For each GT family with more than three members, the full protein sequences
were aligned using ClustalW Version 2.0 with default options. Then maximum likelihood
trees were bulit using PhyML with JTT model.
CAZy Family
GT Family assignment from Carbohydrate Active enZymes (CAZy) database. Domain Assignment
GT related domain identified by Pfam and/or Interpro databases. Source
GT identification method, including CAZy, homolog search, domain search and paralog search. RGAP Paralog Family
Paralog family classification generated by Rice Genome Annotation Project (Lin et al., 2008). Chromosome
The chromosome on which each GT gene is located. 5' end
Position of 5' end of GT coding sequence. 3 'end
Position of 3' end of GT coding sequence. BAC Name
Name of BAC clone from which each GT sequence was derived. GB Accession
The GenBank Accession Number of BAC clone from which each GT sequence was derived. RAP2 Locus
The corresponding locus ID from Rice Annotation Project (RAP) annotation Ver 2. NCBI Blast Link
Displays a link to the NCBI blastp search. Click on the link and you will be
redirected to the current NCBI blastp search result.
TE-related
Sequences that contain regions matching transposable elements. EST/cDNA
Sequences with matching full-length cDNAs or ESTs. Finished/Unfinished
At the time of TIGR rice pseudomolecule release 5, 98.8 % (3,408 BAC/PAC clones) of the
rice genome sequence was "finished" and the remaining "unfinished" regions are
from lower quality sequence that requires additional sequencing passes. PASA Status
The Program to Assemble Spliced Alignments (PASA) was developed and employed
towards the incorporation of EST and FL-cDNA alignments into the
TIGR Arabidopsis genome annotation. Annotated sequences with exact cDNA
matches are listed as "PASA-validated" Sequences with cDNA hits that do not
exactly match are listed as "PASA-failed" This information assists with assessing
the quality of each GT sequence.
The rice GT orthologs in selected dicots were identified by InParanoid Version 2 (Remm et al., 2001). The dicots genomes used to scan for orthologs are Arabidopsis thaliana, Medicago truncatula, Populus trichocarpa and Ricinus
communis.
Transmembrane Domain
TM indicates the presence of one or more predicted transmembrane domains by TMHMM Server Version 2.0. N-terminal Signal Peptide
SignalP indicates presence of predicted N-terminal signal peptide by SignalP Version 3.0. Chloroplast Transit Peptide
ChloroP indicates presence of predicted chloroplast transit peptide by ChloroP Version 1.1. Predicted Subcellular Localization
The subcellular localization of rice GTs, including 'secretory pathway', 'chloroplast', 'mitochondrion' and 'any other location' as predicted byTargetP Version 1.1.
The digital northern data is from TIGR and provides the tissue specific
gene expression evidence for rice loci based on EST data (Jung et al., 2008). The EST evidence was determined using the PASA program which
utilizes a number of alignment programs to maximally align transcripts to the genome. The minimal alignment
allowed by the PASA program is 95% identity over 90% length of the transcript.
Massively Parallel Signature Sequencing (MPSS) data was downloaded from the
Rice MPSS Database. For the mRNA data, the sum of abundances of 17bp-tag signatures for
classes 1, 2, 5, and 7 are listed for each library. mRNA library information is shown
below. For more information please visit the Rice MPSS Database website.
Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W., and B.C. Meyers.
(2006) Plant MPSS databases: signature-based transcriptional resources for
analyses of mRNA and small RNA. Nucleic Acids Research 34, D731-D735.
