Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM: Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer. 2010
Google Scholar
Jass JR: Classification of colorectal cancer based on correlation of clinical, morphological and molecular features. Histopathology. 2007, 50 (1): 113-130. 10.1111/j.1365-2559.2006.02549.x.
Article
CAS
PubMed
Google Scholar
Kruhoffer M, Jensen JL, Laiho P, Dyrskjot L, Salovaara R, Arango D, Birkenkamp-Demtroder K, Sorensen FB, Christensen LL, Buhl L, et al: Gene expression signatures for colorectal cancer microsatellite status and HNPCC. Br J Cancer. 2005, 92 (12): 2240-2248. 10.1038/sj.bjc.6602621.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bienz M, Clevers H: Linking colorectal cancer to Wnt signaling. Cell. 2000, 103 (2): 311-320. 10.1016/S0092-8674(00)00122-7.
Article
CAS
PubMed
Google Scholar
Shitashige M, Naishiro Y, Idogawa M, Honda K, Ono M, Hirohashi S, Yamada T: Involvement of splicing factor-1 in beta-catenin/T-cell factor-4-mediated gene transactivation and pre-mRNA splicing. Gastroenterology. 2007, 132 (3): 1039-1054. 10.1053/j.gastro.2007.01.007.
Article
CAS
PubMed
Google Scholar
Thorsen K, Mansilla F, Schepeler T, Oster B, Rasmussen MH, Dyrskjot L, Karni R, Akerman M, Krainer AR, Laurberg S, et al: Alternative splicing of SLC39A14 in colorectal cancer is regulated by the Wnt pathway. Mol Cell Proteomics. 2011, 10 (1): M110 002998-
Article
PubMed
Google Scholar
Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, et al: Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 2006, 16 (1): 55-65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH: The functional consequences of alternative promoter use in mammalian genomes. Trends Genet. 2008, 24 (4): 167-177. 10.1016/j.tig.2008.01.008.
Article
CAS
PubMed
Google Scholar
Baek D, Davis C, Ewing B, Gordon D, Green P: Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res. 2007, 17 (2): 145-155. 10.1101/gr.5872707.
Article
CAS
PubMed
PubMed Central
Google Scholar
Battey J, Moulding C, Taub R, Murphy W, Stewart T, Potter H, Lenoir G, Leder P: The human c-myc oncogene: structural consequences of translocation into the IgH locus in Burkitt lymphoma. Cell. 1983, 34 (3): 779-787. 10.1016/0092-8674(83)90534-2.
Article
CAS
PubMed
Google Scholar
Marcel V, Hainaut P: p53 isoforms - a conspiracy to kidnap p53 tumor suppressor activity?. Cell Mol Life Sci. 2009, 66 (3): 391-406. 10.1007/s00018-008-8336-3.
Article
CAS
PubMed
Google Scholar
Xu CF, Brown MA, Chambers JA, Griffiths B, Nicolai H, Solomon E: Distinct transcription start sites generate two forms of BRCA1 mRNA. Hum Mol Genet. 1995, 4 (12): 2259-2264. 10.1093/hmg/4.12.2259.
Article
CAS
PubMed
Google Scholar
Van de Wetering M, Castrop J, Korinek V, Clevers H: Extensive alternative splicing and dual promoter usage generate Tcf-1 protein isoforms with differential transcription control properties. Mol Cell Biol. 1996, 16 (3): 745-752.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aerts S, Van Loo P, Thijs G, Mayer H, de Martin R, Moreau Y, De Moor B: TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res. 2005, 33 (Web Server issue): W393-396.
Article
CAS
PubMed
PubMed Central
Google Scholar
Blache P, van de Wetering M, Duluc I, Domon C, Berta P, Freund JN, Clevers H, Jay P: SOX9 is an intestine crypt transcription factor, is regulated by the Wnt pathway, and represses the CDX2 and MUC2 genes. J Cell Biol. 2004, 166 (1): 37-47. 10.1083/jcb.200311021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, et al: Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells. Mol Cell Biol. 2008, 28 (8): 2732-2744. 10.1128/MCB.02175-07.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van der Flier LG, Sabates-Bellver J, Oving I, Haegebarth A, De Palo M, Anti M, Van Gijn ME, Suijkerbuijk S, Van de Wetering M, Marra G, et al: The Intestinal Wnt/TCF Signature. Gastroenterology. 2007, 132 (2): 628-632. 10.1053/j.gastro.2006.08.039.
