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Address correspondence to: Chatchawit.A@chula.ac.th
Authors Chatchawit Aporntewana and Apiwat Mutirangurab
aDepartment of Mathematics, Faculty of Science,
bCenter for Excellence in Molecular Genetics of Cancer and Human Diseases,
Department of Anatomy, Faculty of Medicine,
Chulalongkorn University, Bangkok 10330, Thailand.
Reference Please cite CU-DREAM as,
Aporntewan C, Mutirangura A. Connection Up- and Down-Regulation Expression Analysis of Microarrays (CU-DREAM): A physiogenomic discovery tool, Asian Biomedicine, Vol. 5 No. 2, pp. 257-262, April 2011. DOI: 10.5372/1905-7415.0502.034
Download program Single executetable file: cu-dream.exe (only for Windows)
     This is the first version and compatible with our publication.
     For updates and the latest version, please see below.
User manual: UserManual.pdf
Template: template.xls
Download showcases All six showcases as in the publication.
  1. CU-DREAM identified genes that were up- and down-regulated.
  2. CU-DREAM validated significantly regulated genes.
  3. CU-DREAM determined if two different diseases had a similar effect on gene regulation.
  4. CU-DREAM identified isoform-changed genes.
  5. CU-DREAM determined if cells shared gene regulation mechanisms.
  6. CU-DREAM can identify common gene regulation pathways even when comparing between two different cell types.
Updates
  1. Feb 17, 2011 CU-DREAM looks for the column "Gene Symbol" in the annotation file. However, the column title could vary. Users can specify the column title (i.e. cu-dream GSE1.xls GSE2.xls "column title"). An alternative is to use "RefSeq Transcript ID" column (e.g. cu-dream GSE1.xls GSE2.xls "RefSeq Transcript ID"). CU-DREAM will count the RefSeqs (NM_) instead of gene symbols.

    Download the executable file for this update, click here.

  2. April 16, 2011 CU-DREAM(X) can intersect a GSE dataset with "a gene set." For instance, a user may find the association between down regulation and genes containing transposable elements (TEs). To do so, use cu-dreamx GSE.xls TE.txt (where TE.txt is a text file, each line is a gene symbol). CU-DREAM(X) can count the RefSeqs (NM_) instead of gene symbols (e.g. cu-dreamx GSE.xls TE.txt "RefSeq Transcript ID").

    Download the executable file for this update, click here.

  3. May 17, 2011 CU-DREAM and CU-DREAM(x) save the output in Excel 97-2003 Workbook (.xls) which limits the maximum row at 2^16 = 65,536. Unfortunately, modern microarrays may contain >100,000 probes (rows). To cope with large arrays, we use the latest Excel Workbook (.xlsx) which can store 2^30 = 1,048,576 rows at the maximum.

    Download the executable file for this update (CU-DREAM), click here.
    Download the executable file for this update (CU-DREAMX), click here.

  4. October 28, 2011 In the previous versions of CU-DREAM, gene symbols are case sensitive. So I made it "case insensitive."

    Download the executable file for this update (CU-DREAM), click here.

CU-DREAM citations
  1. C. Aporntewan, C. Phokaew, J. Piriyapongsa, C. Ittiwut, C. Ngamphiw, S. Tongsima, A. Mutirangura. Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2, PLoS ONE 6(3): e17934. DOI: 10.1371/journal.pone.0017934
  2. S. Khowutthitham, C. Ngamphiw, W. Wanichnopparat, K. Suwanwongse, S. Tongsima, C. Aporntewan, A. Mutirangura, Intragenic long interspersed element-1 sequences promote promoter hypermethylation in lung adenocarcinoma, multiple myeloma and prostate cancer, Genes & Genomics, 34(5): 517-528, October, 2012. DOI 10.1007/s13258-012-0058-0.
  3. W. Wanichnopparat, K. Suwanwongse, P. Pin-on, C. Aporntewan, A. Mutirangura, Genes associated with the cis-regulatory functions of intragenic LINE-1 elements, BMC Genomics, 14(205), 27 March 2013. DOI:10.1186/1471-2164-14-205.
  4. V. Termglinchan, W. Wanichnopparat, K. Suwanwongse, C. Teeyapant, K. Chatpermporn, K. Leerunyakul, K. Chuadpia, O. Sirimaneethum, P. Wijitworawong, W. Mutirangura, C. Aporntewan, C. Vinayanuwattikun, A. Mutirangura, Candidate Cancer-Targeting Agents Identified by Expression Profiling Arrays, OncoTargets and Therapy, Vol. 2013, No. 6, pp. 447 - 458, April 2013. DOI: http://dx.doi.org/10.2147/OTT.S42858