•Information→Architecture

•The Architecture details the various modules of SoyKB.

•Information→Data Sources

•The Data Sources lists all the experimental data that is available in SoyKB along with links to the published papers and urls where the data can be directly accessed.

•It also provides details about the contributing labs in case of unpublished datasets.

•Information→Soybean Nutritional Facts

•The “Soybean nutritional facts” link provides useful details and link to other sites providing information on nutritional benefits of soybean.

•Information→Links

•The Links provides links to other useful resources related to soybeans.

•Help→Sign Up/Access Levels

•The information shows details for our new upgraded user registration system and data sharing based on groups.

•Help→Video

•Video shows details about usage of most tools. It will be updated with new features that have been developed.

•About→Contributors

•The “Contributors” link shows details of the SoyKB development team members and collaborating labs.

•About→Latest Developments

•The “Latest Development” link lists all the features and datasets added to SoyKB and also keeps users posted about other features coming in the future.

•This list is updated every month to highlight the updates made.

•About→Funding

•The “Funding” link lists the funding agencies and all projects involved in the SoyKB funding.

•About→Citation

•The Citation link provides a link to the published manuscript, which users can refer to for more details. Users can also cite this manuscript when using SoyKB data in their research.

•About→Contact

•The Contact link can be used by users for support and queries as well as providing the development team feedback about new features to add and reporting any bugs.

•Search →Genes →Enter Glyma06g to search genes on chromosome 6.

•Click on Glyma06g11530.1 to view its gene card page.

•Gene card page shows all types of function annotation information, gene models, chromosomal information, experimental data and other evidence.

•For Search by Multiple Genes→Copy and paste the gene list in provided file “Multiple_Gene_Search_list.txt”→Click Submit.

•Select the appropriate ones from multiple matches→Click confirm and submit.

•Each gene is linked to its individual metabolite card page.

•Change the View Pearson and Spearman comparison cutoff to 0.99→Click Submit.

•Click Gene Families and other links one by one to see pie charts for annotations and line graphs for experimental data.

•Searches can also be done using gene family keyword such as Bzip or with annotation keywords such as Ubiquitin→Click Submit.

•Results page pulls out a list of Glyma IDs with links to gene card pages.

•Use search by chromosome coordinates →Select Gm07 chromosome from pull down list→Enter 40000 to 70000 nucleotide coordinate range→Click Submit.

•Results will show a list of all genes with their coordinates and links to gene card page.

•Search →miRNA→Click Submit all miRNA IDs→Click on TAG_5113378.

•MiRNA card page shows mirna sequence, mirna family, experimental data, link to mirbase entry and target genes predicted.

•Mirna can also be searched starting with target genes→ Enter Glyma05g23540 under Search by miRNA Target Gene→Click Submit.

•It pulls out the results for respective matching mirna with links to gene card and mirna card pages.

•Search →Metabolites→Enter Apigenin→ Click Submit→Click on apigenin out of all available matches.

•Metabolite Card page will show mass to charge ratio and retention time, link to pathway viewer as well as general information from HMDB database.

•Metabolomics experimental data can be seen for all conditions or for one specific condition using the subgraph feature.

•Select Root Hair Hour 18 from pull down list→Click View Sub-Graph to view only that time point.

•For multiple metabolite search→Copy and paste the metabolite list in provided file “Multiple_Metabolite_Search_list.txt” → Click Submit.

•Select the appropriate ones from multiple matches→Click confirm and submit.

•Each metabolite is linked to its individual metabolite card page.

•Click on “Click to view chart under LCMS2009 to view expression data for multiple metabolites.

•Search by experiment option→Select GCMS, Roothair and Stripped root→ Select either for Condition and Polarity→Click Submit.

•Results page will show list of all metabolites identified in this combination of experiments and each metabolite is linked to its metabolite card page.

•Search →SNPs→Select Gm05 chromosome from pull down list→Enter nucleotide range from 1576000 to 1577000 →Click Submit.

