HELP

Description of the problem:

Number of classes: 2
Column of the Experiment Descriptors sheet that defines class variable: OBNSC vs heNSC
Number of genes that passed filtering criteria: 47231
Type of Gene Sets: Kegg Pathway
Number of total investigated Gene Sets: 171
Type of univariate test used: Two-sample T-test
Random variance model was not used because distribution assumptions of this model were not satisfied.

Tests used to find significant gene sets are: LS/KS permutation test, Efron-Tibshirani's GSA maxmean test
The threshold of determining significant gene sets is 0.005
LS/KS permutation test finds gene sets which have more genes differentially expressed among the phenotype classes than expected by chance.
Efron-Tibshirani's test uses 'maxmean' statistics to identify gene sets differentially expressed.

Summary of Results:

75 out of 171 investigated gene sets passed the 0.005 significance threshold
LS/KS permutation test found 72 significant gene sets.
Efron-Tibshirani's maxmean test found 17 significant gene sets (under 200 permutations).

Table - Table of Gene Sets: 75 gene sets sorted by LS permutation p-value (significant p-values are in red)
To access the list of genes within each gene set, click the hyperlinked number of genes for each gene set.

class 1:1, class 2:2
  Kegg PathwayPathway descriptionNumber of genesHeatmap linkLS permutation p-valueKS permutation p-valueEfron-Tibshirani's GSA test p-value
1hsa00010Glycolysis / Gluconeogenesis121heatmap 0.00001 0.096520.115 (+)
2hsa00020Citrate cycle (TCA cycle)49heatmap 0.00001 0.00164 < 0.005 (-)
3hsa00062Fatty acid elongation in mitochondria13heatmap 0.00001 0.00005 < 0.005 (+)
4hsa00100Biosynthesis of steroids25heatmap 0.00001 0.00073 0.02 (+)
5hsa00190Oxidative phosphorylation159heatmap 0.00001 0.00001 < 0.005 (+)
6hsa00193ATP synthesis66heatmap 0.00001 0.00001 < 0.005 (+)
7hsa00230Purine metabolism258heatmap 0.00001 0.00046 0.25 (+)
8hsa00240Pyrimidine metabolism142heatmap 0.00001 0.00001 0.25 (+)
9hsa00280Valine, leucine and isoleucine degradation67heatmap 0.00001 0.00039 0.17 (+)
10hsa00380Tryptophan metabolism138heatmap 0.00001 0.00223 0.235 (+)
11hsa00640Propanoate metabolism62heatmap 0.00001 0.010570.06 (+)
12hsa00650Butanoate metabolism63heatmap 0.00001 0.00217 0.12 (+)
13hsa00790Folate biosynthesis53heatmap 0.00001 0.00043 0.275 (+)
14hsa00900Terpenoid biosynthesis9heatmap 0.00001 0.0004 < 0.005 (+)
15hsa00970Aminoacyl-tRNA biosynthesis40heatmap 0.00001 0.00001 0.23 (+)
16hsa03010Ribosome150heatmap 0.00001 0.00001 < 0.005 (+)
17hsa03050Proteasome49heatmap 0.00001 0.00001 < 0.005 (+)
18hsa04110Cell cycle200heatmap 0.00001 0.00001 0.16 (+)
19hsa04130SNARE interactions in vesicular transport55heatmap 0.00001 0.00186 0.25 (+)
20hsa04510Focal adhesion359heatmap 0.00001 0.0024 < 0.005 (-)
21hsa04520Adherens junction154heatmap 0.00001 0.00092 < 0.005 (-)
22hsa04720Long-term potentiation111heatmap 0.00001 0.0007 < 0.005 (-)
23hsa04810Regulation of actin cytoskeleton357heatmap 0.00001 0.036960.155 (+)
24hsa05120Epithelial cell signaling in Helicobacter pylori infection118heatmap 0.00001 0.026080.09 (-)
25hsa05210Colorectal cancer148heatmap 0.00001 0.00002 0.035 (-)
26hsa05060Prion disease24heatmap 0.00002 0.00048 < 0.005 (+)
27hsa04310Wnt signaling pathway269heatmap 0.00002 0.001 0.045 (-)
28hsa00310Lysine degradation90heatmap 0.00003 0.00393 0.235 (+)
29hsa00620Pyruvate metabolism83heatmap 0.00003 0.025070.07 (+)
30hsa04910Insulin signaling pathway236heatmap 0.00003 0.039140.195 (-)
31hsa00626Nitrobenzene degradation23heatmap 0.00004 0.00009 0.165 (+)
