Creation Time:	2015-07-22 12:01:03

INPUT:

Annotations file:	sample_annotation_file.txt
Gene file:	sample_gene_file.txt
Use of gene file:	normally ordered list
lower limit annotations/process:	4
upper limit annotations/process:	0 (i.e., None)
k (number of perturbed categories):	0 (i.e., each perturbed gene in its own category)
belief:	5
Method:	MCMC with parameter learning with an empty set as initial set
repeats:	5
burnin steps:	1000
MCMC steps:	10000
Maximal value for alpha and beta:	0.346724736551
Probability parameter change:	0.2
seed for RNG:	0

Initial set of processes:
Empty set


INPUT ANALYSIS:

Total number of processes:	8
Total number of genes:	20
Number of perturbed genes:	7



OUTPUT:

Learnt parameters:
alpha (FPR):	0.121353657793
beta (FNR):	0.294716026068
q (penalization parameter):	0.125
penalization per term, i.e., -log(q/(1-q)):	1.94591014906


Best found log likelihood value:	-12.412927251+-0.00154646945353


Order	#(Annotations)	#(Annotations of perturbed genes)	Mean Posterior Probability	Standard Deviation Posterior Probability	p-value	Average Expression Level	Term Name	Explained Perturbed Genes
1	7	5	0.69144	0.0106	2.232e-02	0.555	ProcessA	G1 G2 G4 G5 G6
2	5	4	0.56472	0.01906	3.070e-02	0.557	ProcessC	G1 G2 G6 G7
3	4	2	0.20148	0.02431	4.392e-01	0.415	ProcessH	G3 G5
4	5	1	0.02168	0.00601	9.170e-01	0.287	ProcessD	G1
5	9	3	0.01168	0.00678	7.276e-01	0.26	ProcessB	G2 G3 G7
6	12	4	0.0093	0.00475	7.492e-01	0.277	ProcessF	G2 G3 G4 G7
7	14	4	0.00296	0.00298	9.223e-01	0.249	ProcessG	G2 G3 G4 G7
8	11	4	0.00176	0.0011	6.300e-01	0.266	ProcessE	G2 G4 G5 G7