% / 99.4% / 35.4% / 93.5% / OS008885_f_at / OLE2_ORYSA Q40646 ORYZA SATIVA
98.4% / 39.9% / 100% / 25.1% / 95.3% / OS000217_s_at / gi|1171352 16 kDa oleosin [Oryza sativa]
C = 0.48 / P = 0.91
69.7% / 47.9% / 32.6% / 58.2% / 77.6% / OS000739_at / gi|5734442| hexose transporter [Lycopersicon esculentum]
65.6% / 27.1% / 23.0% / 61.9% / 85.5% / OS017020.1_at / gi|8072390 AC013453_3 Putative ABC transporter [Arabidopsis thaliana]
59.7% / 36.7% / 20.8% / 42.6% / 72.3% / OS012020_i_at / ABCX_PORPU P51241 PORPHYRA PURPUREA.
PROBABLE ATP-DEPENDENT TRANSPORTER YCF16.
38.9% / 91.9% / 12.2% / 45.2% / 87.2% / OS016537.1_at / gi|8777412 indole-3-glycerol phosphate synthase [Arabidopsis thaliana]
63.5% / 90.4% / 7.3% / 45.0% / 88.8% / OS006069.1_at / gi|7262678 AC012188_13 Contains similarity to UDP-galactose transporter
from Homo sapiens gi|2136347.
73.3% / 81.7% / 47.3% / 39.7% / 79.2% / OS009216_at / gi|6358808 AC010675_11 nitrate transporter
0.2% / 89.8% / 22.4% / 7.7% / 93.7% / OS005805.1_at / gi|5231119 AF143202_1 starch phosphorylase L [Solanum tuberosum]
6.1% / 34.8% / 10.6% / 39.9% / 89.2% / OS012600.1_at / gi|3057122 starch synthase DULL1 [Zea mays]
86.4% / 87.8% / 10.4% / 80.0% / 95.7% / OS002074.1_at / gi|2894148| monomeric alpha-amylase inhibitor [Triticum aestivum]
74.9% / 94.5% / 1.8% / 40.9% / 99.4% / OS016215_at / PULA_KLEPN P07206 KLEBSIELLA PNEUMONIAE. PULLULANASE PRECURSOR
65.8% / 59.7% / 6.3% / 51.3% / 96.9% / OS001734.1_at / gi|225102|1208404A trypsin/amylase inhibitor pUP13 [Hordeum vulgare var. distichum]
60.9% / 38.7% / 28.1% / 56.4% / 95.9% / OS000009_at / gi|218201 allergenic protein [Oryza sativa]
30.1% / 25.3% / 56.8% / 28.5% / 99.8% / OS008901.1_f_at / gi|607202| 15kDa grain softness protein [Triticum aestivum]
18.3% / 28.3% / 61.5% / 27.3% / 98.2% / OS002362.1_f_at / gi|166555 avenin
6.9% / 25.5% / 81.7% / 17.9% / 98.8% / OS000235_at / gi|296129| prolamin [Oryza sativa]
15.5% / 11.8% / 79.0% / 22.0% / 98.6% / OS010401.1_f_at / gi|693794 alcohol-soluble avenin-3=23.2 kda protein
[Avena sativa=oat, Narymsky 943, Peptide, 201 aa]
14.9% / 21.6% / 65.8% / 23.4% / 98.0% / OS010430_f_at / gi|18907| pot. B1 hordein [Hordeum vulgare]
16.5% / 2.4% / 71.3% / 11.4% / 99.2% / OS006413.1_at / gi|20227| preprolglutelin
16.3% / 10.0% / 71.7% / 13.6% / 100% / OS013486_i_at / gi|1362180|pir||S57654 glutenin low molecular weight - wheat
4.5% / 7.3% / 86.8% / 16.5% / 97.1% / OS000596.1_at / GU11_ORYSA P07728 ORYZA SATIVA
3.3% / 2.6% / 84.9% / 9.2% / 99.6% / OS000688.1_at / gi|20232| precursor
4.7% / 12.6% / 77.8% / 15.1% / 96.1% / OS000035_at / gi|556407 prolamin
4.3% / 7.1% / 85.7% / 17.1% / 98.4% / OS019545.1_f_at / gi|169969 glycinin
8.8% / 7.5% / 3.9% / 10.0% / 99.0% / OS000083_at / gi|4126693 prolamin [Oryza sativa]
34.4% / 8.1% / 29.9% / 24.6% / 97.6% / OS004900.1_at / gi|20208| glutelin [Oryza sativa]
16.9% / 16.5% / 26.1% / 31.8% / 95.5% / OS005389_at / gi|169805 [Oryza sativa DNA fragment with a miscellaneous signal and
