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Instructions for FARO server:

This server creates a list of functionally associated factors provided a file
consisting of differentially expressed genes for the query factor.
It works for Arabidopsis thaliana for further information look here.
Query list is compared with top 1209 differentially expressed genes of 241
known factors - the compendium.
The model of associations network in the compendium is currently not computed
on the run and was obtained basing on fixed cutoff values. As a consequence
different cutoffs for query factors may lead into one sided associations
(it is only a statistical problem, if associationis real it's always two directional).



Description of the input fields:

  • Name of the factor - if left takes a default value
  • Input file - format described below
  • Cutoff options - may chose only one at a time
    • Overlap size: only factors with percentage of overlapping genes above or equal
      to specified value are considered associated
    • Rank: treats n leading (in terms of overlap size) factors as associated ignoring
      the absolute of overlap (may be of use if very small number of genes overlaps)


Input:

Server processes tab separated text files containing at least 50 entries (genes).

One entry = one line of folowing format:
  • 1st field - the ID (Affymetrix or @locus)
  • 2nd field - indicator of responce direction i.e. +/- sign or
    expressions fold change(only sign is taken into account)
  • Any further content of the line is ignored
Example input file:

255624_at -4.6
254252_at 3.4
250286_at 3
...
...
...
...
At2g42240 2
At2g42250 -1.9
......
......
255912_at 3.5



Output:

List of factors functionally associated, ie:
Factor Number of overlapping genes % of overlapping genes Congruence
mpk4 500 100% 100%
mekk1 273 54.6% 100%
... ... ... ...
  • Factor name is a link to the list of overlapping genes
  • Congruence of a factor is the fraction of the overlaping genes
    which reacted similarly i.e.where over- or under- expressed
    for both query and compendium factor
Number of associated factors for each of the possible percentage cutoffs
5 % 225 factors
10 % 127 factors
...

Shows number of associated factors found for other cutoff values to make
choosing proper value easier.


Output - list of overlapping genes




GETTING HELP

Server problems: