Main ERGO Navigation Tool Bar

The green toolbar found at the top of every page in ERGO^TM contains utilities that can be applied to the entire ERGO^TM database.

As illustrated above, the global green toolbar contains five drop-down menus: Data, Tools, Query, Configure, and Help.

The Data Menu

Many of the features under the Data menu open up the list of genomes but with different columns that are relevant to the particular feature.

The following items are available under the Data menu:

Genome Projects:

Use this option to display information about the genome sequencing projects for the organisms in your account. The basic table has the following default information displayed:

• Stats – A link to the full statistics page for the organism
• Model – A link to get started with curating the functional model for the organism
• DNA Source / Project – The source of the DNA for the genome sequencing project
• Restrictions – Known restrictions on usage of the genomic data
• Organism taxonomy – Organism taxonomy

Models, Overviews:

Use this option to get easy access to the metabolic information for the organisms in your account. The basic table has the following default information displayed:

• Model – A link to get started curating the functional model for the organism
• Model – A link to the metabolic overview
• Model – A link to a hierarchical view of the metabolic overview
• allO – The total number of open reading frames (ORFs) in the genome
• AP – The total number of pathways asserted to be present in the organism

Contigs, G+C%, Kb:

Use this option to display basic statistical information for the organisms in your account. The basic table has the following information displayed by default:

• Stats – A link to the full statistics page for the organism
• Model – A link to to the the collection of genome curation tools
• allO – The total number of open reading frames in the genome and a link to the subsection of the statistics page that displays a full list of the ORFs.
• Cont. – The total number of DNA contigs in the genome and a link to the subsection of the statistics page that displays the contig list.
• Kb – The total amount of DNA in the genome project, in kilobases
• GC% – The G+C percentage of the genome.

Function statistics:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• Model – Curate functional model
• allO – ORFs total count
• unF – Unique functions assigned
• hyF – Unique hypothetical functions assigned
• FO – ORFs with assigned Function
• FsO? – ORFs with Function but no similarities
• fO – ORFs without assigned functions
• fSO – ORFs without function, with Similarity
• fsO – ORFs without function and similarity
• pO – ORFs not in asserted pathways
• FpO? – ORFs with assigned Function but no pathway
• FamO? – ORFs with Pfam matches

Gene Context Statistics:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• allO – ORF total count
• FO – ORFs with assigned Function
• POO – ORFs in Chromosomal Clusters
• FEO – ORFs in Fusion Events
• fcO – ORFs as Fusion components
• fCO – ORFs as Fusion Composites

Pathway Statistics:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• Model – Curate functional model
• allO – ORFs total count
• AP – Pathways asserted total
• PO – ORFs in asserted pathways
• pO – ORFs not in asserted pathways
• FpO? – ORFs with assigned Function but no pathway

Function Overviews:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• Model – Curate functional model
• Model – Overview of functions, graphical
• Model – Overview of functions, text
• allO – ORFs total count
• AP – Pathways asserted total

Curate Functions:

contains a set of tools for functional annotation.

List All Experiments:

displays the set of genomes which have experimental data.

Essentiality Experiments:

displays the set of genomes which have experimental essentiality data.

Genome Deletion Studies:

displays the set of genomes which have genome experimental deletion data.

Library Sequence Data:

displays the set of genomes which have library experimental sequence data.

Microarray Experiments:

displays the set of genomes which have experimental microrray data.

Cluster Statistics:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• Model – Curate functional model
• allO – ORFs total count
• POO – ORFs in Chromosomal Clusters
• CogO? – ORFs in COGs
• FamO? – ORFs with Pfam matches
• Cogs – Clusters, orthologous groups (COGs)
• Pfam – Unique Pfam domains

Gene Context Statistics:

displays the list of genomes along with the following columns

• Stats – Organism full statistics page
• allO – ORFs total count
• FO – ORFs with assigned Function
• POO – ORFs in Chromosomal Clusters
• FEO – ORFs in Fusion Events
• fcO – ORFs as Fusion components
• fCO – ORFs as Fusion Composites

Ortholog Clusters:

Chromosome Clusters:

tool to identify potential operon regions common to pairs of organisms. This tool is only available for organisms with complete genome sequences.

