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| 1 | Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays显示文摘Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prognosis has not significantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technologies-single nucleotide polymorphism (SNP) array and gene expression array-with gene motifs considered transcription factor -binding sites (TFBS). We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS. The potential regulation of SNP-containing motifs affects only when certain mutations occur. These motifs can be identified from a group of co-expressed genes with copy number variation. Then, we used a sliding window to identify motif candidates near SNPs on gene sequences. The candidates were filtered by coarse thresholding and fine statistical testing. Using the regression-based LARS-EN algorithm and a level-wise sequence combination procedure, we identified 28 SNP-containing motifs as candidate TFBS. We confirmed 21 of the 28 motifs with ChIP-chip fragments in the TRANSFAC database. Another six motifs were validated by TRANSFAC via searching binding fragments on coregulated genes. The identified motifs and their location genes can be considered potential biomarkers for myelodysplastic syndromes. Thus, our proposed method, a novel strategy for associating two data categories, is capable of integrating information from different sources to identify reliable candidate regulatory SNP-containing motifs introduced by genetic variation and mutation. | Jing Fan Jennifer G. Dy Chung-Che Chang Xiaobo Zhou | 2013 | Chinese Journal of Cancer2013，32，4： | 2 |
| 2 | An automated pipeline for dendrite spine detection and tracking of 3D optical microscopy neuron images of in vivo mouse models 显示文摘 | FAN Jiang ZHOU Xiao-bo DY G | 2009 | Neuroinformatics2009，7，2： | 1 |
| 3 | An automated pipeline for dendrite spine detection and tracking of 3D optical microscopy neuron images of in vivo mouse models 显示文摘 | FAN Jing ZHOU Xiaobo Dy G J | 2009 | Neuroinformatics2009，7，2： | 1 |
| 4 | How does cyclic electron flow alleviate photoinhibition in Arabidopsis显示文摘 | Takahashi S Milward SE Fan DY | | 0，，03： | 1 |
| 5 | Gene mapping for primary open angle glaucoma显示文摘 | Fan B J Wang DY Lam | 2006 | Clin Biochem2006，39，3： | 1 |
| 6 | Gene mapping for primary open angle glaucoma显示文摘 | Fan B J Wang DY Lam DS | 2006 | Clin Biochem2006，39，： | 1 |
| 7 | Evaluation of a DNA vaccine candidate expressing prM-E-NSlantigens of dengue virus serotype 1 with or without granulocyte-macrophage colony-stimu- lating factor (GM-CSF) in immunogenicity and protection 显示文摘 | Zheng Q Fan DY Gao N | 2011 | Vaccine2011，29，4： | 1 |
| 8 | Fine mapping of new glaucoma locus GLC1M and exclusion of neuregulin 2 as the causative gene显示文摘 | Fan B J Ko WC Wang DY | 2007 | Mol Vis2007，13，： | 1 |
| 9 | Clinical studies in 500 patients with aort- oarteritis显示文摘 | Zheng DY Liu LS Fan DJ | 1990 | Chin Med J (Engl)1990，103，7： | 1 |
| 10 | Tumor suppressor NM23 - H1 is a granzyme A-activated DNase during CTL-mediated apoptosis, and the nucleosome assembly protein SET is its inhibitor显示文摘 | Fan Z Beresford PJ Oh DY | 2003 | Cell2003，112，5： | 1 |
| 11 | Association of polymorphisms of tumor necrosis factor and tumor protein p53 with primary open-angle glaucoma显示文摘 | Fan B J Liu K Wang DY | 2010 | Invest Ophthalmol Vis Sci2010，51，8： | 1 |
| 12 | Tumor-uppressor Nm23 -H1 is a granzyme A-activated DNase during CTL-mediated apoptosis, and the nucleosome assembly protein SET is its inhibitor显示文摘 | FAN Z BERESFORD PJ OH DY | 2003 | Cell2003，112，5： | 1 |
| 13 | Tumor suppressor NM23-H1 is a granzyme A-activated DNase during CTL-mediated apoptosis, and the nucleosome assembly protein SET is its inhibitor 显示文摘 | Fan Z Beresford PJ Oh DY | 2003 | Cell2003，112，5： | 1 |
| 14 | Clinical studies in 500 patients with aortoarteritis显示文摘 | Zheng DY Liu LS Fan DJ | 1990 | Chin Med J1990，103，： | 1 |
| 15 | Citrullinated vimentin stimu- lates proliferation, pro-inflammatory cytokine secretion, and PADI4 and RANKL expression of fibroblast-like synoviocytes in rheumatoid arthritis显示文摘 | Fan LY Wang Q He DY | 2012 | Scand J Rheumatol2012，41，： | 1 |
| 16 | Tumor suppressor NM23-H1 Is a granzyme A-activated D Nase during CTL-mediated apoptosis, and the nucleosome assembly pProtein SET is its inhibitor 显示文摘 | Fan Z Beresford PJ Oh DY | 2003 | Cell2003，112，5： | 1 |
| 17 | Gene mapping for primary open angle glaucoma显示文摘 | Fan BJ Wang DY Lam DSC Pang CP | 2006 | Clin Biochem2006，39，3： | 1 |
| 18 | Severe Kikuchi disease respon- sive to immune modulation显示文摘 | Lin DY Villegas MS 'Fan PL | 2010 | Singapore Med J2010，51，1： | 1 |
| 19 | The possibility of diagnosing osteoporosis by quantitative uhrasound under loading conditions: Preliminary study显示文摘 | Liu Ctt Li DY Fan YB | 2010 | Bone2010，47，3： | 1 |
| 20 | Tumor suppressor NM23- H1 is a granzyme A-activated DNase during CTL-mediated apoptosis, and the nueleosome assembly protein SET is its inhibitor显示文摘 | Fan Z Beresford PJ Oh DY | 2003 | Cell2003，112，5： | 1 |
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