Response projected clustering for direct association with physiological and clinical response data

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Yi, Sung Gon ^a   Park, Taesung ^a   Lee, Jae K ^b  

^a Seoul National University   (South Korea)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEGREE OF ASSOCIATION; GEOMETRICAL PROJECTIONS; HIGH-DIMENSIONAL CLUSTERING; MACROPHAGE DIFFERENTIATIONS; MICROARRAY GENE EXPRESSION; MICROARRAY GENE EXPRESSION DATA; PHYSIOLOGICAL RESPONSE; PROJECTED CLUSTERING;

CELL CULTURE; CHEMOTHERAPY; GENE EXPRESSION; METADATA; PHYSIOLOGICAL MODELS; PHYSIOLOGY; VECTOR SPACES; VECTORS;

CLUSTER ANALYSIS;

DOCETAXEL; TUMOR MARKER; TUMOR PROTEIN;

ANTINEOPLASTIC ACTIVITY; ARTICLE; ATHEROGENESIS; BIOINFORMATICS; BOOTSTRAPPING; CANCER CELL CULTURE; CANCER GROWTH; CANCER INHIBITION; CELL DIFFERENTIATION; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA MICROARRAY; DRUG RESPONSE; DRUG SENSITIVITY; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HUMAN; HUMAN CELL; IN VITRO STUDY; MACROPHAGE; QUANTITATIVE ANALYSIS; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; COMPUTER ASSISTED DIAGNOSIS; EVALUATION; META ANALYSIS; METABOLISM; METHODOLOGY; NEOPLASM; STATISTICS;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; CLUSTER ANALYSIS; DIAGNOSIS, COMPUTER-ASSISTED; GENE EXPRESSION PROFILING; HUMANS; META-ANALYSIS AS TOPIC; NEOPLASM PROTEINS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; STATISTICS AS TOPIC; TUMOR MARKERS, BIOLOGICAL;

EID: 41249096891     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-76     Document Type: Article

References (29)