an open reading frame.], gene product
20.4% / 15.3% / 13.4% / 25.7% / 96.7% / OS000410_f_at / gi|311643| 13kDa prolamin [Oryza sativa]
20.8% / 11.6% / 31.6% / 20.6% / 96.3% / OS000082_at / gi|4126695 prolamin [Oryza sativa]
44.6% / 71.5% / 9.8% / 25.5% / 94.5% / OS015589.1_at / GLGB_ORYSA Q01401 ORYZA SATIVA
53.8% / 36.9% / 10.8% / 31.4% / 96.5% / OS013446.1_f_at / gi|7209261| alpha-gliadin [Triticum aestivum]
22.2% / 39.7% / 14.5% / 20.0% / 93.9% / OS015550_at / gi|4584507| starch branching enzyme II [Solanum tuberosum]
3.7% / 26.9% / 1.0% / 8.4% / 97.8% / OS001637.1_f_at / gi|3093462 ADP-glucose pyrophosphorylase large subunit [Oryza sativa]
20.2% / 24.8% / 1.2% / 20.8% / 95.1% / OS012678_at / gi|226227|1502200A prolamin [Avena sativa]
Node 437
C = 0.19 / P = 0.44
39.3% / 96.1% / 13.0% / 71.1% / 70.9% / OS013252_at / gi|6899922| multifunctional aminoacyl-tRNA ligase-like protein [Arabidopsis thaliana]
62.1% / 82.9% / 45.0% / 64.0% / 66.2% / OS018204_at / gi|4680496 AF119222_8 putative sugar transporter protein [Oryza sativa]
98.0% / 97.1% / 77.2% / 51.5% / 87.6% / OS018385_r_at / ARE2_YEAST P53629 SACCHAROMYCES CEREVISIAE
63.7% / 91.2% / 65.0% / 45.8% / 75.6% / OS009236_at / KSU5_ECOLI P42216 ESCHERICHIA COLI. 3-DEOXY-MANNO-OCTULOSONATE
CYTIDYLYLTRANSFERASE
21.2% / 62.7% / 23.6% / 61.5% / 80.0% / OS023382_at / YA79_HAEIN P45023 HAEMOPHILUS INFLUENZAE. HYPOTHETICAL
AMINO-ACID ABC TRANSPORTER PERMEASE PROTEIN HI0179.
31.6% / 70.7% / 48.7% / 49.1% / 70.7% / OS001622.1_r_at / gi|169767 alpha-amylase
49.3% / 52.7% / 37.3% / 62.7% / 76.6% / OS020548.1_at / AMYG_NEUCR P14804 NEUROSPORA CRASSA. GLUCOAMYLASE PRECURSOR
54.8% / 71.7% / 68.6% / 50.9% / 82.5% / OS006501.1_r_at / TRPC_BACSU P03964 BACILLUS SUBTILIS. INDOLE-3-GLYCEROL
PHOSPHATE SYNTHASE
5.7% / 49.3% / 51.5% / 34.2% / 80.2% / OS012142_at / gi|7339489| phospholipase-like protein [Arabidopsis thaliana]
Node 453
C = 0.10 / P = 0.4
85.1% / 36.0% / 14.3% / 87.8% / 67.0% / OS015390_at / gi|6648208 AC013483_30 putative phosphatidylinositol-4-phosphate
5-kinase [Arabidopsis thaliana]
38.7% / 61.5% / 53.6% / 57.8% / 59.3% / OS021820_r_at / LIP3_MORSP P24640 MORAXELLA SP. LIPASE 3 PRECURSOR
76.0% / 80.4% / 17.9% / 88.8% / 74.1% / OS021398_i_at / G6NT_HUMAN Q02742 HOMO SAPIENS
22.6% / 66.6% / 24.6% / 79.0% / 78.0% / OS006763.1_at / gb|Z95637 acyl-CoA:1-acylglycerol-3-phosphate acyltransferase
from Brassica napus. [Arabidopsis thaliana]
35.4% / 48.5% / 47.7% / 53.8% / 58.5% / OS013884.1_i_at / PTSN_ECOLI P31222 ESCHERICHIA COLI. NITROGEN REGULATORY IIA PROTEIN
47.9% / 51.1% / 15.7% / 79.8% / 81.5% / OS018830_i_at / OPT1_CAEEL Q17758 CAENORHABDITIS ELEGANS.
HYPOTHETICAL OLIGOPEPTIDE TRANSPORTER C06G8.2.
45.0% / 69.0% / 36.5% / 69.9% / 76.8% / OS006772.1_i_at / gi|2981620 mutated 3-ketoacyl-CoA thiolase [Arabidopsis thaliana]
54.6% / 55.0% / 47.9% / 65.8% / 79.8% / OS005686_at / YDEX_ECOLI P77257 ESCHERICHIA COLI.
HYPOTHETICAL ABC TRANSPORTER ATP-BINDING PROTEIN YDEX.
