How could I import data from a Excel file ?

[Luoji]

I am a “brand newcomer” to the cytoscape, and I want to construct a
Metabolic Network. I have got the enzyme number and the reactions
(including the substrates and products), but I don't know how to
structure the data to a proper format which could be identified by
cytoscape.
Can the following format with only three columns be OK?
EC number
substrates products
2.3.1.1
C00002 C00003
... ... ...

[Luoji]

[Maital Ashkenazi]

Hi Luoji,

Cytoscape recognizes a number of formats. You may structure your data as a table (tab delimited or excel), and use Import --> network from table.
Assuming substrates and products are to be represented as nodes, and EC number is the type of interaction, configure the table import dialog as follows:
Source interaction: column 2, Interaction type: column 1, Target interaction: column 2.
After the network is loaded you can set up the visual style to show the directionality of the edges.

This is the relevant manual chapter regarding network file formats and loading networks into Cytoscape:
http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Creating%20Networks

Hope this helps,
Maital

[Shameer Khadar]

Hello Luoji,

You can get more details from the help/tutorial pages :
http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Import%20Fixed-Format%20Network%20Files


Khader Shameer
NCBS - TIFR