Analysis of potential splice factor binding sites
Computational Analysis of Cryptic Splice Sites
... Computational Analysis of Cryptic Splice Sites 3 Based on the results of the authentic and cryptic probabilistic models, the next step was to understand the reason behind the specific choice of the ...
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Functional analysis of transcription factor binding sites in human promoters
... in binding motifs for functional classes of YY1 binding sites, with the repressing cases showing a pre- ference for G at position 4 of the motif (see Figure ...TF binding sites tended ...
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Analysis of variation at transcription factor binding sites in Drosophila and humans
... that binding sites that tolerate a higher load are less functionally ...since binding events limited to minor alleles are likely to be overlooked by a single-genome ChIP analysis, we com- pute ...
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Statistics for Transcription Factor Binding Sites
... TFs are often represented as PFMs. As described in Section 2.4.4, the number of compat- ible words of a PFM depends on the chosen threshold selection method. Here, we focus on the selection methods based on the error ...
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Computational DIO2 rSNP Analysis, Transcriptional Factor Binding Sites and Disease
... TF binding and have been associated with ...The potential alterations in TFBS obtained by computational analyses need to be verified by future protein/DNA electrophoretic mobility gel shift assays and gene ...
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The demarcation of transcription factor binding sites through the analysis of DNase seq data
... Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell ...
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Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites
... tion factor binding sites (TFBSs) in non-coding DNA sequences, which is essential to elucidate transcriptional regulatory networks, has emerged as an obstacle that frustrates many ...comparative ...
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Targeting splice factor kinases and their splice factor in chronic myeloid leukaemia
... The binding of EGF to EGFR activates RTK, which leads to phosphorylate tyrosine residues and trigger intracellular ...a potential downstream to inhibit apoptosis and promote cell ...
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Why Transcription Factor Binding Sites Are Ten Nucleotides Long
... DNA binding sites are typically 10 nt ...such binding sites evolve. Our analysis is based on an inherent trade-off between specificity, which is greater in long binding ...
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Mapping the YY1 and p65 binding sites on the transcription factor LSF
... of Factor Xa Cleavage Since an aim of the study was to determine the specific LSF peptide sequence or sequences responsible for binding p65 and YY1, I developed a new assay to investigate this ...DNA ...
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Identification of transcription factor binding sites using ATAC seq
... Briefly, mouse bone marrow cells were first amplified with a specific cytokine cocktail and then induced to differen- tiate into DC with Flt3 ligand. cDC1 are CD11c+ CD11b+ XCR1+ and pDC are CD11c+ CD11b- B220+ and thus ...
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The design of transcription factor binding sites is affected by combinatorial regulation
... the analysis described above, we also analyzed the number of binding sites upstream from genes whose knockout led to slow and fast growth in different growth mediums (Yeast Deletion Project ...
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TBXA2R rSNPs, Transcriptional Factor Binding Sites and Asthma in Asians
... Similar logic can be used to evaluate the potential TFBS within the other TBXA2R rSNPs found in the table. It should be noted that the minor alleles in the intron 1 rSNPs create more unique TFBS than do the common ...
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Colocalization of Heparin and Receptor Binding Sites on Keratinocyte Growth Factor
... receptor binding site of KGF involved identifying the epitope recognized by the KGF-specific neutralizing monoclonal antibody ...This analysis was conducted with the assumption that 1G4 neutralizes KGF ...
ATF3 rSNPs, transcriptional factor binding sites and human etiology
... transcription factor binding sites ...transcriptional factor binding site (TFBS) can change a transcriptional factor’s (TF) ability to bind its TFBS [11-14], in which case the TF would ...
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AKT3 rSNPs, Transcriptional Factor Binding Sites and Human Disease
... Human diseases or conditions that have been signifi- cantly associated with rSNPs of the AKT3 gene are shown in the Table 1 along with rSNP allele-specific TFBS. What a change in the rSNP alleles can do, is to alter the ...
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Developing algorithms for the in silico identification of transcription factor binding sites
... ConTrav2 During this PhD we developed an update to the previously published ConTra web-tool. This web-tool provides the wet-lab biologist with a user-friendly tool to interactively explore and visualize TFBSs, predicted ...
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Psoriasis drug development and GWAS interpretation through in silico analysis of transcription factor binding sites
... The goals of this study are to use expression profiling data from psoriasis lesions to identify TFs and cis-regu- latory elements mediating psoriasis plaque development. We identify differentially expressed genes (DEGs) ...
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Transcription Factor Binding Site Analysis
... methylated sites were validated by bisulfite ...transcription factor target genes, Shyr C, Pearson Correlation and Spearman Correlation do not take the sizes of the vectors into ...regulatory ...
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Mapping genome-wide transcription factor binding sites in frozen tissues
... also performed all tissue preparations in large batches consisting of several distinct tissue types, and these took only 1 hour to perform. The approach also ensures that tissues remain frozen during the preparation ...
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