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Author --> Publications
Show the publications which have an author whose name contains the given string. Default: Close. Expression --> Genes
Find genes that express above a given value in the given sample. Default: above 1000 TPM in RT (root tip). Note: if you'd like to study differential expression, make one list of genes with expression above a certain amount in a sample and another with expression below a certain amount in a different sample. Intersect the two lists and you have genes that satisfy both criteria. Expression sample/value --> Genes
Find genes that have high expression in a given tissue in at least one of the expression experiments. (Default: expression>100 in Nodules.) Gene --> Expression
Display the expression in various tissues from various studies for the given gene. Default: Phvul.002G040500. Gene --> GO Terms
Given a gene, provide its GO ontology annotations. Default: Phavu.002G040500. Gene --> Homologues
Given a gene, show its homologues (based in this mine on common gene family membership). Default: Phavu.002G040500. Gene --> Homologues for given species
Given genes, find their homologous genes in a given species. Default: homologues of Glyma.01G000100 in Cicer arietinum. Gene --> Homologues from Species
Given genes, find their homologous genes in a given species Gene --> Ontology Terms
Given a gene, provide its ontology annotations. Default gene: Glyma.12G011700. Gene --> Proteins and Sequences
Display the proteins and their (truncated) sequences associated with a given gene. Default: CDCFrontier.Ca_00007. Gene --> Transcripts and Sequences
Display the transcripts and their (truncated) sequences for a given gene. Default: Phvul.002G040500. Gene description --> Genes
List genes whose description contains the given string. Default: HD-ZIP. Gene description --> Proteins
Show proteins for genes whose description contains the given string. Default: HD-Zip. Gene description --> Transcripts
Show the transcripts for genes whose description contains the given string. Default: HD-Zip. GO Term --> Genes
Find the genes that are annotated by the given GO term. (Default: photosynthesis.) GO Term --> Genes + Upstream Flanking Regions
Find genes associated with a term in the description of GO terms, along with their upstream flanking regions. Default: "nodule". GO Term --> Proteins
Find proteins that are translated by genes associated with the given GO term. Default: photosynthesis. Keyword --> Publications
Find publications containing the given keyword in the title. Default: expression. Phenotype --> GWAS
Find GWAS that show segregation for the desired phenotype. Default: Seed weight. Phenotype --> QTLs
Find the QTLs which are associated with the given phenotype. Default: Plant height. Protein Domain --> Proteins
Find the proteins which have protein HMM matches that belong to the requested protein domain, e.g. PF01582. Protein Domain --> Proteins, Genes
Find proteins and genes for which the protein domain has the given Interpro short name. Proteins for Genes
Given a gene or genes, get their proteins Region --> Genes
Find genes within a given region. Default: Pv01:1000000-2000000. Region --> Genetic Markers
Find genetic markers that are located within the given genomic region. Default: Pv01:1000000-2000000. Region --> Synteny Blocks
Show the synteny blocks (containing pairs of syntenic regions) within the given region. Default: Aradu.A01:1000000-3000000. Title --> Publications
Find publications containing the given string in the title. Default: climbing. TO Term --> QTLs
Search for QTLs associated with the given Trait Ontology term. (Default: seed weight.)

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