Gene Co-expression Network analysis of Lung Adenocarcinoma Cell Carcinoma data
| dc.contributor.author | Uddin, Md. Saif | |
| dc.contributor.author | Ahamed, Md. Tanvir | |
| dc.date.accessioned | 2017-10-25T10:25:52Z | |
| dc.date.available | 2017-10-25T10:25:52Z | |
| dc.date.issued | 2016-11-20 | |
| dc.description | Supervised by Tareque Mohmud Chowdhury Assistant Professor Department of Computer Science and Engineering | en_US |
| dc.description.abstract | A gene co-expression analysis on Lung adenocarcinoma data was done to find modules of genes that might highly impact the growth of this type of tumor. Along with that, cancer survival data was used to relate modules to prognostic significance for survival time. Analysis on microarray data revealed modules that were significant in gene enrichment analysis and 4 genes - TTk, C6orf173, CENPE, DCC1 were found that were significant in terms of survival time. A second analysis was done on a second set of RNAseq data and the significant genes in modules was found there, were also found in the RNAseq data implying that these genes might indeed play a crucial role in Lung adenocarcinoma. | en_US |
| dc.identifier.citation | 1. Langfelder, P. & Horvath, S. (2008) WGCNA: an R package for weighted correlation network analysis. 2. Horvath, S., et al. "Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target." Proceedings of the National Academy of Sciences 103.46 (2006): 17402-17407. 3. A Research for Weighted Gene Co-expression Network Model.Jun Wang, Weiping Wang, Wen Liu, Zhong Zhou, Xiaoying Wang. 4. Yip A, Horvath S: Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics 2007, 8:22.. 5. Li A, Horvath S: Network Neighborhood Analysis With theMulti-node Topological Overlap Measure. Bioinformatics 2007,23(2):222-231 6. Langfelder P, Zhang B, Horvath S: Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.Bioinformatics 2008, 24(5):719-720. 7. Ghazalpour A, Doss S, Zhang B, Plaisier C, Wang S, Schadt E, Thomas A, Drake T, Lusis A, Horvath S: Integrating Genetics and Network Analysis to Characterize Genes Related to Mouse Weight. PloS Genetics 2006, 2(8):e130 8. Fuller T, Ghazalpour A, Aten J, Drake T, Lusis A, Horvath S:Weighted Gene Co-expression Network Analysis StrategiesApplied to Mouse Weight. Mammalian Genome 2007,6(18):463-472 9. Oldham M, Horvath S, Geschwind D: Conservation and Evolution of Gene Co-expression Networks in Human and Chimpanzee Brains. Proc Natl Acad Sci USA 2006, 103(47):17973-17978. 10. Horvath S, Dong J: Geometric interpretation of Gene Coexpression Network Analysis. PLoS Computational Biology 2008. P a g e 43 | 42 11. Dudoit S, Yang Y, Callow M, Speed T: Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002. 12. (2006) FDT: fields: Tools for Spatial Data. Tech. rep., National Center for Atmospheric Research, Boulder, CO 2007 [http://www.image.ucar.edu/GSP/Software/Fields] 13. Hu Z, Snitkin ES, DeLisi C: VisANT: an integrative framework for networks in systems biology. Brief Bioinform 2008,9(4):317-325. 14. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 2003, 13(11):2498-2504. 15. Mutation and Expression of the DCC Gene in Human Lung Cancer. Takashi Kohno, Takako Sato, Satoshi Takakura, Kimiko Takei, Kaoru Inoue, Michiho Nishioka, and Jun Yokota,2000. 16. DAVID - Gene enrichment analysis tool. https://david.ncifcrf.gov/home.jsp | en_US |
| dc.identifier.uri | http://hdl.handle.net/123456789/103 | |
| dc.language.iso | en | en_US |
| dc.publisher | IUT, CSE | en_US |
| dc.title | Gene Co-expression Network analysis of Lung Adenocarcinoma Cell Carcinoma data | en_US |
| dc.type | Thesis | en_US |