[BiO BB] gene regulatory network reconstruction and pathway finding from the micro-array data

[Li Fan]

Hi,

I am a graduate student in CS dept.  I am dointg some work in learning
gene regulatory network from the
micro-array data.   On major problem I am facing is that it is very hard
to evaluate the results.
For example, I have runned experiments on 6211 yeast genes and my
experimental results suggest that gene
YBR231C  is  "directly " connected with

YAR014C  YBR261C   YBR237W   YBR215W   YBL111C    YER138C     YBR169C
YAR073W    YBL064C        YBR022W      YCR093W     YBR025C   YDR180W
YCR040W     YGL130W
YBR213W     YBR160W

(sorted according to descending probability score)

However, it is hard to judge to what extent the program has succeeded.  I
know Nir Friedman has done a
fundamental experiment
http://www.cs.huji.ac.il/labs/compbio/expression/.    But it is still
difficult to give
a direct comparisan because Friedman's experiment is only on the 800 cell
cycle genes, not on the all 6000 genes.
Further more, only few edges are listed with comments from biologists in
that paper.

So could somebody give me some suggestions about the benchmark which can
be used to evaluate the success
of the bayes network structure learning algorithm(which is used to learn
the genetic structure)?

Thanks a lot

Fan Li