SimpleMine Users' Guide
SimpleMine is designed for biologists who want to get essential information for a list of genes without any command-line or programming skill. We consider the following as "essential information" based on user feedback. Please feel free to contact us if you want to include more information on the list.
Names, Identifiers, Sequences, Species
WormBase Gene ID
Reference UniProt ID
Genetics, Phenotypes, Interactions
Genetic Map Position
RNAi Phenotype Observed: Display the phenotype ontology names sorted in alphabetic order.
Allele Phenotype Observed: Display the phenotype ontology names sorted in alphabetic order.
Coding_exon Non_silent Allele: Among those alleles that were sequenced, we exclude polymorphisms and alleles that fall in any coding exon. Alleles are sorted and displayed according to the following order of their types: Deletion, Insertion, Substitution, Tandem_duplication. Each allele entry contains three bar-separated fields: allele name, allele type, and molecular change.
Interacting Gene: We only display experimentally confirmed gene interactions.
Expr_pattern Tissue: Anatomical expression based on GFP, immunoprecipitation, In_situ, etc.
Genomic Study Tissue: Tissue enrichment based on the microarray, RNA-Seq, and proteomics studies.
Expr_pattern LifeStage: Developmental expression based on GFP, immunoprecipitation, In_situ, etc.
Genomic Study LifeStage: Developmental expression based on the microarray, RNA-Seq, and proteomics studies.
Human Orthologs and Disease
Functional Annotation and References
Gene Ontology Association: Display the names of gene ontology terms that were annotated to the gene sorted in alphabetic order
Concise Description: Outdated manually written descriptions of the gene functions.
Automated Description: Up-to-date gene description machine generated based on the current WormBase data.
Expression Cluster Summary: Gene regulation, molecular regulation, and tissue enrichment summary based on the microarray, RNA-Seq, and proteomics studies.
Reference: Primary research articles that studied the gene.