Genome Walk:

comparative genomics tool that allows the user to select a reference organism as well as more or more closely related organisms to project upon. The result is a spreadsheet matching open reading frames in the reference organism to open reading frames in the selected organisms.

Genome Align:

allows user to select a target organism and query organism and performs a BLAST search of the entire genome of the query organism against the entire genome of the target organism. The results identify genes in the target organism that are not present in the query organism. Also included in the results are displays of the BLAST hits from the query organism against the individual segments of the target organism.

The Tools Menu

Compare Cluster Sets:

Protein Family Clustering:

tool to cluster open reading frames (RIDs) in user-selected organisms by protein family / function. The user selects organisms, and is allowed to fill in spreadsheet cells and add rows for missing RIDs from a specified organism. The output is a display of RIDs clustered by protein function.

Similarity Clustering:

a set of tools to identify genes that are either common among a set of organisms or genes that are unique to a specific subset of organisms.

Workbench:

a set of clustering tools

Organism Signatures:

a tool for identifying families or genes that differentiate two sets of organisms.

Batch Annotation:

a tool for submitting batch annotations. The user must prepare and submit a tab delimited file containing ERGO^TM RIDs and annotations.

Curate Functions:

same tool found under Data, Curate Functions

The Query Menu

By Keywords:

allows the user to search the ERGO^TM database using one or more keywords. The first panel allows users to narrow the search by selecting specific data categories such as ORFs, Pathways, Enzymes, etc. A maximum of 4 keywords may be entered along with AND/OR Boolean operators. Additionally, the search may be limited to a specific organism. This restricts the results to the organism(s) selected. The user may also choose to impose maximum output table length restrictions.

By Sequence:

Alternatively, a user is able to search the ERGO^TM database by a DNA or protein sequence. This is advantageous in cases when functional annotations may be absent, incorrect, or lacking the appropriate keyword. For example, suppose a user would like to search for the enzyme aminopeptidase P in Pichia pastoris. If the protein or DNA sequence is known, it can be used to search the Pichia pastoris genome using BLAST. This will locate aminopeptidase P in Pichia pastoris, even if it had been annotated simply as a peptidase.

By Pattern:

allows the user to upload a patscan search pattern.

By Protein Properties:

allows a search for proteins based on properties such as length, molecular weight, and isoelectric point. The results can also be filtered by function by entering a keyword, such as “peptidase”. If more than one search field is entered, an implied AND is imposed, such that all proteins in the search results will fall into all ranges specified by the user.

By User Annotation:

facilitates searches for open reading frames annotated by specific non-master users or by user models such as Pfam, COGs, or GenBank? .

Query Pathways:

the MPW database is no longer active. Although some pathway queries will return results, this query is largely non-functional.

Query Enzymes:

facilitates searches for enzymes based on name or EC number. The search can be limited to a selected organism or taxon, or to a specific tissue or organelle.

Query Ortholog Clusters:

Color Features:

Export Genome Data:

genomes that are less than 100 megabases in length may be exported in either EMBL format (whole genome) or FASTA format (DNA, protein, and contig). Data is exported in a compressed format (.zip).

The Configure Menu

Set User Name:

allows user to set or change the username.

Set Preferred Organism:

allows user to set a preferred organism which will appear on a brown menu bar. By setting a preferred organism, the user can quickly access organism-specific information and tools. This is advantageous when a user frequently works with a particular genome. Only a single preferred organism can be set.

Set Organism Group:

sets an organism group that is used in all pages that use sets of organisms.

Log Out:

logs out of ERGO^TM.

The Help Menu

How to Contact Us: where to go to report software or database problems, to request features, or for general inquiries.

Introduction for Users: contains a brief introduction and history of the ERGO^TM platform.

Alphabetical Genome List: provides an alphabetical list of genomes currently in the ERGO^TM database along with the genome size (in kb), number of contigs, and source of the DNA.

Data and Code Locations: contains information about the internal file structure of the ERGO^TM database.

Data Access Routines: a collection of programming tutorials relating to data access in ERGO^TM.

-- TheresaWalunas - 02 Apr 2008