ftfert.blogg.se - Cytoscape directed graph

#CYTOSCAPE DIRECTED GRAPH WINDOWS#

In order to move nodes (proteins, chemical compounds etc.) one first has to click on the yellow icon below the "Help" link. The thickness of an edge correlates with the number of interactions found for the same subject, object and interaction symbol.

#CYTOSCAPE DIRECTED GRAPH WINDOWS#

Clicking on an arrow/edge results in opening new windows with the complete entry information, one for each entry. Hovering over arrows/edges opens an info box with detailed information about the underlying interactions.

Pop-up windows show the information that is basis of the interactions.

"cell%" finds every interaction with a term that begins with "cell". "all Fields" is chosen, all host-pathogen interactions of the database are shown. Wildcard: Finds all interactions within the search space. The latter is a GO term that includes the words 'cell' and 'death' in the synonym of GO:0001781 : neutrophil apoptotic process (neutrophil programmed cell death by apoptosis).įinds only exactly 'cell death' but not 'neutrophil apoptotic process' you will retrieve 'cell death' and 'neutrophil apoptotic process'. It can also be used in a double-quoted search term.įinds every term that contains the words 'cell' and 'death' anywhere (also synonyms!), i.e. "type IV pilus" will not find type IV pilus-dependent motility which would happen without quotes)

The search space can be restricted by setting the search term into double quotes (e.g.

A drop-down menu allows combining the two queries with the Boolean operators AND, OR and NOT. By clicking on Refine query a second search field is opened.

Combined queries can be performed by using Refine query.

Per default, the search covers all fields. only within genes/proteins, biological processes etc. The first box of the search options ( Field) allows searching within a specific type of data, e.g.This type of query is highly unspecific as it includes also information such as gene/protein name synonyms and authors names from referenced literature. flag is sufficient to find everything concerning flagella). Queries are not case-sensitive and search all database content that includes the query term (e.g. One can find interactions of the pathogen itself and interactions between pathogen and host.Per default the search space includes all types of data concerning pathogen-host relations.