Module-based functional pathway enrichment analysis of a protein-protein interaction network to study the effects of intestinal microbiota depletion in mice

Molecular Medicine Reports

Volumn 9, Issue 6, 2014, Pages 2205-2212

  Jia, Zhen Y I ^a   Xia, Yang ^a   Tong, Danian ^a   Yao, Jing ^a   Chen, Hong Q I ^a   Yang, Jun ^a  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

Author keywords

Intestinal microbiota depletion; Modules; Pathway enrichment analysis; Protein protein interaction network

Indexed keywords

LINOLEIC ACID; XENOBIOTIC AGENT; PROTEIN BINDING;

ARACHIDONIC ACID METABOLISM; ARTICLE; CELL METABOLISM; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; CYP4F14 GENE; CYTOCHROME P450 4B1 ISOZYME GENE; DOWN REGULATION; DRUG METABOLISM; GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE ONTOLOGY; INTESTINE FLORA; LIPID METABOLISM; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PROTEIN PROTEIN INTERACTION; TACHYKININ PRECURSOR 1 GENE; UPREGULATION; ANIMAL; GENE REGULATORY NETWORK; INTESTINE; METABOLISM; MICROBIOLOGY; MICROFLORA; MOLECULAR GENETICS; MOUSE; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION;

ANIMALS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; INTESTINES; MICE; MICROBIOTA; MOLECULAR SEQUENCE ANNOTATION; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION;

EID: 84899670003     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2014.2137     Document Type: Article

References (36)

