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
Functional Enrichment of A. thaliana Global v1.0 network In-house perl scrip

The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro.

Functional Enrichment of A. thaliana K90 GIL networks In-house perl script

The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro...

Functional Enrichment of A. thaliana Global, Tissue and K90 GIL networks In-house perl script

The Feltus-lab in-house enrichment Perl script (modeled after DAVID) was used for testing functional enrichment of InterPro...

MSU v6.0 Oryza sativa whole genome download Manual Download
MSU v7.0 Oryza sativa whole genome download Manual Download
Maize B73 Genes Manual download from maizesequence.org

Gene predictios from the filtered set of the B73 Zea mays genome.  Sequences were downloaded from the maizesequence.org FTP site.

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

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.

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.