Difference between revisions of "UserGuide:SimpleMine"
Line 42: | Line 42: | ||
Allele Phenotype Observed | Allele Phenotype Observed | ||
− | + | Coding_exon Non_silent Allele: Among those alleles that were sequenced, we exclude polymorphisms and alleles fell in exon, 5' UTR or 3' UTR. | |
− | Interacting Gene | + | Interacting Gene: We only display experimentally confirmed gene interactions. |
'''Expression''' | '''Expression''' | ||
− | Expr_pattern Tissue | + | Expr_pattern Tissue: Anatomical expression based on GFP, immunoprecipitation, In_situ, etc. |
− | Genomic Study Tissue | + | Genomic Study Tissue: Tissue enrichment based on microarray, RNA-Seq, and proteomics studies. |
− | Expr_pattern LifeStage | + | Expr_pattern LifeStage: Developmental expression based on GFP, immunoprecipitation, In_situ, etc. |
− | Genomic Study LifeStage | + | Genomic Study LifeStage: Developmental expression based on microarray, RNA-Seq, and proteomics studies. |
− | |||
− | |||
Line 69: | Line 67: | ||
'''Functional Annotation and References''' | '''Functional Annotation and References''' | ||
− | Gene Ontology Association | + | Gene Ontology Association: Gene Ontology terms that were annotated to the gene. |
+ | |||
+ | Concise Description: Outdated manually written descriptions of the gene functions.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 microarray, RNA-Seq, and proteomics studies. | |
− | Reference | + | Reference: Primary research articles that studied the gene. |
Revision as of 23:17, 1 July 2020
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 in the list.
Names, Identifiers, Sequences, Species
WormBase Gene ID
Public Name
Species
Sequence Name
Other Name
Transcript
Operon
WormPep
Protein Domain
UniProt
Reference UniProt ID
TreeFam
RefSeq_mRNA
RefSeq_protein
Genetics, Phenotypes, Interactions
Genetic Map Position
RNAi Phenotype Observed
Allele Phenotype Observed
Coding_exon Non_silent Allele: Among those alleles that were sequenced, we exclude polymorphisms and alleles fell in exon, 5' UTR or 3' UTR.
Interacting Gene: We only display experimentally confirmed gene interactions.
Expression
Expr_pattern Tissue: Anatomical expression based on GFP, immunoprecipitation, In_situ, etc.
Genomic Study Tissue: Tissue enrichment based on 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 microarray, RNA-Seq, and proteomics studies.
Human Orthologs and Disease
Disease Info
Human Ortholog
Functional Annotation and References
Gene Ontology Association: Gene Ontology terms that were annotated to the gene.
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 microarray, RNA-Seq, and proteomics studies.
Reference: Primary research articles that studied the gene.