Omics Data Analysis

Gene Expression Data Analysis

• Paint gene expression data onto metabolic map. Data can be uploaded from a file, imported from PortEco or GEO, or imported from a recently visited group. From the Cellular Overview page, choose the data source from the options in the navigation box on the right.
• Paint gene expression data onto regulatory map. Data can be uploaded from a file, imported from PortEco or GEO, or imported from a recently visited group. From the Regulatory Overview page, choose the data source from the options in the navigation box on the right.
• Paint gene expression data onto pathway diagram. Data can be uploaded from a file. From any pathway page, choose the option Customize or Overlay Omics Data on Pathway Diagram from the options in the navigation box on the right, and check the box Superimpose Omics Data on Pathway.
• Table of over/under-expressed pathways. Data can be uploaded from a file, imported from PortEco or GEO, or imported from a recently visited group. From the Cellular Overview page, choose the data source from the options in the navigation box on the right. In the resulting form, select As a table of pathway diagrams from among the Show data options.
• Enrichment analysis. Enrichment analysis is a computational technique for identifying known categories of objects (e.g., pathways) that are statistically over-represented in a set of objects (e.g. genes that are significantly up-regulated in an expression experiment). For example, enrichment analysis allows us to ask whether a set of genes contains more genes regulated by a given transcriptional regulator than one would expect to occur by chance. In order to perform an enrichment analysis, you must create a SmartTable containing the genes of interest. Make sure the SmartTable contains only those genes that are significantly over- or under-expressed, not the entire dataset. From the page for the SmartTable, choose an enrichment option and fill out the dialog (in most cases, it will be sufficient to use the defaults). (NB: each entity in the column must come from the same organism)

Metabolomics Data Analysis

• Paint metabolomics data onto metabolic map. Data can be uploaded from a file or imported from a recently visited group. From the Cellular Overview page, choose the data source from the options in the navigation box on the right. When uploading a file, be sure to specify that the items in the first column are compound names and/or identifiers.
• Paint metabolomics data onto pathway diagram. Data can be uploaded from a file. From any pathway page, choose the option Customize or Overlay Omics Data on Pathway Diagram from the options in the navigation box on the right, and check the box Superimpose Omics Data on Pathway. Be sure to specify that the items in the first column are compound names and/or identifiers.
• Table of over/under-activated pathways. Data can be uploaded from a file or imported from a recently visited group. From the Cellular Overview page, choose the data source from the options in the navigation box on the right. In the resulting form, select As a table of pathway diagrams from among the Show data options.
• Enrichment analysis. Enrichment analysis is a computational technique for identifying known categories of objects (e.g., pathways) that are statistically over-represented in a set of objects (e.g. metabolites whose concentration has changed in a metabolomics experiment). In a metabolomics context, enrichment analysis allows us to ask whether a set of compounds contains more metabolites from a given metabolic pathway than one would expect to occur by chance. In order to perform an enrichment analysis, you must create a group containing the compounds of interest. Make sure the group contains only those compounds that are significant in some way, not the entire dataset. From the page for the group, choose the Compounds enriched for pathways option and fill out the dialog (in most cases, it will be sufficient to use the defaults).

Genome Data Analysis

• Genome browser tracks. External datasets can be shown alongside the display of a replicon region, in form of additional tracks that are uploaded by the user. The supported tracks file format is GFF, version 2. Data can be imported from a website URL, or by uploading a file.