δ-TRIMAX: Extracting triclusters and analysing coregulation in time series gene expression data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7534 LNBI, Issue , 2012, Pages 165-177

  Bhar, Anirban ^a   Haubrock, Martin ^a   Mukhopadhyay, Anirban ^b   Maulik, Ujjwal ^c   Bandyopadhyay, Sanghamitra ^d   Wingender, Edgar ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b UNIVERSITY OF KALYANI   (India)

^c JADAVPUR UNIVERSITY   (India)

^d INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

Affirmation score; Gene ontology; KEGG Pathway; Mean squared residue; Time series gene expression data; TRANSFAC; Tricluster

Indexed keywords

AFFIRMATION SCORE; GENE ONTOLOGY; KEGG PATHWAY; MEAN-SQUARED RESIDUE; TIME-SERIES GENE EXPRESSION DATA; TRANSFAC; TRICLUSTER;

BIOINFORMATICS; GENES; THREE DIMENSIONAL COMPUTER GRAPHICS; TIME SERIES; TRANSCRIPTION FACTORS;

ALGORITHMS;

EID: 84866727006     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_13     Document Type: Conference Paper

References (23)

1. Benjamini, Y., Hochberg, Y.: Controlling the False Discovery Rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 57(1), 289-300 (1995)
2. Benjamini, Y., Yekutieli, D.: The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics 29(4), 1165-1188 (2001)
3. Chen, D., et al.: JunD and JunB integrate prostaglandin E2 activation of breast cancer-associated proximal aromatase promoters. Mol. Endocrinol. 25(5), 767-775 (2011)
4. Cheng, Y., Church, G.M.: Biclustering of expression data. In: Proc. Int. Conf. Int. Syst. Mol. Biol., pp. 93-103 (2000)
5. Chhabra, A., et al.: Expression of transcription factor CREB1 in human breast cancer and its correlation with prognosis. Oncology Reports 18(4), 953-958 (2007)
6. Mukhopadhyay, A., et al.: A novel coherence measure for discovering scaling biclusters from gene expression data. Journal of Bioinformatics and Computational Biology 7(5), 853-868 (2009)
7. Prelic, A., et al.: A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics 22, 1122-1129 (2006)
8. Wingender, E., et al.: The TRANSFAC system on gene expression regulation. Nucleic Acids Res. 29(29), 281-283 (2001)
9. Boyle, E.I., et al.: GO::TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20(18), 3710-3715 (2004)
10. Lanigan, F., et al.: Homeobox transcription factor muscle segment homeobox 2(Msx2) correlates with good prognosis in breast cancer patients and induces apoptosis in vitro. Breast Cancer Research 12(R59) (2010)
11. Carroll, J.S., et al.: Genome-wide analysis of estrogen receptor binding sites. Nature Genetics 38(11) (November 2006)
12. Magnani, L., et al.: PBX1 genomic pioneer function drives ERα signaling underlying progression in breast cancer. PLOS Genetics 7(11) (November 2011)
13. Fougere, M., et al.: NFAT3 transcription factor inhibits breast cancer cell motility by targeting the Lipocalin 2 gene. Oncogene 29(15), 2292-2301 (2010)
14. Yoeli-Lerner, M., et al.: Akt blocks breast cancer cell motility and invasion through the transcription factor NFAT. Molecular Cell 20(4), 539-550 (2005)
15. Khan, S., et al.: Role of specificity protein transcription factors in estrogeninduced gene expression in mcf-7 breast cancer cells. Journal of Molecular Endocrinology 39, 289-304 (2007)
16. Tommasi, S., et al.: Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. Breast Cancer Research 11(R14) (2009)
17. Lee, S.Y., et al.: Homeobox gene Dlx-2 is implicated in metabolic stress-induced necrosis. Molecular Cancer 10(113) (2011)
18. Zhang, S.Y., et al.: E2F-1: a proliferative marker of breast neoplasia. Cancer Epidemiology, Biomarkers & Prevention 9, 395-401 (2000)
19. Maeda, T., et al.: TEF-1 transcription factors regulate activity of the mouse mammary tumor virus LTR. Biochemical and Biophysical Research Communications 296(5), 1279-1285 (2002)
20. Stevens, T.A., et al.: BARX2 and estrogen receptor-alpha (ESR1) coordinately regulate the production of alternatively spliced esr1 isoforms and control breast cancer cell growth and invasion. Oncogene 25, 5426-5435 (2006)
21. Jauliac, S., et al.: The role of NFAT transcription factors in integrin-mediated carcinoma invasion. Nature Cell Biology 4(7), 540-544 (2002)
22. Falcon, S., Gentleman, R.: Using GOstats to test gene lists for GO term association. Bioinformatics 23(2), 257-258 (2007)
23. Zhao, L., Zaki, M.J.: TRICLUSTER: An effective algorithm for mining coherent clusters in 3D microarry data. In: SIGMOD (June 2005)