•Results are displayed for SNPs between Williams vs Forrest and BGI GWAS data as well as Soja datasets.

•SNPs falling in gene coding regions provide a link to the respective GlymaID and link to the gene card page.

•Links to QTL and traits is also provided for SNPs overlapping in those regions.

•Search →PI→Enter PI532458→Click Submit.

•For Multiple PI lines input PI lines separated by comma→Enter PI103079,FC32175,PI532458→Click Submit.

•Search →Traits→Enter protein→ Click Submit.

•Change chromosome from pull down list to see regions on different chromosome.

•Genes following in various QTL regions are color coded as per the QTL region.

•Click on the Expand/Fold links under the SNPs or GWAS section to the see the SNPs which fall in each QTL.

•Lastly the Soja Inversion and Deletions data is also available color coded as per the QTLs.

•Click→Chromosome Visualizer link for accessing the graphical viewer for traits and QTLs.

•Browse →Gene Family →Transcription factor → Click Select Family Search →Select BZIP Transcription factor from pull down →Click Confirm and Submit for Search.

•Click any GlymaID of interest to view its gene card page.

•Browse →3D Protein Structure Viewer → Enter Glyma16g01990.1 →Click Submit.

•Click Glyma16g01990_1.pdbf at bottom to open PDB format file for protein 3D Structure or Right-Click and use Save as option to download file.

•Browse →Homeologous Genes → Enter Glyma19g09610.1→Click Submit.

•Results are presented in two tables based on entire Glyma CDS and based on every exon respectively one below the other.

•Click GlymaID to view its gene card page.

•Browse →Phosphorylation→ Enter Glyma17g34850.1→Click Submit.

•Results are loaded in a new page linking to P3DB database.

•Click Glyma:Glyma17g34850.1 or Details to see the detailed phosphorylation positions.

•Browse →G. Soja→Expand individual tables to view the analysis results for comparative study between G. max and G. soja.

•Click GlymaID to view its gene card page.

•Browse →Genome Browser.

•Expand the tracks below using the +/- signs and select the data to be visualized from amongst GWAS, Soja and RNA-SEQ.

•Various visualization options can be used from amongst hide, dense, squish, pack and full.

•Navigation controls on top of the page can be used for better visualization.

•Browse →In Silico Breeding Program→Germplasm Browser.

•Click on Linoleic, Oil and Protein from Chemical descriptors→ Also click on Nematcyst from Other descriptots→Click Submit.

•The results are available in a a tabular format.

•All columns can be sorted and searched with values.

•Entire table can be exported as .csv file.

•Browse →In Silico Breeding Program→QTL and Trait Browser.

•Click on Insect trait→Select Gm01 Chromosome number from Pull down list → Click Submit.

•The results are available in a a tabular format.

•All columns can be sorted and searched with values.

•Entire table can be exported as .csv file.

•The bottom panels show the functional annotation pie charts for Gene family, Pfam, Panther and KOG as well experimental data heatmaps for transcriptomics and proteomics data for all genes falling in these QTLs.

•Browse →In Silico Breeding Program→QTL Viewer.

•Click →Chromosome Visualizer button to view the graphical QTL viewer.

•Select the Gm01 Chromosome→Select Oil, Protein and Nematode traits check boxed under Traits→Select SNP and RFLP check boxes under Molecular Markers.

•The QTL regions for individual traits are colored according to the traits, markers are shown with respective colors as well as individual genes as small green boxes on forward and reverse strand separately.

•Move the dark blue box on top panel by dragging it or change the size by dragging the sides to adjust the size.

•The second panel shows more detailed view of region inside the top panel blue box.

•Click on the QTL regions in second panel to save the gene list individually or use the save link above the panel to save all genes in second panel.

•Use << and >> arrows to jump to left and right or use < and > arrows to move slowly.

•Use the + and – to zoom in and out respectively.

•The hide/show layer links can be used to collapse and expand panels as needed.

