|Oryza sativa Global Co-Expression Network v1.0||WGCNA + RMT||
A gene co-expression network was constructed for Oryza sativa using all public Affymetrix microarray samples available at the time.
|Zea mays Global Co-Expression Network v1.0||WGCNA + RMT||
A gene co-expression network was constructed for Zea Mays using all public Affymetrix microarray samples available at the time.
|NCBI Taxonomy Tree Import||Tripal Phylogeny Module NCBI Taxonomy Importer||
Used to import NCBI taxonomy details for organisms in this database.
|Tos17 Retrotransposon Study. Miyao, et. al. Plant Cell 2003||Thermal asymmetric interlaced PCR protocol and a suppression PCR protocol||
Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon rich regions of the genome. Plant Cell 2003;15:1771-1780.
Because retrotransposons are the major component of plant genomes, analysis of the target site selection of retrotransposons is important for understanding the structure and evolution of plant genomes. Here, we examined the target site specificity of the rice retrotransposon Tos17, which can be activated by tissue culture. We have produced 47,196 Tos17-induced insertion mutants of rice. This mutant population carries ∼500,000 insertions. We analyzed >42,000 flanking sequences of newly transposed Tos17 copies from 4316 mutant lines. More than 20,000 unique loci were assigned on the rice genomic sequence. Analysis of these sequences showed that insertion events are three times more frequent in genic regions than in intergenic regions. Consistent with this result, Tos17 was shown to prefer gene-dense regions over centromeric heterochromatin regions. Analysis of insertion target sequences revealed a palindromic consensus sequence, ANGTT-TSD-AACNT, flanking the 5-bp target site duplication. Although insertion targets are distributed throughout the chromosomes, they tend to cluster, and 76% of the clusters are located in genic regions. The mechanisms of target site selection by Tos17, the utility of the mutant lines, and the knockout gene database are discussed.
|RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates||SNP genotyping array||
|Arabidopsis thaliana Tissue Co-expression Network Compendium v1||RMTGeneNet||
For this project all available Affymetrix micorarrays for Arabidopsis thaliana from the platform NCBI GEO GPL198, were manually organized into tissue specific groups. Each group underwent network construction.
|Oryza sativa GIL-Hive Co-expression Network v1||RMTGeneNet||
A Gene Interaction Layer (GIL) Hive is a collection of networks constructed after clustering of input samples. Each cluster is then used to create a unique network. For this project a GIL-Hive was constructed for Oryza sativa using all available Affymetrix samples from the GPL2025 platform at the time. This resulted in 25 distinct networks.
|Arabidopsis thaliana GIL-Hive Co-expression Network v1||RMTGeneNet||
A Gene Interaction Layer (GIL) Hive is a collection of networks constructed after clustering of input samples. Each cluster is then used to create a unique network. For this project a GIL-Hive was constructed for Arabidopsis thaliana using all available Affymetrix samples from the GPL198 platform at the time. This resulted in 90 distinct networks.
|Arabidopsis thaliana Global Co-expression Network v1||RMTGeneNet||
A gene co-expression network for Arabidopsis thaliana. The network was constructed using all public Affymetrix microarrays from the NCBI GEO platform GPL198 at the time.
|Import of dbSNPs for Arabdidopsis, Zea Mays and Oryza sativa||manual download & processing||
SNPs were downloaded in bulk from the NCBI dbSNP FTP repository for Arabidopsis thaliana, Oryza sativa and Zea Mays in XML format. The XML was coverted to FASTA formatted files containing the SNP and 5' and 3' flanking sequences. These sequences were aligned to the TAIR10, Rice MSU v6.0, and the MaizeSequence.org B73 genome assemblies respectively using blat. Only SNPs that mapped uniquely along the full length of the flanking sequence were kept and uploaded to this database.