BIOST 2055
Statistical methods and data mining in microarray analysis
Spring 2011
Class location: Room A622, Crabtree Hall
Class schedule: Wednesday, Friday 9:30-10:45AM
Course homepage: http://www.biostat.pitt.edu/biost2055/11
Lab location: 3073 (3rd floor), Department of Computational Biology, BST3, 3501 Fifth Avenue. (BST3 is a secured building. Bring your Pitt ID to enter for the five lab sessions.)
Lecturer: George C. Tseng
Homepage: http://www.pitt.edu/~ctseng
Office hour: by appointment
Office: 303 Parran Hall
Email address: ctseng@pitt.edu
Telephone number: 412-624-5318
TA: Xingbin Wang
Office hour: Wed and Fri 2:00-3:00
Offce: Crabtree A431
Email: xbw1@pitt.edu (homework please send to biost2055@gmail.com)
syllabus
final project instructions
Lecture Slides
01/05 LectureW1_Intro_Class, LectureW1_Intro_Bio
01/07 LectureW1_Intro_Bio
Students with no knowledge of R software should start to study the tutorial and learn R programming language:
LectureW2_simple_R_Tutorial, LectureW2_more_complete_R_intro
01/12 LectureW2_Intro_Array
01/14 LectureW2_Affy_cDNA_preprocessing
01/19 LectureW3_Lab1,
LectureW3_R_code_BRCA1,
LectureW3_Lab1_RMA_tutorial,
LectureW3_R_code_MAplot,
LectureW3_dChip,
LectureW3_CEL_files,
LectureW3_CDF_file,
HW1
01/21 LectureW3_DE
01/26 LectureW4_Classification2
01/28 LectureW4_Classification2,
LectureW4_Theorem
02/02 LectureW5_Lab2,
HW2
02/04 LectureW5_Dimension_Reduction,
LectureW5_Dimension_Reduction_Theory
02/09 LectureW6_Clustering1
02/11 LectureW6_Clustering2
02/16 LectureW7_Lab3, LectureW7_cellCycleData,
HW3, data_simu_tight_clust,
tclust_package
02/18 LectureW7_pathway_motifFindaing
02/23 LectureW8_SP_LA
02/25 LectureW8_Genomic_Meta
03/02 LectureW9_Lab4,
LectureW9_data,
LectureW9_H4,
LectureW9_HW4_data
03/04 LectureW9_Network
03/16 LectureW10_Other_arrays
03/18 LectureW10_GWAS (by guest lecturer Eleanor Feingold
03/23 LectureW11_MS_Intro, LectureW11_MS_case_study
03/25 LectureW11_Next_gen_Sequencing (by guest lecturer Mike Barmada)
03/30 The guest lecture on NGS by Mike Barmada will take place in A215
Final project groups:
4/1
F: Devinney, Katelynn M; Houze, Matin; Chen, Rui
G: Chang, Lun-Ching; Lin, Huimin; Ma, Hua
H: Jia, Jia; Liao, Ge; Tang, Shaowu
4/6
D: Huang, Hsin-Hui; Ji, Hao; Liu, Qing
E: Li, Xiaoxue; Lin, Yun; Yang, Shuting
B: Adomako-Ankomah, Yaw; Ren, Yi; Yan, Peng
4/8
A: Shi, Haiwen; Won, SeungHyun; Joyeeta Dutta-Moscato
C: Buhule, Olive Darlia; Hong, Chang Sook; Singhabahu, Dilrukshika Manori
Data sets for final project:
Breast cancer data
Clin Cancer Res. 2007 Jun 1;13(11):3207-14. Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series. Desmedt C, Piette F, Loi S, Wang Y, Lallemand F, Haibe-Kains B, Viale G, Delorenzi M, Zhang Y, d'Assignies MS, Bergh J, Lidereau R, Ellis P, Harris AL, Klijn JG, Foekens JA, Cardoso F, Piccart MJ, Buyse M, Sotiriou C; TRANSBIG Consortium.
Lancet. 2003 May 10;361(9369):1590-6. Gene expression predictors of breast cancer outcomes. Huang E, Cheng SH, Dressman H, Pittman J, Tsou MH, Horng CF, Bild A, Iversen ES, Liao M, Chen CM, West M, Nevins JR, Huang AT. (group E)
Int J Cancer. 2007 Mar 1;120(5):1070-5. Prediction of metastasis from low-malignant breast cancer by gene expression profiling. Thomassen M, Tan Q, Eiriksdottir F, Bak M, Cold S, Kruse TA. (group B)
Cancer Res. 2006 Nov 1;66(21):10292-301. Genetic reclassification of histologic grade delineates new clinical subtypes of breast cancer. Ivshina AV, George J, Senko O, Mow B, Putti TC, Smeds J, Lindahl T, Pawitan Y, Hall P, Nordgren H, Wong JE, Liu ET, Bergh J, Kuznetsov VA, Miller LD.
J Clin Oncol. 2007 Apr 1;25(10):1239-46. Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade. Loi S, Haibe-Kains B, Desmedt C, Lallemand F, Tutt AM, Gillet C, Ellis P, Harris A, Bergh J, Foekens JA, Klijn JG, Larsimont D, Buyse M, Bontempi G, Delorenzi M, Piccart MJ, Sotiriou C. (group D)
Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13550-5. Epub 2005 Sep 2. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J.
Breast Cancer Res. 2005;7(6):R953-64. Epub 2005 Oct 3. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedrén S, Bergh J. (group C)
Lancet. 2005 Feb 19-25;365(9460):671-9. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Wang Y, Klijn JG, Zhang Y, Sieuwerts AM, Look MP, Yang F, Talantov D, Timmermans M, Meijer-van Gelder ME, Yu J, Jatkoe T, Berns EM, Atkins D, Foekens JA.
Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10393-8. Epub 2003 Aug 13. Breast cancer classification and prognosis based on gene expression profiles from a population-based study. Sotiriou C, Neo SY, McShane LM, Korn EL, Long PM, Jazaeri A, Martiat P, Fox SB, Harris AL, Liu ET. (group F)
J Natl Cancer Inst. 2006 Feb 15;98(4):262-72. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, Van de Vijver MJ, Bergh J, Piccart M, Delorenzi M.
Nature. 2002 Jan 31;415(6871):530-6. Gene expression profiling predicts clinical outcome of breast cancer. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. (group A)