•The LOD scores (demo) data can also be added to this view.

•Select check boxes next to GWAS and Soja under the Single Nucleotide Polymorphism.

•Also select all check boxes under Insertions/Deletions.

•The panels can also be reordered by clicking and dragging then up and done as needed.

•Browse →In Silico Breeding Program→PI-Trait Search.

•Click→PI Cards→Enter PI103079→ Click Submit.

•For multiple PI search Enter PI103079,FC32175,PI532458→ Click Submit.

•Click→Trait Cards→Enter Protein→ Click Submit.

•Browse →Fast Neutron Mutant Data→Search by CGD_ID→Enter FN151→Click Submit.

•To search by Glyma ID →Enter Glyma05g24980→ Click Submit.

•To search by Confidence level →Select Low or High from Pull down list→ Click Submit.

•To search by Chromosome →Select Gm04 Chromosome number from Pull down list→Enter range for nucleotide coordinates from 24891885 to 24999201 → Click Submit.

•Browse →Differential Expression→Select Data type→select Dataset→Choose from available methods.

•Select upto four datasets to compare at the same time.

•Enter value for fold change and p-value to filter the results-> Click Submit.

•Results are presented in five different tabs and click on any one to view them.

•Gene/Protein/Metabolite lists for each dataset will be shown in Gene Lists tab, along with fold change, p-vlaue and q-value->Click Show Entire list to view results.

•Click Venn Diagram tab to see the individual list of genes on the right and also intersection between all datasets.

•Click on any intersection to view list of genes common between those datasets and use download to save the list.

•Click on save picture to save the Venn diagram image.

•Click Volcano Plot tab to view the plot for significant and insignificant genes/proteins in red and blue respectively.

•Click Function tab to view the pie charts for gene family, Pfam, Panther and KOG by selecting any of them and click Submit.

•Click on Show Entire list or Download List buttons to view and save the list of gene functions respectively.

•Click Pathway tab to view list of all pathways identified for each dataset and corresponding gene names in each pathway.

•Tools→Affymetrix Probe ID Mapper→Enter Gma.1014→Click Submit.

•Click on Gma.10141.1.A1_at to see this probes mapping to genes.

•Search can also be done using gene Glyma02g47940→Click Submit.

•Probes mapping to this gene will be displayed.

•Batch search is coming soon for probe IDs and genes.

•Tools→Gene Pathway Viewer →Enter list of genes from provided file “GenePathwayViewer_list.txt”→Click Submit.

•Gene Pathway Viewer is loaded and shows all pathways for each gene.

•Use +/- to expand and collapse the pathways list on left panel.

•Mouse over the highlighted circles for viewing the gene name.

•Clicking over the highlighted circle will show the gene name in bottom panel, which is linked to the gene card page.

•Commonly represented pathways between entered list is shown on top.

•Pathways can be browsed using the pull down list→Click View Pathway button.

•Use Full Screen button for visualization in full mode.

•Pathways can be saved by highlighted genes using the Save Image button.

•Tools→Metabolite Pathway Viewer→Enter list of metabolites from provided file “MetabolitePathwayViewer_list.txt”→Click Submit.

•Metabolite Pathway Viewer is loaded and shows all pathways for each metabolite.

•Use +/- to expand and collapse the pathways list on left panel.

•Mouse over the highlighted circles for viewing the metabolite name.

•Clicking over the highlighted circle will show the metabolite expression data in bottom panel.

•Commonly represented pathways between entered list is shown on top.

•Pathways can be browsed using the pull down list→Click View Pathway button.

•Use Full Screen button for visualization in full mode.

•Pathways can be saved by highlighted metabolites using the Save Image button.

•Tools→Motif Sampler with WebLogo→Copy and Paste the example genes list from provided file “MotifSampler_Weblogo_list.txt” →Select check box next to CDS→Click Get Sequence Data→Copy All.