Article
CAS
PubMed
Google Scholar
Blom N, Gammeltoft S, Brunak S: Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol. 1999, 294 (5): 1351-1362. 10.1006/jmbi.1999.3310.
Article
CAS
PubMed
Google Scholar
la Cour T, Kiemer L, Molgaard A, Gupta R, Skriver K, Brunak S: Analysis and prediction of leucine-rich nuclear export signals. Protein Eng Des Sel. 2004, 17 (6): 527-536. 10.1093/protein/gzh062.
Article
CAS
PubMed
Google Scholar
Emanuelsson O, Brunak S, von Heijne G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc. 2007, 2 (4): 953-971. 10.1038/nprot.2007.131.
Article
CAS
PubMed
Google Scholar
Bendtsen JD, Nielsen H, von Heijne G, Brunak S: Improved prediction of signal peptides: SignalP 3.0. J Mol Biol. 2004, 340 (4): 783-795. 10.1016/j.jmb.2004.05.028.
Article
PubMed
Google Scholar
Huang HY, Chien CH, Jen KH, Huang HD: RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res. 2006, 34 (Web Server issue): W429-434.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, et al: UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res. 2010, 38 (Database issue): D75-80.
Article
CAS
PubMed
Google Scholar
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al: The Pfam protein families database. Nucleic Acids Res. 2010, 38 (Database issue): D211-222.
Article
CAS
PubMed
Google Scholar
Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, et al: Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006, 38 (6): 626-635. 10.1038/ng1789.
Article
CAS
PubMed
Google Scholar
Yamashita R, Sathira NP, Kanai A, Tanimoto K, Arauchi T, Tanaka Y, Hashimoto SI, Sugano S, Nakai K, Suzuki Y: Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res. 2011
Google Scholar
Cheong J, Yamada Y, Yamashita R, Irie T, Kanai A, Wakaguri H, Nakai K, Ito T, Saito I, Sugano S, et al: Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. DNA Res. 2006, 13 (4): 155-167. 10.1093/dnares/dsl008.
Article
CAS
PubMed
Google Scholar
Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, et al: Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. BMC Genomics. 2011, 12 (1): 313-10.1186/1471-2164-12-313.
Article
CAS
PubMed
PubMed Central
Google Scholar
Thorsen K, Sorensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AM, Kruhoffer M, Laurberg S, Borre M, Wang K, et al: Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics. 2008, 7 (7): 1214-1224. 10.1074/mcp.M700590-MCP200.
Article
CAS
PubMed
Google Scholar
An Y, Zhou Y, Ren G, Tian Q, Lu Y, Li H, Li K, Su T, Xu B, Chen S, et al: Elevated expression of MGb2-Ag/TRAK1 is correlated with poor prognosis in patients with colorectal cancer. Int J Colorectal Dis. 2011
Google Scholar
Wang D, Claus CL, Rajkumar P, Braunstein M, Moore AJ, Sigvardsson M, Anderson MK: Context-dependent regulation of hematopoietic lineage choice by HEBAlt. J Immunol. 2010, 185 (7): 4109-4117. 10.4049/jimmunol.0901783.
Article
CAS
PubMed
Google Scholar
Wang D, Claus CL, Vaccarelli G, Braunstein M, Schmitt TM, Zuniga-Pflucker JC, Rothenberg EV, Anderson MK: The basic helix-loop-helix transcription factor HEBAlt is expressed in pro-T cells and enhances the generation of T cell precursors. J Immunol. 2006, 177 (1): 109-119.
Article
CAS
PubMed
Google Scholar
Starr TK, Allaei R, Silverstein KA, Staggs RA, Sarver AL, Bergemann TL, Gupta M, O'Sullivan MG, Matise I, Dupuy AJ, et al: A transposon-based genetic screen in mice identifies genes altered in colorectal cancer. Science. 2009, 323 (5922): 1747-1750. 10.1126/science.1163040.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto S, Matsushima K, Mizushima-Sugano J, Yamashita R, Nakai K, et al: Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res. 2009, 37 (7): 2249-2263. 10.1093/nar/gkp066.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gardina PJ, Clark TA, Shimada B, Staples MK, Yang Q, Veitch J, Schweitzer A, Awad T, Sugnet C, Dee S, et al: Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics. 2006, 7: 325-10.1186/1471-2164-7-325.
