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. 2014 Dec 11;8(12):e3392. doi: 10.1371/journal.pntd.0003392

Table 3. Pathway enrichment analysis of 1406 ESPs in the EgPSCs transcriptomes.

Category Terma Pathway databaseb Pathway Idc Sample numberd Background numbere P-Valuef Corrected P-valuef
Carbohydrate metabolism
Pentose phosphate pathway KEGG cel00030 13 18 9.41E-10 4.21E-08
Glycolysis/Gluconeogenesis KEGG cel00010 19 40 2.62E-08 8.80E-07
Gluconeogenesis Reactome — 12 19 4.87E-08 1.51E-06
Glycolysis Reactome — 7 8 9.66E-08 2.60E-06
Starch and sucrose metabolism KEGG cel00500 10 26 0.000253 0.004432
Fructose and mannose metabolism KEGG cel00051 8 23 0.001801 0.0226766
Amino sugar and nucleotide sugar metabolism KEGG cel00520 10 32 0.001974 0.0241093
Glucose metabolism Reactome — 18 30 2.63E-10 1.32E-08
Carbon metabolism KEGG cel01200 24 78 1.50E-05 0.0003552
Biosynthesis of amino acids KEGG cel01230 17 65 0.001585 0.0212919
Signal transduction
Heterotrimeric G-protein signaling pathway PANTHER P00026 7 8 9.66E-08 2.60E-06
Calcium signaling pathway KEGG cel04020 13 37 0.000157 0.0030182
IFN-alpha/beta pathways Reactome — 3 5 0.001394 0.0193684
TGF-beta receptor signaling Reactome — 3 6 0.003739 0.0367554
Apoptosis signaling pathway PANTHER P00006 7 18 0.00122 0.0182041
Proteins metabolism
Protein folding Reactome — 22 23 6.32E-21 8.49E-19
Metabolism of proteins Reactome — 64 293 1.75E-05 0.0003918
Mitochondrial protein import Reactome — 9 22 0.000238 0.0043566
Chaperonin-mediated protein folding Reactome — 16 19 1.57E-13 1.59E-11
Post-chaperonin tubulin folding pathway Reactome — 8 9 1.28E-08 5.16E-07
Activation of chaperones by ATF6-alpha Reactome — 5 7 3.41E-05 0.000723
Calnexin/calreticulin cycle Reactome — 5 12 0.002474 0.0293186
Gene expression
MicroRNA (miRNA) biogenesis Reactome — 6 16 0.002776 0.0310737
Genetic information processing
Spliceosome KEGG cel03040 25 103 0.000786 0.0121906
Transport and catabolism
Phagosome KEGG cel04145 37 55 2.53E-21 5.10E-19
Disease pathway
Huntington disease PANTHER P00029 39 41 2.31E-34 9.29E-32
Parkinson disease PANTHER P00049 15 31 3.76E-07 9.46E-06
Others
Cytoskeletal regulation by Rho GTPase PANTHER P00016 15 18 1.07E-12 7.16E-11
CCT/TriC Reactome — 15 18 1.07E-12 7.16E-11
mRNA splicing - minor pathway Reactome — 13 39 0.0003 0.0050358
N-glycan trimming in ER and CNX/CRT Reactome — 6 13 0.000599 0.0096585
Adenine and hypoxanthine salvage pathway PANTHER P02723 3 6 0.003739 0.0367554
a

KEGG enrichment analysis was performed by KOBAS 2.0 (http://kobas.cbi.pku.edu.cn/home.do).

Caenorhaditis elegans pathways were used as a reference. The ESP corresponding to each pathway can be found in Table S9.

b

Pathway databases mapped by KOBAS including KEGG pathway: http://www.genome.jp/kegg/pathway.htm1; reactome: http://www.reactome.org/ReactomeGWT/entrypoint.htm1; PANTHER: http://www.patherdb.org/.

c

Pathway identified in specific database.

“-” means not given.

d

The number of input proteins mapped to the particular pathway.

e

The number of identified proteins mapped to the particular pathway.

f

Only significant results (p<0.05) were shown.

The statistical method was a hypergeometric test, whereas the FDR correction method was from Benjamini and Hochberg (1995).