1. + T lymphocytes Oxford Journal of Medicine 1999, 92:463-471
2. Cassidy J Bissett D Spence RAJ Payne M Oxford Handbook of Oncology. Oxford University 2002
3. Bouchard MF Taniguchi H Viger RS Protein kinase A-dependent synergism between GATA factors and the nuclear receptor, liver receptor homolog-1, regulates human aromatase (CYP19) PII prooter activity in breast cancer cells Endocrinology 2006, 146:4905-4916 10.1210/en.2005-0187
4. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns PNAS 1998, 95:14863-14868 24541 9843981 10.1073/pnas.95.25.14863
5. Tamayo P Slonim D Mesirov J Zhu Q Kitareewan S Ditrovsky E Lander ES Golub TR Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation PNAS 1999, 96:2907-2912 15868 10077610 10.1073/pnas.96.6.2907
6. Hasti T Tibshirani R Eisen MB Alizadeh A Levy R Staudt L Chan WC Botstein D Brown PO 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns Genome Biology 2000,1 research0003.1 0003.21 10.1186/gb-2000-1-2-research0003
7. Alter O Brown PO Botstein D Singular value decomposition for genome-wide expression data processing and modeling PNAS 2000, 97:10101-10106 27718 10963673 10.1073/pnas.97.18.10101
8. Park T Yi S-G Lee S Lee SY Yoo D-H Ahn J-I Lee Y-S Statistical tests for identifying differentially expressed genes in time-course microarray experiments Bioinformatics 2003, 19:694-703 10.1093/bioinformatics/ btg068 12691981
9. van de Vijver MJ He YD van't Veer LJ Dai H Hart AAM Voskuil DW Schreiber GJ Peterse JL Roberts C Marton MJ Parrish M Atsma D Witteveen A Glas A Delahaye L van der Velde T Bartelink H ROdenhuis S Rutgers ET Friend SH Bernards R A gene-expression signature as a predictor of survival in breast cancer The New England Journal of Medicine 2002, 347:1999-2009 10.1056/NEJMoa021967 12490681
10. West M Blanchette C Dressman H Huang E Ishida S Spang R Zuzan H Olson JA Marks JR Nevins JR Predicting the clinical status of human breast cancer by using gene expression profiles Proc Natl Acad Sci USA 2001, 98(20):11462-7 58752 11562467 10.1073/pnas.201162998
11. Developmental Therapeutic Program NCI/NIH
12. Cho H Shashkin P Gleissner CA Dunson DM Jain N Lee J Miller Y Ley K Induction of Dendritic Cell-like Phenotype in Macrophages during Foam Cell Formation Physiological Genomics 2007, 29:149-160 10.1152/ physiolgenomics.00051.2006 17244792
13. MedMaster Patient Drug Information, US National Library of Medicine, NIH GNF Genome Informatics Applications & Datasets, the Genomics Institute of the Novartis Research Foundation (GNF)
14. Jain N Thatte J Braciale T Ley K O'Connell M Lee JK Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays Bioinformatics 2003, 19(15):1945-1951 10.1093/ bioinformatics/btg264 14555628
15. Shi LM Fan Y Lee JK Waltham M Andrews DT Scherf U Paull KD Weinstein JN Mining and visualizing large anticancer drug databases Journal of Chem Inf & Com Sci 2000, 40:367-379 10.1021/ci990087b
16. Beißbarth T Speed TP GOstat: Find statistically overrepresented gene ontologies within a group of genes Bioinformatics 2004, 20:1464-1465 10.1093/bioinformatics/bth088 14962934
17. Primiano T Baig M Maliyekkel A Chang B-D Fellars S Sadhu J Axenovich SA Holzmayer TA Roninson IB Identification of potential anticancer drug targets through the selection of growth-inhibitory genetic suppressor elements Cancer cell 2003, 4:41-53 10.1016/S1535-6108(03)00169-7 12892712
18. Li Z Xia L Lee LM Khaletskiy A Wang J Wong JYC Li J-J Effector genes altered in MCF-7 human breast cancer cells after exposure to fractionated ionizing radiation Radiation research 2001, 155:543-553 10.1667/0033-7587(2001)155[0543:EGAIMH]2.0.CO;2 11260656
19. Hu R-J Lee MP Connors TD Johnson LA Burn TC Su K Landes GM Feinberg AP A 2.5-Mb transcript map of a tumor-suppressing subchromosomal transferable fragment from 11p15.5, and isolation and sequence analysis of three novel genes Genomics 1997, 46:9-17 10.1006/geno.1997.4981 9403053
20. Moggs JG Murphy TC Lim FL Moore DJ Stuckey R Antrobus K Kimber I Orphanides G Anti-proliferative effect of estrogen in breast cancer cells that re-express ERα is mediated by aberrant regulation of cell cycle genes Journal of Molecular Endocrinology 2005, 34:535-551 10.1677/jme.1.01677 15821115
21. Sampath D Greenberger LM Beyer C Hari M Liu H Baxter M Yang S Rios C Discafani C Preclinical pharmacologic evaluation of MST-997, an orally active taxane with superior in vitro and in vivo efficacy in pacitaxel- and docetaxel-resistant tumor models Clinical Cancer Research 2006, 12:3459-3469 10.1158/1078-0432.CCR-05-2349 16740771
22. Lin X Duan X Liang Y-Y Su Y Wrigton KH Long J Hu M Davis CM Wang J Brunicardi FC Shi Y Chen Y-G Meng A Feng X-H PPM1A functions as a Smad phosphatase to terminate TGFβ Signaling Cell 2006, 125:915-928 10.1016/j.cell.2006.03.044 16751101
23. Amiel A Leopold L Gronich N Yukla M Fejgin MD Lishner M The influence of different chromosomal aberrations on molecular cytogenetic parameters in chronic lymphocytic leukemia Cancer Genetics and Cytogenetics 2006, 167:145-149 10.1016/j.cancergencyto.2005.11.019
24. Meije CB Hakvoort TBM Swart GWM Westerhof W Lamers WH Das PK Gene expression patterns in melanocytic cells: Candidate markers for early stage and malignant transformation Journal of Pathology 2002, 196:51-58 10.1002/path.1017 11748642
25. Watari A Takaki K Higashiyama S Li Y Satomi Y Takao T Tanemura A Yamaguchi Y Katayama I Shimakage M Miyashiro I Takami K Kodama K Yutsudo M Suppression of tumorigenicity, but not anchorage independence, of human cancer cells by new candidate tumor suppressor gene CapG Oncogene advance online publication 2006:1-8
26. Ricote M Valledor AF Glass CK Decoding transcriptional programs regulated by PPARs and LXRs in the macrophage: Effects on lipid homeostasis, inflammation, and atherosclerosis Arterioscler Thromb Vasc Biol 2004, 24:230-239 10.1161/01.ATV.0000103951.67680.B1 14592855
27. Benjamini Y Hochberg Y Controlling the false discovery rate: A practical and powerful approach to multiple testing Journal of Royal Statistical Society, series B 1995, 57:289-300
28. Kerr MK Churchill GA Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments PNAS 2001, 98:8961-8965 55356 11470909 10.1073/pnas.161273698
29. Tseng GC Wong WH Tight clustering: A resampling-based approach for identifying stable and tight patterns in data Biometrics 2005, 61:10-16 10.1111/j.0006-341X.2005.031032.x 15737073