Network Projects

The following network construction projects are available on this site. Click a project name to browse the network and any subgraphs.
Name Method Description
NCBI Taxonomy Tree Import Tripal Phylogeny Module NCBI Taxonomy Importer

Used to import NCBI taxonomy details for organisms in this database.

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.

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.

RiceDiversity 44K SNP assay, 34 trait GWAS study, Nat Comm Sept 2011. MSU6 coordinates SNP genotyping array

details

TAIR10 Genes Manual download of TAIR10 genes

Manual download of GFF file from TAIR which includes chromosomes, genes, mRNA and UTRs. File obtained is found at TAIR FTP site

Tos17 Retrotransposon Study. Miyao, et. al. Plant Cell 2003 Thermal asymmetric interlaced PCR protocol and a suppression PCR protocol

Reference

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.

Abstract

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.

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.