Colon Cancer Project

DNA microarrays provide a global assessment of patterns of gene expression and our hope is to use these as a means of improving the diagnosis and treatment of colorectal cancer. This work involves finding genes whose expression patterns correlate with a range of clinical outcomes, including survival and response to therapy. Ultimately, our hope is to find genes that are mechanistically associated with the development of the disease and its progression and to use these for the development of new therapeutics. This work is being carried out in collaboration with Timothy J. Yeatman of the H.Lee Moffitt Cancer Center with support from the US National Cancer Institute (grant U01-CA8552-01A1).

Additional work focuses on the use of candidate genes identified in these genomic screens to elucidate the pathways and networks that they control. Using a combination of RNA interference and microarray analysis, combined with a directed Bayesian Network approach to data analysis, we hope to better understand the mechanisms that are used to regulate tumor progression and to develop a general methodology for approaching the analysis of mammalian gene expression networks.

Colon Cancer pulications

A concise guide to cDNA microarray analysis.
Biotechniques. 2000 Sep;29(3):548-50, 552-4, 556 passim.
Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R, Hughes JE, Snesrud E, Lee N, Quackenbush J.

An optimized protocol for analysis of EST sequences.
Nucleic Acids Res. 2000 Sep 15;28(18):3657-65.
Liang F, Holt I, Pertea G, Karamycheva S, Salzberg SL, Quackenbush J..

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species.
Nucleic Acids Res. 2001 Jan 1;29(1):159-64.
Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J. 

Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray.
Cancer Res. 2001 Nov 1; 61(21):7792-7.
Hegde P, Qi R, Gaspard R, Abernathy K, Dharap S, Earle-Hughes J, Gay C, Nwokekeh NU, Chen T, Saeed AI, Sharov V, Lee NH, Yeatman TJ, Quackenbush J.

Effects of ischemia on gene expression.
J Surg Res. 2001 Aug;99(2):222-7.
Huang J, Qi R, Quackenbush J, Dauway E, Lazaridis E, Yeatman T.

Identification of tumor markers in models of human colorectal cancer using a 19,200-element complementary DNA microarray.
Cancer Res. Nov 2001;61:7792-7797.
Priti Hegde, Rong Qi, Renee Gaspard, Kristie Abernathy, Sonia Dharap, Julie Earle-Hughes, Cheryl Gay, Nnenna U. Nwokekeh, Tingan Chen, Alexander I. Saeed, Vasily Sharov, Norman H. Lee, Timothy J. Yeatman, and John Quackenbush.

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.
Nature Genetics. Dec 2001;29:365-371.
Alvis Brazma, Pascal Hingamp, John Quackenbush, Gavin Sherlock, Paul Spellman, Chris Stoeckert, John Aach, Wilhelm Ansorge, Catherine A. Ball, Helen C. Causton, Terry Gaasterland, Patrick Glenisson, Frank C.P. Holstege, Irene F. Kim, Victor Markowitz, John C. Matese, Helen Parkinson, Alan Robinson, Ugis Sarkans, Steffen Schulze-Kremer, Jason Stewart, Ronald Taylor, Jaak Vilo & Martin Vingron.

Standards for Microarray Data.
Science. 2002 Oct 18;298(5593):539.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J; Microarray Gene Expression Data (MGED) Society.

Editorial: An open letter to the scientific community.
Bioinformatics. 2002;18(112002):1409.
Catherine A. Ball, Gavin Sherlock, et al.

A Concise Guide to cDNA Microarray Analysis.
BioTechniques. Sept 2002;29:548-562.
P. Hegde, R. Qi, K. Abernathy, C. Gay, S. Dharap, R. Gaspard, J.E. Hughes, E. Snesrud, N. Lee and J. Quackenbush.

Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Genome Biol. 2002 Oct 24;3(11):research0062.
Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J.

Identification of Src transformation fingerprint in human colon cancer.
Oncogene. 2002 Oct 17;21(47):7256-65.
Malek RL, Irby RB, Guo QM, Lee K, Wong S, He M, Tsai J, Frank B, Liu ET, Quackenbush J, Jove R, Yeatman TJ, Lee NH.

Osteopontin identified as lead marker of colon cancer progression, using pooled sample expression profiling.
J Natl Cancer Inst. 2002 Apr 3;94(7):513-21.
Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ.

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.
BioTechniques. Oct 2002;33(4):924-930.
H. Kim, B. Zhao, E.C. Snesrud, B.J. Haas, C.D. Town, and J. Quackenbush.

Osteopontin identified as colon cancer tumor progression marker.
C R Biol. 2003 Oct-Nov;326(10-11):1041-3.
Agrawal D, Chen T, Irby R, Quackenbush J, Chambers AF, Szabo M, Cantor A, Coppola D, Yeatman TJ.