•Select the motif sequence length as 5, number of motifs to search and display as 5 each→Click Submit.

•The results page displays all predicted motifs and shows the sequence name, start, end, score, strand and site information for each.

•The weblogo for each motif can be created using the Create WebLOGO button.

•Tools→Blast Sequence Alignment→ Choose file to upload from provided file ”BlastSeqAlignment_Batch_list.txt”→Click Upload.

•Select Blastn and Glyma1.cds.fa from Nucleotide database pull down list→ Click Submit.

•Results for the sequences can be seen individually by clicking on the sequence name on the top.

•All matching hits can be seen listed one below the other and alignment can be viewed by clicking on the provided link.

•All gene names are linked to individual gene card pages.

•For single sequence query → Copy and paste sequence from provided file ”BlastSeqAlignment_Single_list.txt”→ Click Submit.

•Tools→Multiple Sequence Alignment→Copy and Paste from the provided file “MultipleSeqAlignment_list.txt” or upload the file using Choose file option→Click Submit.

•Results for alignment can be viewed as well as downloaded→Click Download button next to results.

•Click ViewTree button to see the Phylogeny tree.

•Tools→Protein BioViewer→ Enter Glyma17g34850.1 →Click Submit.

•Protein Bioviewer displays the protein primary sequence, secondary sequence, phosphorylation, amino acid properties, domains and trans-membrane helix information.

•The domains are linked to their individual websites for more details.

•Tools→Chromosome Visualizer→Select the Gm01 Chromosome→Select Oil, Protein and Nematode traits check boxed under Traits→Select SNP and RFLP check boxes under Molecular Markers.

•The QTL regions for individual traits are colored according to the traits, markers are shown with respective colors as well as individual genes as small green boxes on forward and reverse strand separately.

•Move the dark blue box on top panel by dragging it or change the size by dragging the sides to adjust the size.

•The second panel shows more detailed view of region inside the top panel blue box.

•Click on the QTL regions in second panel to save the gene list individually or use the save link above the panel to save all genes in second panel.

•Use << and >> arrows to jump to left and right or use < and > arrows to move slowly.

•Use the + and – to zoom in and out respectively.

•The hide/show layer links can be used to collapse and expand panels as needed.

•The LOD scores (demo) data can also be added to this view.

•Select check boxes next to GWAS and Soja under the Single Nucleotide Polymorphism.

•Also select all check boxes under Insertions/Deletions.

•The panels can also be reordered by clicking and dragging then up and done as needed.

•Tools→Heatmap→Copy and Paste gene list in the provided file “Heatmap_list.txt” →Select SolexaTranscriptomicsData from Transcriptomics (Solexa/Illumina) pull down list→Click Select All→Click Draw Heatmap button.

•The heatmap color scale shows the intervals for experimental data ranges.

•Tools→Scatter Plot→Select SolexaTranscriptomicsData from pull down list→Select top 2 conditions by clicking on check box next to them→Click Draw Scatter Plot button.

•The scatter plot also shows the r-square value between the selected samples.

•Tools-> Targeted Sequence Selection-> Upload a text file with Chromosome and positions separated by space or tab.

•Enter range 200 for extracting +/- 200 base pair sequence around the entered positions.

•Use download link to save the results file.

•Data Files→Download Data→Copy and paste gene list from provided file “Download_Data_list” →Select Sequences radio button → Select CDS→ Click Submit.

•The data will be downloaded to a text file.

•Login before using this tool.

•Data Files→Upload Data→ Click Choose File and select the provided file “Upload_Data_Transcriptomics_list” to be uploaded→Enter Name and Contact information in the text box→Select Transcriptomics.

•Data Files→Extract Genome Sequence→Select Gm01 chromosome number from pull down list→Enter 50000 to 60000 as coordinate range→Click Submit.

•The sequence will be extracted on the results page for the entered range.

•Data Files→Public Data Files->Click on the View and download data link for access to the NGS raw read and analyzed GBS datasets.