90.8% / 78.2% / 39.1% / 77.8% / 78.8% / OS006283_at / gi|3869206 Phosphate Transporter 4 [Arabidopsis thaliana]
88.8% / 73.1% / 22.6% / 88.2% / 77.0% / OS012835_at / PITH_STRHA P41132 STREPTOMYCES HALSTEDII.
PUTATIVE LOW-AFFINITY INORGANIC PHOSPHATE TRANSPORTER
37.7% / 59.9% / 14.9% / 27.9% / 39.7% / OS010689.1_at / PA2M_MOUSE P31482 Q60871 MUS MUSCULUS
30.5% / 49.7% / 55.0% / 76.8% / 51.9% / OS003342_at / ABC transporter-7
90.6% / 97.8% / 2.6% / 73.1% / 97.4% / OS015423_at / gi|5430757 AC007504_12 Putative acyl CoA synthetase [Arabidopsis thaliana]
96.1% / 93.5% / 95.7% / 99.6% / 88.6% / OS009917_at / gi|6850341 AC022354_3 putative peptide transporter [Arabidopsis thaliana]
95.7% / 92.5% / 96.3% / 92.7% / 89.8% / OS017766.1_at / gi|6714447 AC011620_10 putative phospholipase D [Arabidopsis thaliana]
65.0% / 62.5% / 59.3% / 67.0% / 73.7% / OS008739.1_at / gi|4587543 AC006577_10 Belongs to the PF|00657 Lipase/Acylhydrolase
with GDSL-motif family.
87.0% / 85.5% / 84.3% / 70.5% / 80.9% / OS016223_at / PPI1_RABIT P48738 ORYCTOLAGUS CUNICULUS
92.3% / 83.5% / 78.8% / 62.5% / 84.9% / OS009020.1_r_at / gi|254616 bifunctional subtilisin/alpha-amylase inhibitor,
RASI [Oryza sativa=rice, seeds, bran, Peptide, 176 aa]
99.8% / 79.4% / 93.9% / 95.3% / 89.4% / OS002073.1_at / gi|18916| bifunctional alpha-amylase/subtilisin inhibitor [Hordeum vulgare]
97.4% / 94.9% / 87.6% / 78.8% / 91.6% / OS010384_at / gi|6358806 AC010675_9 putative peptide transporter [Arabidopsis thaliana]
Node 423
C = 0.30 / P = 0.42
60.1% / 88.6% / 90.2% / 89.6% / 70.1% / OS020923_at / CRTI_PHYBL P54982 PHYCOMYCES BLAKESLEEANUS.
PHYTOENE DEHYDROGENASE
24.4% / 83.7% / 71.1% / 66.4% / 64.2% / OS019211_at / Y877_METJA Q58287 METHANOCOCCUS JANNASCHII.
PUTATIVE ABC TRANSPORTER PERMEASE PROTEIN MJ0877.
38.3% / 72.5% / 40.5% / 66.6% / 72.5% / OS022874_at / TRPC_AZOBR P26938 AZOSPIRILLUM BRASILENSE.
INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE
66.8% / 83.3% / 43.4% / 81.9% / 79.0% / OS009890_f_at / FABG_HAEIN P43713 HAEMOPHILUS INFLUENZAE.
3-OXOACYL-[ACYL-CARRIER PROTEIN] REDUCTASE
56.8% / 79.6% / 51.7% / 62.3% / 62.1% / OS021397.1_i_at / FCGN_HUMAN P55899 HOMO SAPIENS
87.6% / 96.3% / 61.7% / 95.9% / 85.9% / OS018238_at / ACO1_YEAST P21147 SACCHAROMYCES CEREVISIAE
48.7% / 81.1% / 46.8% / 62.9% / 67.6% / OS021939.1_i_at / LEG9_RAT P97840 O08588 RATTUS NORVEGICUS
1.4% / 99.2% / 76.0% / 95.1% / 88.4% / OS020669_at / ACH1_YEAST P32316 SACCHAROMYCES CEREVISIAE
21.6% / 80.7% / 37.1% / 58.7% / 70.3% / OS009158_at / gi|6714431 AC012328_22 putative cellulose synthase catalytic
subunit [Arabidopsis thaliana]
12.8% / 93.1% / 74.5% / 71.5% / 85.7% / OS020524.1_at / AMYM_BACST P19531 BACILLUS STEAROTHERMOPHILUS.
MALTOGENIC ALPHA-AMYLASE PRECURSOR
31.0% / 84.9% / 79.4% / 66.0% / 86.2% / OS022546_at / PTSB_VIBAL P22825 VIBRIO ALGINOLYTICUS. PTS SYSTEM,
SUCROSE-SPECIFIC IIBC COMPONENT
0.4% / 99.0% / 80.4% / 89.2% / 88.2% / OS006321.1_at / gi|5052025 AF155815_1 glycerol-3-phosphate acyltransferase [Oryza sativa]