Genome Function INtegrated Discover (GFINDer)
Category Genomics>Genetic Data Analysis/Tools
Abstract Genome Function INtegrated Discover (GFINDer) is a Web-accessible three-tier multi-database system developed to automatically enrich lists of user-classified genes with several functional and phenotypic controlled annotations, and to statistically evaluate them in order to identify annotation categories significantly over- or underrepresented in each considered gene class.
Genomic controlled annotations from Gene Ontology (GO - i.e. Biological Process, Cellular Component, and Molecular Function categories), KEGG (i.e. Biochemical Pathways), Pfam (i.e. Protein Domains), InterPro, and the Online Mendelian Inheritance in Man (OMIM) database were integrated in GFINDer and several categorical tests were implemented for their analysis.
Multiple controlled vocabularies of inherited disorder phenotypes were obtained by normalizing and hierarchically structuring disease accompanying signs and symptoms from OMIM clinical synopsis sections.
The two (2) controlled vocabularies, suitable for computational purposes, describe the Phenotypes and 'Phenotype Locations' associated with inherited disorders or genetic loci.
GFINDer modular architecture is well suited for further system expansion and for sustaining increasing workload.
Testing results showed that GFINDer analyses can highlight 'gene functional' and phenotypic characteristics and differences, demonstrating its value in supporting 'genomic biomedical' approaches aiming at understanding the complex biomolecular mechanisms underlying patho-physiological phenotypes, and in helping the transfer of genomic results to medical practice.
GFINDer is organized in 'distinct modules'; each providing specific functionalities. All modules are accessible through the manufacturer's web-site, via menu selection.
1) Upload: You can upload your file containing your gene ID's list.
2) Annotation: You can view your gene ID's list enriched with functional annotations. You can choose which annotation you want to display and the sorting simply by choosing annotation sort order in combo-boxes.
3) Exploration --
- a) Gene Ontologies: this module performs exploration of Gene Ontology based functional classification of genes in the uploaded gene id list. The result shows the distribution of genes in the uploaded list among Gene Ontology categories (GO category terms).
- Genes are also linked to additional annotations available through EBI QuickGO system that displays the current GO term in the ontology tree and provides the list of genes that belong to that selected GO category term. You can choose the ontology/ontologies to consider for the exploration and their correspondent levels of GO term coverage and specificity within the GO tree.
- You can also choose to analyze your gene list only on terminal terms (ignoring the GO structure) or on All terms i.e. including each GO term associated with any of your genes and all its parents terms.
- You can choose also to filter evidence codes, i.e. to include in the results only those categories that are linked to genes with the specified 'evidence code'.
- Finally you can choose the minimum number of genes associated with each GO term to be included in the output and a sort criterion.
- An advanced feature is the ability of re-exploring the GO hierarchy for any subset of genes sharing a common classification simply by clicking on the histogram bar of a specific GO category, or selecting only the required GO categories and clicking the "View subset categories" button.
- b) Biochemical Pathways: this module performs exploration of KEGG Pathway based functional classification of genes in the uploaded gene id list. The result shows the distribution of genes in the uploaded list among KEGG biochemical Pathways.
- Genes are also linked to additional annotations available through KEGG's DBGET system and you can get the list of genes that belong to a selected KEGG category. You can also choose the minimum number of genes associated with each KEGG pathway to be included in the result output and a sort criterion.
- c) Protein Families & Domains: this module performs exploration of Protein Family and Domain based functional classification of genes in the uploaded gene id list. The result shows the distribution of genes among Pfam Protein Domains or InterPro Protein Families, Domains, and functional sites.
- Genes are also linked to additional annotations available through the Sanger Institute Pfam Web system or the InterPro Web system, from where you can get a list of genes that belong to a selected Pfam or InterPro category.
- You can also choose the minimum number of genes associated with each Pfam or InterPro category to be included in the result output and a sort criterion.
- d) Genetic Disorders: this module performs exploration of OMIM based functional classification of genes in the uploaded gene id list. The result shows the distribution of genes among OMIM Genetic Disorder or Phenotype classifications.
- Genes are also linked to additional annotations available through the NCBI OMIM Web system, from where you can get a list of genes that belong to a selected OMIM category.
- You can also choose the minimum number of genes associated with each OMIM category to be included in the result output and a sort criterion.
4) Statistics: these modules allow you to perform significance statistical tests automatically applied to each Gene Ontology, KEGG Biochemical Pathway, Pfam Protein Domain or InterPro Protein Family, Domain, or Functional site, OMIM Genetic Disorder or Phenotype, or Cytogenetic Location category associated with the genes in your uploaded sequence ID's list.
5) Logistic Regression: this module allows performing a Logistic Regression analysis on the Protein Family or Domain categories associated with an uploaded sequence ID's list.
6) Utilities --
- a) Categorization: this module allows you to create a new classification column for your sequence ID's list or manage the current classification column.
- You can annul the column (i.e. setting the class value "0" for all genes),delete it, or create a new classification in the selected column based on a GO, Pathways, Protein Families or domains, Genetic Disorders or Phenotypes, or Cytogenetic location controlled vocabulary term search.
- You can search through these categories by keywords, select some of them and the system will put, in the classification column, the selected value for each gene that belongs to the selected categories.
- You can also create your own categories using the keyword search engine by selecting some of the categories resulting from the search and specifying a name for a new category that groups all the selected.
- You can also perform a statistical analysis on these new categories.
- b) GO Browser: it allows you to browse the Gene Ontology tree in a top- down or bottom-up way starting from a specified GO term.
You can also perform a search on terms that contains a specified keyword.
System Requirements
Web-based.
Manufacturer
- BioMedical Informatics Laboratory
- Dipartimento di Bioingegneria
- Politecnico di Milano
- piazza Leonardo da Vinci 32
- 20133 Milano, Italy
Manufacturer Web Site GFINDer
Price Contact manufacturer.
G6G Abstract Number 20421
G6G Manufacturer Number 104050