UNC MICROARRAY DATABASE
LCCC
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This site provides the service for microarray data storage, retrieval, analysis, and visualization. Access to non-public data is limited to registered University of North Carolina - Chapel Hill researchers and their collaborators. For published data, please see published data. To register for access please see registration form for more specific information.

If you have further questions regarding access, please e-mail the UNC-Chapel Hill Microarray Database curators at: UNC MD curators

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Clinical data collection Collection of
Genomic Predictors and
Clinical Data
Genomic publications Collection of
Publications


software program

Software Programs

MapSplice
MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J.
Nucleic Acids Res, 38(18):e178, 2010.

Software webpage. Open access PDF at Nucleic Acids Res.

Coclustering versus biclustering
LAS: Biclustering algorithm for finding large average submatrices in high dimensional data. Finding large average submatrices in high dimensional data.
A.A. Shabalin, V.J.Weigman, C.M. Perou, and A.B. Nobel.
Annals of Applied Statistics, 3(3), 985-1012, 2009.

Software webpage. Limited access PDF at AoAS. Open access PDF at arxiv.org.

Illustration of cross-platform normalization (XPN).
XPN: Cross-platform normalization method for combining gene expression data from different studies. Merging two gene-expression studies via cross-platform normalization.
A.A. Shabalin, H. Tjelmeland, C. Fan, C.M. Perou, and A.B. Nobel.
Bioinformatics, 24(9):1154, 2008.

Software webpage. Open access PDF at Bioinformatics.

FastMap GUI
FastMap: Fast method for performing eQTL analyses in homozygous populations, including permutation based assessment of significance. FastMap: Fast eQTL mapping in homozygous populations.
D.M. Gatti, A.A. Shabalin, T.C. Lam, F.A. Wright, I. Rusyn, and A.B. Nobel.
Bioinformatics, 25(4):482, 2009.

Software webpage. Open access PDF at Bioinformatics.

FastMap GUI
SWITCHdna: SupWald Identification of dna-copy Changes Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival.
V.J. Weigman, H. H. Chao, A.A. Shabalin, et al.
Breast Cancer Research and Treatment, Nov 2011

Software website.  Open access PDF at Breast Cancer Research and Treatment.

DWD
DWD: Distance Weighted Discrimination.
Adjustment of Systematic Microarray Data Biases.
M. Benito, J. Parker, Q. Du, J. Wu, D. Xiang, C. Perou, J. Marron
Bioinformatics 20:105-144, 2004

Software: website.

Subtyping
SubTyping: Guide to Intrinsic Subtyping.
 A. Prat, J. Parker, C. Perou

Guide: website.
publication

Recent Publications

Carey et al. TBCRC 001: Randomized Phase II Study of Cetuximab in Combination With Carboplatin in Stage IV.

Carey et al. Journal of Clinical Oncology 2012. 30(21):2615-2623
Xu et al. Lunatic Fringe deficiency cooperates with the Met/Caveolin gene amplicon to induce basal-like breast cancer.

Xu et al. Cancer Cell 2012. 21(5):626-641
Liu et al. LKB1/STK11 Inactivation Leads to Expansion of a Prometastatic Tumor Subpopulation in Melanoma.

Liu et al. Cancer Cell 2012. 21(6):751-764

Hutti et al. Oncogenic PI3K mutations lead to NF-kB-dependent cytokine expression following growth.

Hutti et al. Cancer Research 2012. 72:3260-3269

Esserman et al. Chemotherapy response and recurrence-free survival in neoadjuvant breast cancer depends on biomarker
profiles: results from the I-SPY 1 TRIAL (CALGB 150007/150012; ACRIN 6657).

Esserman et al. Breast Cancer Research and Treatment. 2012 132(3):1049-62

Weigman et al. Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival.


Weigman et al. Breast Cancer Research and Treatment, 2011. 133(3):865-80

Keller et al.

Defining the cellular precursors to human breast cancer.

Keller et al. PNAS, 2012. 109(8):2772-7

TCGA et al.

Integrated genomic analyses of ovarian carcinoma.

The Cancer Genome Atlas Research Network,
Nature 2011 474(7353):609-15


Abell et al.
MAP3K4/CBP-regulated H2B acetylation controls epithelial-mesenchymal transition in trophoblast stem cells.

Abell et al. Cell Stem Cell. 2011 8(5):525-37

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Database Service Schedule

The database is backed up during weekend nights. Some of these backups require the database to be shutdown and making it unavailable.