32hsa00440Aminophosphonate metabolism29heatmap 0.00004 0.001 0.165 (+)
33hsa03020RNA polymerase37heatmap 0.00005 0.007870.205 (+)
34hsa00030Pentose phosphate pathway41heatmap 0.00006 0.067570.045 (+)
35hsa00071Fatty acid metabolism81heatmap 0.00007 0.080070.035 (+)
36hsa00330Arginine and proline metabolism85heatmap 0.00007 0.097450.125 (+)
37hsa04120Ubiquitin mediated proteolysis92heatmap 0.00007 0.00053 0.41 (+)
38hsa00251Glutamate metabolism46heatmap 0.00008 0.073190.185 (+)
39hsa04360Axon guidance229heatmap 0.00008 0.089660.14 (-)
40hsa05010Alzheimer@47heatmap 0.00009 0.055980.255 (+)
41hsa00511N-Glycan degradation19heatmap 0.0001 0.00014 0.345 (+)
42hsa00530Aminosugars metabolism45heatmap 0.0001 0.032750.155 (-)
43hsa01510Neurodegenerative Disorders77heatmap 0.00014 0.077060.135 (+)
44hsa00340Histidine metabolism66heatmap 0.00015 0.00364 0.25 (+)
45hsa03022Basal transcription factors53heatmap 0.00027 0.06649 < 0.005 (-)
46hsa05020Parkinson@27heatmap 0.00027 0.005940.145 (+)
47hsa01032Glycan structures - degradation46heatmap 0.00045 0.00102 0.29 (+)
48hsa04150mTOR signaling pathway95heatmap 0.00047 0.273270.13 (-)
49hsa04540Gap junction153heatmap 0.00059 0.016740.145 (-)
50hsa04530Tight junction225heatmap 0.0006 0.070170.16 (-)
51hsa00051Fructose and mannose metabolism70heatmap 0.00091 0.127610.3 (+)
52hsa00930Caprolactam degradation30heatmap 0.00094 0.092040.09 (+)
53hsa04010MAPK signaling pathway498heatmap 0.00112 0.63310.16 (-)
54hsa04710Circadian rhythm27heatmap 0.00131 0.014680.06 (-)
55hsa03060Protein export16heatmap 0.0014 0.00025 0.175 (+)
56hsa00400Phenylalanine, tyrosine and tryptophan biosynthesis14heatmap 0.00145 0.083060.075 (+)
57hsa00450Selenoamino acid metabolism53heatmap 0.00146 0.014160.245 (+)
58hsa00290Valine, leucine and isoleucine biosynthesis16heatmap 0.00151 0.006050.24 (+)
59hsa00410beta-Alanine metabolism40heatmap 0.00168 0.01130.12 (+)
60hsa00561Glycerolipid metabolism102heatmap 0.00212 0.164840.165 (+)
61hsa00903Limonene and pinene degradation41heatmap 0.00233 0.044280.225 (+)
62hsa00532Chondroitin sulfate biosynthesis24heatmap 0.00234 0.0007 0.31 (+)
63hsa04670Leukocyte transendothelial migration203heatmap 0.00249 0.623320.145 (-)
64hsa00710Carbon fixation41heatmap 0.00269 0.144820.125 (+)
65hsa04330Notch signaling pathway81heatmap 0.0027 0.041240.47 (+)
66hsa00670One carbon pool by folate25heatmap 0.00274 0.148250.215 (+)
67hsa00600Sphingolipid metabolism65heatmap 0.00286 0.020530.355 (+)
68hsa04612Antigen processing and presentation141heatmap 0.00333 0.17877 < 0.005 (+)
69hsa00362Benzoate degradation via hydroxylation6heatmap 0.00371 0.019570.13 (+)
70hsa00510N-Glycan biosynthesis62heatmap 0.004 0.133490.35 (+)
71hsa00904Diterpenoid biosynthesis5heatmap0.0102 0.0024 < 0.005 (-)
72hsa00052Galactose metabolism62heatmap0.01908 0.00444 0.385 (+)
73hsa00780Biotin metabolism14heatmap0.052320.01355 < 0.005 (-)
74hsa05030Amyotrophic lateral sclerosis (ALS)32heatmap0.106580.43079 < 0.005 (-)
75hsa006232,4-Dichlorobenzoate degradation6heatmap0.17510.28288 < 0.005 (+)

Links to the genes within gene sets:
Gene Sets 1 - 75

Filtering parameters:

R version 2.12.0 (2010-10-15)
Name of the project file: Hany_Project.xls
Time of the analysis: Sun Aug 28 12:40:26 2011

BRB-ArrayTools Version: 4.2.0 - Beta_2 (June 2011)
Project annotated by SOURCE (source.stanford.edu), searched by gene identifier: Symbol, on 7/22/2011 3:40:29 PM

  • Spot Filters: OFF


  • Average the replicate spots within an array: OFF

  • Normalization:

    • Normalize (center) each array using quantile normalization.

  • Gene Filters: OFF


  • Gene Subsets: OFF