Difference between revisions of "UserGuide:SimpleMine"
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== SimpleMine Users' Guide == | == 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 | + | 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''' | '''Names, Identifiers, Sequences, Species''' | ||
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Genetic Map Position | Genetic Map Position | ||
| − | RNAi Phenotype Observed | + | RNAi Phenotype Observed: Display the phenotype ontology names sorted in alphabetic order. |
| − | Allele Phenotype Observed | + | 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 | + | 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. | Interacting Gene: We only display experimentally confirmed gene interactions. | ||
| Line 51: | Line 51: | ||
Expr_pattern Tissue: Anatomical expression based on GFP, immunoprecipitation, In_situ, etc. | 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. | + | 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. | 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. | + | Genomic Study LifeStage: Developmental expression based on the microarray, RNA-Seq, and proteomics studies. |
| Line 67: | Line 67: | ||
'''Functional Annotation and References''' | '''Functional Annotation and References''' | ||
| − | Gene Ontology Association: | + | 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. | Concise Description: Outdated manually written descriptions of the gene functions. | ||
| Line 73: | Line 73: | ||
Automated Description: Up-to-date gene description machine generated based on the current WormBase data. | 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. | + | 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. | Reference: Primary research articles that studied the gene. | ||
Revision as of 07:00, 12 August 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 on 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: 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.
Expression
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
Disease Info
Human Ortholog
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.
