Abstract:Tumor metastasis is the leading cause of death for gastric cancer. Metastasis is the main reason for the failure of clinical treatment for gastric cancer. In order to find metastasis-related genes and abnormal signal transduction pathway of high-invasive gastric cancer, samples of gastric cancer with liver metastasis were collected for microarray detection; up-regulated or down-regulated genes in all three cases were simultaneously screened out. Subsequently, from the preliminary screened genes, molecular pathways possibly impacting liver metastasis from gastric cancer were investigated by the Gene Cluster with Literature Profiles (GenCLip) analysis software. Many biological effects including apoptosis have been validated. Functional analysis of differentially expressed genes revealed that a variety of biological pathways, such as blood circulation and gas exchange, vasodilation and vasoconstriction regulation, and immune defense, could be significantly activated. Besides, gene sequences, specific keywords or gene regulatory networks were further searched by GenCLiP. We conclude that data mining allows to quickly identify a series of special signal transduction pathways involving abnormally expressed genes.
. Data mining of microarray for differentially
expressed genes in liver metastasis from gastric cancer[J]. Front. Med., 2010, 4(2): 247-253.
Ling XU MM, Feng WANG MM, Xuan-Fu XU MD, Wen-Hui MO BM, Rong WAN MD, Chuan-Yong GUO MD, Xing-Peng WANG MD, . Data mining of microarray for differentially
expressed genes in liver metastasis from gastric cancer. Front. Med., 2010, 4(2): 247-253.
Chambers A F, Groom A C, MacDonald I C. Dissemination and growthof cancer cells in metastatic sites. Nat Rev Cancer, 2002, 2(8): 563–572 doi: 10.1038/nrc865
Golub T R, Slonim D K, Tamayo P, Huard C, Gaasenbeek M, Mesirov J P, Coller H, Loh M L, Downing J R, Caligiuri M A, Bloomfield C D, Lander E S. Molecular classification of cancer: class discovery andclass prediction by gene expression monitoring. Science, 1999, 286(5439): 531–537 doi: 10.1126/science.286.5439.531
Perou C M, Sørlie T, Eisen M B, van de Rijn M, Jeffrey S S, Rees C A, Pollack J R, Ross D T, Johnsen H, Akslen L A, Fluge O, Pergamenschikov A, Williams C, Zhu S X, Lønning P E, Børresen-Dale A L, Brown P O, Botstein D. Molecular portraits of human breast tumours. Nature, 2000, 406(6797): 747–752 doi: 10.1038/35021093
Sørlie T, Perou C M, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen M B, van de Rijn M, Jeffrey S S, Thorsen T, Quist H, Matese J C, Brown P O, Botstein D, Eystein Lønning P, Børresen-Dale A L. Gene expression patterns of breast carcinomas distinguish tumor subclasseswith clinical implications. Proc Natl Acad Sci U S A, 2001, 98(19): 10869–10874 doi: 10.1073/pnas.191367098
Jensen L J, Saric J, Bork P. Literature mining for the biologist:from information retrieval to biological discovery. Nat Rev Genet, 2006, 7(2): 119–129 doi: 10.1038/nrg1768
Chaussabel D, Sher A. Mining microarray expression data by literature profiling. Genome Biol, 2002, 3(10): RESEARCH0055
Jenssen T K, Laegreid A, Komorowski J, Hovig E. A literature network of human genes for high-throughputanalysis of gene expression. Nat Genet, 2001, 28(1): 21–28 doi: 10.1038/88213
Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet, 2004, 36(7): 664 doi: 10.1038/ng0704-664
