Expression data conditions similarity matrix coming soon.
Jbrowse genome browser supported by Coge to view Rna-seq and methylation datasets added to SoyKB.
New upgraded combined gene and metabolite pathway viewer available.
RNA-seq data added for seed germination stages for private access.
New Gene Model Glycine Max Wm82.a2.v1 along with mapping to the old gene models added into gene card page.
Iplant username update/signup for SoyKB users implemented. Users with current Iplant accounts can add/verify their usernames and new users can sign-up for Iplant username and add information in SoyKB. Iplant username will be used for data access control for tools such as Jbrowse using Coge and future analysis pipelines access.
User analysis jobs section added under the user profile page for easy access to results for jobs submitted for certain SoyKB tools.
Function enrichment analysis capacity added under Tools and also in Differential Expression Suite of Tools.
Soybean SNP50K array data added to SoyKB. Users can browse this data for multiple PI lines under SNP search.
RNAseq Dataset4 and Epigenomics dataset for 4 genotypes PAMP treatment conditions now available for public access.
eFP Browser for transcriptomics expression data visualization coming soon.
SoyKB website hosting migrating to IPlant infrastructure. No changes to website URL for users.
New soybean gene models incorporated from V9.0 on Phytozome.
Mutant Finder Tool added to identify mutants available for a soybean gene in lotus and medicago mutant database.
Root and Leaf nutrient conditions expression with ammonia, urea, nitrate and symbiosis added to gene card and differential expression analysis.
RNA-seq data added for flooding and drought susceptible and tolerant soybean lines for Nguyen lab access.
RNA-seq data added for hormone treatments for soybean lines for Nguyen lab access.
SoyKB update manuscript published in Nucleic Acids Research Database Issue. (link)
Heat stress timepoints metabolomics data added to metabolite card pages and differential expression analysis for root hair and stripped roots.
SNPViz tool added for visualizing SNP and GBS data using phylogeny trees.
Proteomics data for heat stress time points added for root hair and stripped root for private access for Stacey lab.
Detailed user manual added for SoyKB users under Help menu.
Forrest vs Williams82 SNP data added to Chromosome Visualizer.
Cultivar names added for 31 BGI datasets on SNP card, Chromosome Visualizer and Data source pages.
Users can now select GmComposite2003 or GmConsensus40 genetic maps option for viewing in In Silico Breeding Program and trait card pages.
GBS resequencing data for 25 soybean lines added for Nguyen lab access.
Users option to save gene and metabolite expression charts as images added.
Differential expression analysis tool added which provided access to gene lists, Venn diagrams, Volcano plots, Function and Pathway analysis.
mirna information added on gene card pages.
Traits information added on PI card pages.
List of PIs for a specific trait added on trait card pages.
Download option added for batch Affymetrix probe ID search.
Users can request membership to available groups for data sharing and viewing access.
NGS raw read sequencing data for Magellan and PI438489B 250 population added for access under Public data link in SoyKB.
List of all genes belonging to an individual pathway can now be accessed via Gene pathway viewer link under Tools.
View sub-graph feature added to transcriptomics charts for easy viewing.
Targeted Sequence Selection tool added to SoyKB for extracting genomic sequence for a user specified list of SNP positions and selected +/- nucleotide bp range.
Insertion and Deletion searches added on SNP card pages.
Users can upload any PDB file and visualize 3D protein structure in SoyKB.
Multiple datasets for miRNA and PARE library target gene validation added for Stacey lab private access.
QTL and trait data for Nguyen lab added for private access.
Summary details added for In Silico Breeding Program tools.
Circos circular genome visualization tool added.
SNP data added for 41 NAM parents for Bilyeu lab for private access.
Upstream 500, 1000 and 2000 nucleotide sequences added to gene card page for all genes.
SCN condition microarray and rna-seq datasets added for Mitchum lab.
Homologous genes from other species like Arabidopsis, Medicago, Lotus, Sorghum and others added on gene card page.
Gene search feature added to Chromosome Visualizer tool.
miRNA search by sequence and small RNA data added to SoyKB.
Datasets selection option added to download data page for omics experiments.
Methods selection option added to Phylogeny.
Gene Ontology and EC functions added to gene cards page.
Deleting groups and group memberships option added to SoyKB.
Multiple Affymetrix microarray, cDNA array, Oligo array and RNA-seq transcriptomics experimental conditions samples from Dr. Steve Clough's lab added to SoyKB.
Multiple Sequence Alignment and Phylogeny Tree tools added.
Heatmaps, Scatter plots and Hierarchial Clustering tools added for experimental data.
User registration system upgraded with new feature to create groups, invite members and data sharing data based on group memberships added to SoyKB.
Epigenomics data added for 4 genotypes in PAMP treatment conditions for private access.
Fast Neutron Mutant data added for private access.
Protein BioViewer for amino acid characteristics, domains and secondary structure visualization.
Batch sequence similarity search using Blast added.
In Silico Breeding Program for PI, QTL and Traits information added under "Browse" navigation menu.
PI and Trait card search added on the navigation menu under "Search".
PI and Trait card search added to the "Quick Search" dropdown menu.
Gene card pages updated with QTL information.
SNP card pages updated with QTL information.
52 new transcriptomics conditions data added for private access.
Gene Ontology and EC annotations added.
Comparison against G. soja.
Phosphorylation data for soybean added for public access.
Added mirna search by target gene names.
Added affy probe search by gene names.
Demo video added.
Chromosome Visualizer tool added for integration of QTL, Traits, SNPs and Insertion/Deletion data for breeders.
GWAS SNPs, Insertion and Deletion data added for 31 soybean genotypes from BGI to Chromosome Visualizer and SNPs Search.
G. Soja SNPs, Invertion and Deletion data added to Chromosome Visualizer and SNPs Search.