Pathway Comparison Results

Description of the problem:

Number of classes: 2
Number of genes: 8324
Number of genes that passed filtering criteria: 8324
Number of investigated pathways: 211 BioCarta and 77 KEGG (288 total)
Random variance model was used

Pathways which discriminate among classes:

Table – Sorted by p-value of the LS permutation test.
The first 4 pathways are significant at the nominal 0.01 level of the LS permutation test or KS permutation test

Pathway id Pathway description Number of genes LS Permutation p-value KS Permutation p-value
1 Kegg: hsa00600 Sphingoglycolipid Metabolism 9 0.00448 0.00287
2 BioCarta: h_granulocytesPathway Adhesion and Diapedesis of Granulocytes 5 0.02492 0.00951
3 BioCarta: h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase 5 0.0933 0.00956
4 BioCarta: h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle 5 0.17392 0.00926

Table Significant pathways consist of the following genes:

Pathway id Pathway description Unique id Description Clone GB acc UG cluster Gene symbol Geometric mean of ratios
( Disease / Normal )		 p-value
1 hsa00600 Sphingoglycolipid Metabolism H000076_01 UDP-glucose ceramide glucosyltransferase H000076_01 D50840 152601 UGCG 0.81 0.01527
2 hsa00600 Sphingoglycolipid Metabolism H001062_01 N-acylsphingosine amidohydrolase (acid ceramidase) H001062_01 U70063 75811 ASAH 0.761 0.00155
3 hsa00600 Sphingoglycolipid Metabolism H001185_01 Arylsulfatase A H001185_01 NM_000487 88251 ARSA 0.904 0.14918
4 hsa00600 Sphingoglycolipid Metabolism H001229_01 Arylsulfatase E (chondrodysplasia punctata 1) H001229_01 X83573 74131 ARSE 1.079 0.26811
5 hsa00600 Sphingoglycolipid Metabolism H002064_01 Galactosidase, beta 1 H002064_01 M34423 79222 GLB1 0.816 0.01277
6 hsa00600 Sphingoglycolipid Metabolism H007128_01 Cerebroside (3'-phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase H007128_01 D88667 17958 CST 1.105 0.2026
7 hsa00600 Sphingoglycolipid Metabolism H008567_01 Sialidase 1 (lysosomal sialidase) H008567_01 AF040958 118721 NEU1 0.833 0.01207
8 hsa00600 Sphingoglycolipid Metabolism H012673_01 Serine palmitoyltransferase, long chain base subunit 2 H012673_01 AB011098 59403 SPTLC2 1.034 0.55588
9 hsa00600 Sphingoglycolipid Metabolism H014980_01 Glucosidase, beta; acid (includes glucosylceramidase) H014980_01 NM_000157 282997 GBA 0.882 0.09493
10 h_granulocytesPathway Adhesion and Diapedesis of Granulocytes H002233_01 Selectin P ligand H002233_01 NM_003006 79283 SELPLG 1.164 0.02755
11 h_granulocytesPathway Adhesion and Diapedesis of Granulocytes H002931_01 Selectin L (lymphocyte adhesion molecule 1) H002931_01 M25280 82848 SELL 0.942 0.32569
12 h_granulocytesPathway Adhesion and Diapedesis of Granulocytes H002944_01 Interleukin 8 H002944_01 M17017 624 IL8 1.499 0.02976
13 h_granulocytesPathway Adhesion and Diapedesis of Granulocytes H003221_01 Lymphotoxin beta receptor (TNFR superfamily, member 3 H003221_01 L04270 1116 LTBR 0.856 0.08611
14 h_granulocytesPathway Adhesion and Diapedesis of Granulocytes H003784_01 Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor H003784_01 M24283 168383 ICAM1 0.798 0.01573
15 h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase H001367_01 Protein kinase C, alpha H001367_01 X52479 169449 PRKCA 0.894 0.11314
16 h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase H003826_01 Protein kinase C-like 1 H003826_01 U33053 2499 PRKCL1 0.921 0.28641
17 h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase H008350_01 Myosin phosphatase, target subunit 2 H008350_01 AB007972 130760 MYPT2 0.895 0.27031
18 h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase H010567_01 Homo sapiens protein kinase C-alpha mRNA, partial 3' UTR H010567_01 AF035594 279856 1.117 0.17118
19 h_myosinPathway PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase H011336_01 Guanine nucleotide binding protein (G protein), q polypeptide H011336_01 U43083 296261 GNAQ 1.156 0.00709
20 h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle H001660_01 Dynamin 1 H001660_01 L07807 166161 DNM1 1.1 0.19358
21 h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle H005952_01 Gephyrin H005952_01 AB037806 13405 GPHN 0.897 0.1513
22 h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle H007996_01 GABA(A) receptor-associated protein H007996_01 NM_007278 7719 GABARAP 0.892 0.02784
23 h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle H013966_01 Hypothetical protein H013966_01 AJ011916 84359 HSA011916 1.056 0.2844
24 h_gabaPathway Gamma-aminobutyric Acid Receptor Life Cycle H015514_01 Hypothetical protein MGC2941 H015514_01 NM_024297 288217 MGC2941 1.071 0.26215

Date and time of the analysis:

Name of the project file: Project.xls
Time of the analysis: Thu Apr 28 09:07:44 2005