Difference between revisions of "UserGuide:SimpleMine"

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Allele Phenotype Observed
 
Allele Phenotype Observed
  
Sequenced Allele
+
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.
 
 
Expression Cluster Summary
 
  
  
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'''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Concise Description: Outdated manually written descriptions of the gene functions.
  
Concise Description
+
Automated Description: Up-to-date gene description machine generated based on the current WormBase data.
  
Automated Description
+
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.

Latest 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.