Article
PubMed
PubMed Central
Google Scholar
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersen CL, Jensen JL, Orntoft TF: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004, 64 (15): 5245-5250. 10.1158/0008-5472.CAN-04-0496.
Article
CAS
PubMed
Google Scholar
Andersen CL, Christensen LL, Thorsen K, Schepeler T, Sorensen FB, Verspaget HW, Simon R, Kruhoffer M, Aaltonen LA, Laurberg S, et al: Dysregulation of the transcription factors SOX4, CBFB and SMARCC1 correlates with outcome of colorectal cancer. Br J Cancer. 2009, 100 (3): 511-523. 10.1038/sj.bjc.6604884.
Article
CAS
PubMed
PubMed Central
Google Scholar
van de Wetering M, Sancho E, Verweij C, de Lau W, Oving I, Hurlstone A, van der Horn K, Batlle E, Coudreuse D, Haramis AP, et al: The beta-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells. Cell. 2002, 111 (2): 241-250. 10.1016/S0092-8674(02)01014-0.
Article
CAS
PubMed
Google Scholar
Schmid CD, Praz V, Delorenzi M, Perier R, Bucher P: The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res. 2004, 32 (Database issue): D82-85.
Article
CAS
PubMed
PubMed Central
Google Scholar
French PJ, Peeters J, Horsman S, Duijm E, Siccama I, van den Bent MJ, Luider TM, Kros JM, van der Spek P, Sillevis Smitt PA: Identification of differentially regulated splice variants and novel exons in glial brain tumors using exon expression arrays. Cancer Res. 2007, 67 (12): 5635-5642. 10.1158/0008-5472.CAN-06-2869.
Article
CAS
PubMed
Google Scholar
Xi L, Feber A, Gupta V, Wu M, Bergemann AD, Landreneau RJ, Litle VR, Pennathur A, Luketich JD, Godfrey TE: Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer. Nucleic Acids Res. 2008, 36 (20): 6535-6547. 10.1093/nar/gkn697.
Article
CAS
PubMed
PubMed Central
Google Scholar
Satow R, Shitashige M, Kanai Y, Takeshita F, Ojima H, Jigami T, Honda K, Kosuge T, Ochiya T, Hirohashi S, et al: Combined functional genome survey of therapeutic targets for hepatocellular carcinoma. Clin Cancer Res. 2010, 16 (9): 2518-2528. 10.1158/1078-0432.CCR-09-2214.
Article
CAS
PubMed
Google Scholar
Taylor BS, Schultz N, Hieronymus H, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, et al: Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010, 18 (1): 11-22. 10.1016/j.ccr.2010.05.026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25 (17): 3389-3402. 10.1093/nar/25.17.3389.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wernersson R, Rapacki K, Staerfeldt HH, Sackett PW, Molgaard A: FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB. Nucleic Acids Res. 2006, 34 (Web Server issue): W84-88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, Jones DT: Protein structure prediction servers at University College London. Nucleic Acids Res. 2005, 33 (Web Server issue): W36-38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Julenius K, Molgaard A, Gupta R, Brunak S: Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology. 2005, 15 (2): 153-164.
Article
CAS
PubMed
Google Scholar
Jensen LJ, Gupta R, Staerfeldt HH, Brunak S: Prediction of human protein function according to Gene Ontology categories. Bioinformatics. 2003, 19 (5): 635-642. 10.1093/bioinformatics/btg036.
Article
CAS
PubMed
Google Scholar
Hamilton TL, Stoneley M, Spriggs KA, Bushell M: TOPs and their regulation. Biochem Soc Trans. 2006, 34 (Pt 1): 12-16.
Article
CAS
PubMed
Google Scholar
Kato S, Sekine S, Oh SW, Kim NS, Umezawa Y, Abe N, Yokoyama-Kobayashi M, Aoki T: Construction of a human full-length cDNA bank. Gene. 1994, 150 (2): 243-250. 10.1016/0378-1119(94)90433-2.
Article
CAS
PubMed
Google Scholar