http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D731
Code
Tittle
# 0f Signatures
NYR
14 days - Young Roots
1,944,785
NRA
60 days - Mature Roots - Replicate A
2,675,567
NRB
60 days - Mature Roots - Replicate B
2,617,770
NGD
10 days - Germinating seedlings grown in dark
2,512,579
NST
60 days - Stem
2,095,983
NYL
14 days - Young leaves
2,249,147
NLA
60 days - Mature Leaves - Replicate A
1,073,991
NLB
60 days - Mature Leaves - Replicate B
1,348,557
NLC
60 days - Mature Leaves - Replicate C
1,263,549
NLD
60 days - Mature Leaves - Replicate D
1,254,824
NME
60 days - Crown vegetative meristematic tissue
2,568,641
NPO
Mature Pollen
2,310,574
NOS
Ovary and mature stigma
2,499,264
NIP
90 days - Immature panicle
2,661,421
NGS
3 days - Germinating seed
1,861,571
NCA
35 days - Callus
2,131,255
NSR
14 days - Young roots stressed in 250 mM NaCl for 24h
1,842,226
NSL
14 days - Young leaves stressed in 250 mM NaCl for 24h
2,531,362
NDR
14 days - Young roots stressed in drought for 5 days
2,190,870
NDL
14 days - Young leaves stressed in drought for 5 days
2,613,140
NCR
14 days - Young roots stressed in 4C cold for 24h
2,401,553
NCL
14 days - Young leaves stressed in 4C cold for 24h
2,322,924
XC00
Unwounded Control-Nipponbare Xa21-0hr
1,190,318
XC06
Mock treatment-6hr
1,367,076
XC24
Mock treatment-24hr
1,165,716
XR03
X.oryzae-R-3hr
1,134,269
XR06
X.oryzae-R-6hr
1,269,616
XR12
X.oryzae-R-12hr
1,542,183
XR24
X.oryzae-R-24hr
1,055,586
XR48
X.oryzae- R-48hr
1,248,814
XS03
X.oryzae-S-3hr
1,466,965
XS06
X.oryzae-S-3hr
1,419,178
XS12
X.oryzae- S-12hr
1,444,840
XS24
X.oryzae- S24hr
1,264,383
XS48
X.oryzae-S-48hr
1,175,368
MR03
M. grisea-R-3hr
1,422,272
MR06
M. grisea-R-6hr
1,054,700
MR12
M. grisea-R-12hr
1,331,343
MR24
M. grisea-R-24hr
1,435,098
MR48
M. grisea-R-48hr
1,367,250
MS03
M. grisea-S-3hr
1,584,229
MS06
M. grisea-S-6hr
1,354,948
MS12
M. grisea-S-12hr
1,086,361
MS24
M. grisea-S-24hr
1,022,535
MS48
M. grisea-S-48hr
1,518,407
MS96
M. grisea-S-96hr
1,061,873
MC00
Mock treatment-0hr
1,372,860
MC24
Mock treatment-24hr
1,402,116
I9RO
Roots
2,162,940
I9RR
Roots - Replicate
2,156,164
I9LA
Leaves
1,606,175
I9LB
Leaves - Replicate
1,005,937
I9LC
Leaves
1,144,192
I9LD
Leaves - Replicate
1,146,212
I9ME
Merismatic Tissue
2,112,790
FRO
F1 Hybrid 60days Mature Root
2,436,387
FRR
F1 Hybrid 60days Mature Root-Repl
2,205,884
FLA
F1 Hybrid 60days Mature Leaf Replicate A
1,171,478
FLB
F1 Hybrid 60days Mature Leaf Replicate B
1,040,468
FLC
F1 Hybrid 60days Mature Leaf Replicate C
1,056,621
FLD
F1 Hybrid 60days Mature Leaf Replicate D
1,419,115
FME
F1 Hybrid 60days Meristematic tissue
3,045,290
PSC
rice developing seeds, 6 days old cypress high milling(99-1710)
1,266,713
PSI
rice developing seeds,6 days old, Ilpumbyeo - High Taste
1,201,584
PSL
rice developing seeds, 6 days old, LaGrue-Low Milling
1,082,099
PSN
rice developing seed, 6 days old, Nipponbare-Grain quality control
1,207,914
PSY
rice developing seeds,6 days old, YR15965Acp33 - Low Taste
1,190,250
PLA
rice leaf, beet armyworm damaged, 24 hr(99-1726)
1,150,869
PLW
rice leaf, water weevil damaged, 24 hr
1,012,170
PLC
rice leaf, mechanical damaged, 24 hr
1,213,577
For the small RNA data, the sum of abundances for signatures are listed for each
library. Small RNA library information is shown below.
Code
Title
Total
Sequences
Genome
Matched
Reads
Distinct
Genome
Matched
Reads
t/r/sn/snoRNA
Matched
Reads
STM
Stem
520,676
381,597
50,766
19,113
SNU
Germinating seedlings
701,631
542,567
28,574
18,813
FLR
Nipponbare Immature panicles- 90 days old plants
1,731,548
1,111,811
150,743
49,681
SNM
Germinating seedlings infected with Magnaporthe grisea (strain 70-15)
Affmetrix Platform
The Affymetrix array contains probes to query 51,279 transcripts representing two rice subspecies, with approximately 48,564 japonica transcripts and 1,260 transcripts representing indica. The arrays were designed using NCBI UniGene Build #52 (May 7, 2004) incorporating predicted genes from GenBank and the TIGR Os1 v2 data set (ftp.tigr.org FASTA, 89.3 MB). The NCBI GEO platform Accession Number is GPL2025.