Regulation of caspase expression and apoptosis by adenomatous polyposis coli.
Cancer Res. 2003 Aug 1;63(15):4368-74.
Chen T, Yang I, Irby R, Shain KH, Wang HG, Quackenbush J, Coppola D, Cheng JQ, Yeatman TJ.

Shear-induced cyclooxygenase-2 via a JNK2/c-Jun-dependent pathway regulates prostaglandin receptor expression in chondrocytic cells.
J Biol. Chem. 2003 Aug;278(31):28388-28394.
James P. Abulencia, Renee Gaspard, Zachary R. Healy, William A. Gaarde, John Quackenbush, and Konstantinos Konstantopoulos

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Genome Res. 2003;13:1542-1551.
Takeya Kasukawa, Masaaki Furuno, Itoshi Nikaido, Hidemasa Bono, David A. Hume, Carol Bult, David P. Hill, Richard Baldarelli, Julian Gough, Alexander Kanapin, Hideo Matsuda, Lynn M. Schriml, Yoshihide Hayashizaki, Yasushi Okazaki, and John Quackenbush

Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
Genome Res. 2003;13:327-340.
Heenam Kim, Erik C. Snesrud, Brian Haas, Foo Cheung, Christopher D. Town, and John Quackenbush.

Open-source software accelerates bioinformatics.
Genome Biology. Sept. 2003;4(336):1-4.
John Quackenbush.

Using the TIGR Gene Index Databases for biological discovery.
Current Protocols in Bioinformatics. Nov. 2003; Chapter 1: Unit 1.6.
Lee Y, Quackenbush J.

Microarrays- guilt by association.
Science. Oct 2003;302:240-241.
John Quackenbush.

Enrichment of gene-coding sequences in Maize by genome filtration.
Science. Dec 2003;302:2118-2120.
C. A. Whitelaw, W. B. Barbazuk, G. Pertea, A. P. Chan, F. Cheung, Y. Lee, L. Zheng, S. van Heeringen, S. Karamycheva, J. L. Bennetzen, P. SanMiguel, N. Lakey, J. Bedell, Y. Yuan, M. A. Budiman, A. Resnick, S. Van Aken, T. Utterback, S. Riedmuller, M. Williams, T. Feldblyum, K. Schubert, R. Beachy, C. M. Fraser, J. Quackenbush.

Multi-platform, multi-site, microarray-based human tumor classification.
Am J Pathol. 2004 Jan;164(1):9-16.
Bloom G, Yang IV, Boulware D, Kwong KY, Coppola D, Eschrich S, Quackenbush J, Yeatman TJ.

The limits of log-ratios.
BMC Biotechnol. 2004 Mar 8;4(1):3.
Sharov V, Kwong KY, Frank B, Chen E, Hasseman J, Gaspard R, Yu Y, Yang I, Quackenbush J.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
PLoS Bio. Jun 2004;2(6):1-20.
Imanishi, et al.

Orthologous gene-expression profiling in multi-species models: search for candidate genes.
Genome Bio. Apr 2004;5(R34):1-13.
Dmitry N Grigoryev, Shwu-Fan Ma, Rafael A Irizarry, Shui Qing Ye, John Quackenbush and Joe GN Garcia.

Cardiac transcriptional response to acute and chronic angiotensin II treatments.
Physiol Genomics. May 2004;18:152-166.
Jennie E. Larkin, Bryan C. Frank, Renee M. Gaspard, Irena Duka, Haralambos Gavras, and John Quackenbush.

Genetic regulation of endotoxin-induced airway disease.
Genomics. 2004 Jun; 83(6):961-9.
Donald N. Cook, Shuibang Wang, Yonghong Wang, Gabriel P. Howles, Gregory S. Whitehead, Katherine G. Berman, Tony D. Church, Bryan C. Frank, Renee M. Gaspard, Yan Yu, John Quackenbush, and David A. Schwartz.

Submission of microarray data to public repositories.
PLoS Biology. Sept 2004;2(9):1276-1277.
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, John C. Matese, Helen Parkinson, John Quackenbush, Martin Ringwald, Susanna-Assunta Sansone, Gavin Sherlock, Paul Spellman, Chris Stoeckert, Yoshio Tateno, Ronald Taylor, Joseph White, Neil Winegarden.

Multiple-laboratory comparison of microarray platforms.
Nature Methods. May 2005;2(5):345-349.
Rafael A Irizarry, Daniel Warren, Forrest Spencer, Irene F Kim, Shyam Biswal, Bryan C Frank, Edward Gabrielson, Joe G N Garcia, Joel Geoghegan, Gregory Germino, Constance Griffin, Sara C Hilmer, Eric Hoffman, Anne E Jedlicka, Ernest Kawasaki, Francisco Martinez-Murillo, Laura Morsberger, Hannah Lee, David Petersen, John Quackenbush, Alan Scott, Michael Wilson, Yanqin Yang, Shui Qing Ye & Wayne Yu.