1. Qin J, Li R, Raes J, et al: A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65, 2010.
2. Tremaroli V and Backhed F: Functional interactions between the gut microbiota and host metabolism. Nature 489: 242-249, 2012.
3. Gerritsen J, Smidt H, Rijkers GT and de Vos WM: Intestinal microbiota in human health and disease: the impact of probiotics. Genes Nutr 6: 209-240, 2011.
4. Jernberg C, Lofmark S, Edlund C and Jansson JK: Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156: 3216-3223, 2010.
5. Arroyo G, Penas E, Pedrazuela A and Prestamo G: Intestinal microbiota in rats fed with tofu (soy curd) treated under high pressure. Eur Food Res Technol 220: 395-400, 2005.
6. Bjorksten B, Sepp E, Julge K, Voor T and Mikelsaar M: Allergy development and the intestinal microflora during the first year of life. J Allergy Clin Immunol 108: 516-520, 2001. (Pubitemid 32978019)
7. Ohigashi S, Sudo K, Kobayashi D, et al: Changes of the intestinal microbiota, short chain fatty acids, and fecal pH in patients with colorectal cancer. Dig Dis Sci 58: 1717-1726, 2013.
8. Rawls JF: Enteric infection and inflammation alter gut microbial ecology. Cell Host Microbe 16: 73-74, 2007.
9. Human Microbiome Jumpstart Reference Strains Consortium, Nelson KE, Weinstock GM, Highlander SK, et al: A catalog of reference genomes from the human microbiome. Science 328: 994-999, 2010.
10. Reikvam DH, Erofeev A, Sandvik A, et al: Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression. PLoS One 6: e17996, 2011.
11. R. Irizarry, L. Gautier, and L. Cope. An R package for analyses of Affymetrix oligonucleotide arrays. In: The Analysis of Gene Expression Data: Methods and Software. G. Parmigiani, E. S. Garrett, R. A. Irizarry, and S. L. Zeger (eds). Springer-Verlag, Berlin, pp102-119, 2003.
12. Smyth GK: limma: linear models for microarray data. In: Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Gentleman R, Carey VJ, Huber W, Irizarry RA and Dudoit S (eds). Springer New York, NY, pp397-420, 2005.
13. Shao X, Huang B, Lee JM, Xu F and Espejo A: Bayesian method for multirate data synthesis and model calibration. AIChE J 57: 1514-1525, 2011.
14. Hur AB, Elisseeff A and Guyon I: Identification of co-regulation patterns by unsupervised cluster analysis of gene expression data. US Patent 8,489,531. Filed February 2, 2011; issued July 16, 2013.
15. Szklarczyk D, Franceschini A, Kuhn M, et al: The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-D568, 2011.
16. Shannon P, Markiel A, Ozier O, et al: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504, 2003. (Pubitemid 37428274)
17. Bader GD and Hogue CW: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2, 2003.
18. Smoot M, Ono K, Ideker T and Maere S: PiNGO: a Cytoscape plugin to find candidate genes in biological networks. Bioinformatics 27: 1030-1031, 2011.
19. Kanehisa M and Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30, 2000. (Pubitemid 30047706)
20. Xue J, Zhao C and Liang A: Pathway analysis of the differential expression genes of oligonucleotide microarray of airway allergic diseases using GenMAPP. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 25: 371-373, 2011 (In Chinese).
21. Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC and Conklin BR: GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 31: 19-20, 2002.
22. Velagapudi VR, Hezaveh R, Reigstad CS, et al: The gut microbiota modulates host energy and lipid metabolism in mice. J Lipid Res 51: 1101-1112, 2010.
23. Bäckhed F: Programming of host metabolism by the gut microbiota. Ann Nutr Metab 58: 44-52, 2011.
24. Espey MG: Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Radic Biol Med 55: 130-140, 2013.
25. Tamaki Y, Arai T, Sugimura H, et al: Association between cancer risk and drug-metabolizing enzyme gene (CYP2A6, CYP2A13, CYP4B1, SULT1A1, GSTM1, and GSTT1) polymorphisms in cases of lung cancer in Japan. Drug Metab Pharmacokinet 26: 516-522, 2011.
26. Roos PH, Belik R, Follmann W, et al: Expression of cytochrome P450 enzymes CYP1A1, CYP1B1, CYP2E1 and CYP4B1 in cultured transitional cells from specimens of the human urinary tract and from urinary sediments. Arch Toxicol 80: 45-52, 2006. (Pubitemid 41830994)
27. Jang SJ, Kang JH, Lee TS, et al: Prodrug-activating gene therapy with rabbit cytochrome P450 4B1/4-ipomeanol or 2-aminoanthracene system in glioma cells. Nucl Med Mol Imaging 44: 193-198, 2010.
28. Antonovic L: A physiological role of cytochromes P450 4Fs: mouse model (unpublished dissertation). The University of Texas, AAI3218710, 2006.
29. Li N, Liu JY, Qiu H, et al: Use of metabolomic profiling in the study of arachidonic acid metabolism in cardiovascular disease. Congest Heart Fail 17: 42-46, 2011.
30. Gaullier JM, Halse J, Hoye K, et al: Supplementation with conjugated linoleic acid for 24 months is well tolerated by and reduces body fat mass in healthy, overweight humans. J Nutr 135: 778-784, 2005. (Pubitemid 40464104)
31. Gaullier JM, Halse J, Hoye K, et al: Conjugated linoleic acid supplementation for 1 y reduces body fat mass in healthy overweight humans. Am J Clin Nutr 79: 1118-1125, 2004. (Pubitemid 41095966)
32. Kreider RB, Ferreira MP, Greenwood M, Wilson M and Almada AL: Effects of conjugated linoleic acid supplementation during resistance training on body composition, bone density, strength, and selected hematological markers. J Strength Cond Res 16: 325-334, 2002.
33. Graham GJ, Stevens JM, Page NM, et al: Tachykinins regulate the function of platelets. Blood 104: 1058-1065, 2004. (Pubitemid 39038026)
34. Brain SD: Sensory neuropeptides: their role in inflammation and wound healing. Immunopharmacology 37: 133-152, 1997.
35. Mayer EA: Gut feelings: the emerging biology of gut-brain communication. Nat Rev Neurosci 12: 453-466, 2011.
36. Vijay-Kumar M, Aitken JD, Carvalho FA, et al: Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328: 228-231, 2010.