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#General#

CrossTalkB requires a combination of following tab seperated files for analysis.

• 1 Network file or 1 pre processed network
• 1-2 Group files

NOTE: using a pre processed network file will increase the speed of the analysis exponentially

#Network file#

NOTE: Statistics in CrossTalkB hold only for undirected networks

• Format:
  • tab separated files only, \t.
• Header:
  • the file should contain a header line marked with an hash tag, #.
• Column:
  • 1-2 ; node ID which span the link
  • 3 ; score of the link
• Rows:
  • each row represents a link

##Example## In this example we have in the first row two genes MRPL3 and HNRNPF which are connected in the network. The connection has a weight/score of 3.949.

#!bash
#1:Gene1    2:Gene2 3:PFC   4:FBS_max
ENSG00000075651 ENSG00000183684 0.269   5.906
ENSG00000075651 ENSG00000147133 0.137   5.068
ENSG00000075651 ENSG00000197122 0.782   8.185
ENSG00000075651 ENSG00000156049 0.150   5.170
ENSG00000075651 ENSG00000141522 0.386   6.442
ENSG00000075651 ENSG00000177674 0.130   5.008
ENSG00000075651 ENSG00000185624 0.946   9.763
ENSG00000075651 ENSG00000125676 0.757   8.042
ENSG00000075651 ENSG00000146122 0.483   6.842

#Group file#

• Format:
  • tab separated files only, \t.
• Header:
  • the file should contain a header line marked with an hash tag, #.
• Column:
  • 1 ; node ID
  • 2 ; group ID
• Rows:
  • each row contains an element of a group and the group name it is part of.

##Example##

#!bash
#Node GroupName
ENSG00000101247 Pathway1
ENSG00000108510 Pathway1
ENSG00000130528 Pathway1
ENSG00000065150 Pathway1
ENSG00000158258 Pathway2
ENSG00000170423 Pathway2
ENSG00000240344 Pathway2
ENSG00000171346 Pathway2
ENSG00000198925 Pathway2
ENSG00000155511 Pathway2

#Pre processed network#

A pre processed network file can be obtained calculated by CrossTalkB, see create a pre processed network. The statistics are based on the information provided in this file. The authors highly discourage from using some other files for this purpose.