The Affymetrix raw data was downloaded from NCBI GEO, including 14 series: GSE4438, GSE4471, GSE6737, GSE6893, GSE6901, GSE6908, GSE7197, GSE7256, GSE7951, GSE8380, GSE9498, GSE10857, GSE10872 and GSE12069. We used the MAS 5.0 method provided by the affy R package to convert probe level data to expression values. The trimmed mean target intensity of each array was arbitrarily set to 500. The data within this database was log transformed. There is a little difference between this MAS 5.0 normalization method that we used and the MAS 5.0 provided by Affmetrix Inc. Affymetrix normalization is usually done after summarization and the normalization we used was carried out before summarization. The Rice Multi-platform Microarrary Search tool was used to get the corresponding Affymetrix probe sets for rice GTs and only unique probe sets that match unique rice loci were included in this database. If several unique probe sets are available for one certain rice GT, we only select one probe set with the highest expression and this probe set is indicted by the symbol '*'.
Agilent Platform
Probes on this array are designed to selections from the extensive rice (japonica) cDNA library of Japan National Institute of Agrobiological Sciences. It contains 22,575 oligos. The NCBI GEO platform Accession Number is GPL892. Twenty one series, GSE4409, GSE5286, GSE5853, GSE5906, GSE6124, GSE6125, GSE6126, GSE6244, GSE6362, GSE6600, GSE7192, GSE7530, GSE7531, GSE7532, GSE8811, GSE9450, GSE9765, GSE10098, GSE11021, GSE11157 and GSE11158, corresponding to 164 samples were downloaded from NCBI GEO. Then all the values in these data sets were converted to log2 scale for comparison. The oligo selection method is same with the Affymetrix platform.
BGI/Yale Platform Oryza sativa Genome Oligo Set Version 1.0 was used in this dataset, which was designed by the Beijing Genomics Institute (BGI) and contains 60,727 70-mer oligos representing both the indica and japonica genomes. Oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes from the BGI rice genome build and other public resources. The NCBI GEO platform Accession Number is GPL1829. This data was also downloaded from NCBI GEO, including 7 series GSE2211, GSE2360, GSE2619, GSE6533, GSE2691, GSE6552 and GSE11712, corresponding to 97 samples. In the case of multiple oligos that match single loci, the selection method was the same as with the Affymetrix platform.
NSF 20K Platform
The NSF funded rice oligo array version 2 (NSF 20K) developped by the Ronald Lab at UC Davis and the TIGR, contains 20,190 unique probes for rice. The number of total spots including empty and controls is 21,120. The NCBI GEO platform Accession Number is GPL2091. Click here to see the detailed information about this microarray platform.
The NSF 20K microarray data about rice GTs was from an experiment "NSF 20K Oligo Arrays to Dissect Rice Defense Response Pathways " carried out by Guo-liang Wang and Pamela Ronald et al. The NCBI GEO Accession Number is GSE9653. This experiment is a two-condition experiment, 10 mutants vs wild type control with treatment or without treatment, including 114 slides. After obtaining raw data, we performed LOWESS normalization within and between arrays using the R-package, LMGene. In the website, we provide two options: intensity data for either channel (log transformed) and log2 ratio between the two channels. Click here to see the detailed information about the experiment design. In the case of multiple oligos that match single loci, the selection method was the same as with the Affymetrix platform.
NSF 45K Platform
We used the oligonucleotide identification tool, PICKY 2.0, to design the 50- to 70-mer oligos that comprise the NSF45K array. NSF45K arrays contain 43,311 oligonucleotide probes that target 45,116 gene models out of a total of 61,420 target transcript sequences in the TIGR V3 rice gene set release. This array is printed on two slides, NSF45Ka and NSF45Kb. NSF45Ka contains 23,040 oligos including 240 oligos corresponding to the hygromycin phosphotransferase (hph) gene (GenBank Accession: AF354045), a selectable marker used in transgenic rice generation. NSF45Kb contains 20,727 oligos including 216 hph oligos. The hph oligos serve as positive controls for experiments comparing transgenic plants with wild type plants. These show approximately 10-fold induction relative to non-transgenic samples. Alternatively, the hph spots serve as negative controls for non-transgenic samples.
Light and dark responses are fundamental to a plants biology and produce dramatic differences in gene expression. To verify that the NSF45K array can be used to obtain biologically meaningful data, we performed an experiment to identify rice genes involved in the response of rice to light and dark treatments. For the light vs. dark experiment, we carried out expression-profiling on RNA from leaves of two-week old plants grown in a natural light-dark cycle (light-grown) in comparison to RNA from leaves of plants grown in a natural light dark cycle for a week and then transferred to constant darkness for the second week (dark-grown). In this validation experiment our aim was to identify genes that are universally important to the light/dark response in rice and thus to de-emphasize genotypic differences in the response. Hence, as our biological replicates we employed four different rice varieties with representatives of the two subspecies of rice, japonicas Kitaake, Nipponbare, and Taipei309; and indica, IR24. For statistical purposes, we conducted an additional set of hybridizations with the dyes used to label each sample swapped for each genotype (i.e., technical replicates).
