BioProfiling: Help

Methods

We would recommend you to read method description before using BioProfiling.

Reference Gene networks

BioProfiling is using two different reference gene networks: Reactome pathway database and Intact database of protein interactions. A reference gene network (external knowledge) is supposed to modulate the spreading of a signal in the cell from one gene to another.

BioProfiling OUTPUT

Mapping Of your Genes

Your gene Ids are mapped to NCBI gene Entrez IDs . The number of recognised genes (blue number) reports how many of your genes can be mapped. However not all of them have been annotated in Reactome or Intact database. The number of genes ( red number ) reports how many of your genes are annotated (can be mapped) to REACTOME (INTACT).
Attention!!! Please note that only these genes are used to find functional intersection between your lists

Direct Intersection (between list a and b)

This is just to count how many genes are common between list a and b.

Functional Intersection (between list a and b)

As output, the genes from the list a are ranked by significance (p-value) of the connectivity score in relation to the list b. Table 1 reports top genes from list a.
Column "P-value FDR" reports p-values adjusted by FDR (see methods) In brackets, the p-value computed by Monte Carlo simulation procedure is given.
Column "Network Model CytoScape" provides link to online visualization using cytoscape. The network model shows connectivity between the corresponding gene "a" and genes from list b.
Column "Download Meduza files" provides link to download visualization files for Meduza application (the same network model).

CytoScape Figure Legend

  • rectangle - gene from list a
  • circle - gene from list b
  • diamond - gene from lista and b
  • triangles - missing genes added to the model (i.e. not from list a or b
  • colors - indicate pathways (black color = no pathway)
  • star - name of the pathway (GO term)

Meduza Figure Legend

See instructions on the Meduza Model downloading page.

How to produce high quality Network Figures

You can produce high quality Network Figures either using cytoscape or meduza programs.
You can use online cytoscape capabilities to align and edit your network. Please use Controls menu in the right top corner (cytoscape online). You can select several layout options (use menu Layout). We recommend to try several layout options ("cola", "cose", etc). You can save your model either as image (.png) or JSON format. The JSON file can be opened and edited by cytoscape on your computer. Example of the figure prepared with online cytoscape is presented in figure 1.

Figure 1. Example of network model