Alako B T, Veldhoven A, van Baal S, Jelier R, Verhoeven S, Rullmann T, Polman J, Jenster G. CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics, 2005, 6(1): 51 doi: 10.1186/1471-2105-6-51
Rubinstein R, Simon I. MILANO--custom annotation of microarray results using automatic literature searches. BMC Bioinformatics, 2005, 6(1): 12 doi: 10.1186/1471-2105-6-12
Plake C, Schiemann T, Pankalla M, Hakenberg J, Leser U. AliBaba: PubMedas a graph. Bioinformatics, 2006, 22(19): 2444–2445 doi: 10.1093/bioinformatics/btl408
Li S, Wu L, Zhang Z. Constructing biological networks throughcombined literature mining and microarray analysis: a LMMA approach. Bioinformatics, 2006, 22(17): 2143–2150 doi: 10.1093/bioinformatics/btl363
Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. Automatic extraction of gene ontology annotation and its correlation with clustersin protein networks. BMC Bioinformatics, 2007, 8(1): 243 doi: 10.1186/1471-2105-8-243
Huang Z X, Tian H Y, Hu Z F, Zhou Y B, Zhao J, Yao K T. GenCLiP: a software program for clustering gene listsby literature profiling and constructing gene co-occurrence networksrelated to custom keywords. BMC Bioinformatics, 2008, 9(1): 308 doi: 10.1186/1471-2105-9-308
Livak K J, Schmittgen T D. Analysis of relative gene expression data using Real-Time quantitativePCR and the 2-▵▵Ct method. Methods, 2001, 25(4): 402–408 doi: 10.1006/meth.2001.1262
Fukuhara D, Kanai Y, Chairoungdua A, Babu E, Bessho F, Kawano T, Akimoto Y, Endou H, Yan K. Protein characterization of NA+-independentsystem L amino acid transporter 3 in mice: a potential role in supplyof branched-chain amino acids under nutrient starvation. Am J Pathol, 2007, 170(3): 888–898 doi: 10.2353/ajpath.2007.060428
Ashida S, Nakagawa H, Katagiri T, Furihata M, Iiizumi M, Anazawa Y, Tsunoda T, Takata R, Kasahara K, Miki T, Fujioka T, Shuin T, Nakamura Y. Molecular features of the transition from prostatic intraepithelialneoplasia (PIN) to prostate cancer: genome-wide gene-expression profilesof prostate cancers and PINs. Cancer Res, 2004, 64(17): 5963–5972 doi: 10.1158/0008-5472.CAN-04-0020
Okada K, Katagiri T, Tsunoda T, Mizutani Y, Suzuki Y, Kamada M, Fujioka T, Shuin T, Miki T, Nakamura Y. Analysis of gene-expression profiles in testicular seminomas using a genome-widecDNA microarray. Int J Oncol, 2003, 23(6): 1615–1635
Yandell M D, Majoros W H. Genomics and natural language processing. Nat Rev Genet, 2002, 3(8): 601–610
Chambers A F, Groom A C, MacDonald I C. Dissemination and growthof cancer cells in metastatic sites. Nat Rev Cancer, 2002, 2(8): 563–572 doi: 10.1038/nrc865
Hu P, Bader G, Wiqle D A, Emili A. Computational prediction of cancer-gene function. Nat Rev Cancer, 2007, 7(1): 23–34 doi: 10.1038/nrc2036
Pawson T, Nash P. Assembly of cell regulatory systems through protein interaction domains. Science, 2003, 300(5618): 445–452 doi: 10.1126/science.1083653
Barrios-Rodiles M, Brown K R, Ozdamar B, Bose R, Liu Z, Donovan R S, Shinjo F, Liu Y, Dembowy J, Taylor I W, Luga V, Przulj N, Robinson M, Suzuki H, Hayashizaki Y, Jurisica I, Wrana J L. High-throughput mapping ofa dynamic signaling network in mammalian cells. Science, 2005, 307(5715): 1621–1625 doi: 10.1126/science.1105776
Jiang H, Kang D C, Alexandre D, Fisher P B. RaSH, a rapid subtraction hybridization approach for identifyingand cloning differentially expressed genes. PNAS, 2000, 97(23): 12684–12689 doi: 10.1073/pnas.220431297