Transcription factor binding site (TFBS)
Jaccard index based similarity measure to compare transcription factor binding site models
... tative TFBS recognized by PWMs at given threshold levels rather than the PWMs per ...tentative TFBS are close to the maximal PWM scores; only the matrix elements with high values contribute to the score of ...
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MCOIN: a novel heuristic for determining transcription factor binding site motif width
... of TFBS motifs (Figure ...FruR binding sites (Figure 2) show that the outermost motif positions are very poorly conserved, providing little information above that of background ...
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An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
... The fact that TFBS sequences are usually very short means that the same or very similar sequences tend to occur by chance at a relatively high frequency. Conse- quently one of the main goals in the prediction of ...
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Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
... the binding site are independent, and the contribution at one position of the binding site to the overall affinity does not de- pend on the identity of nucleotides in other positions of the ...
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Identification of human T-cell lymphotropic virus type I 21-base-pair repeat-specific and glial cell-specific DNA-protein complexes.
... Competition EMS analyses with oligonucleotides containing transcription factor binding site sequences indicate the involvement of a cyclic AMP response element binding protein in the for[r] ...
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Regulation of bovine beta defensin expression
... on transcription factor binding site prediction by comparison to a PWM database, it can also be used to discover motifs describing other types of DNA ...
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Sequences Just Upstream of the Simian Immunodeficiency Virus Core Enhancer Allow Efficient Replication in the Absence of NF-κB and Sp1 Binding Elements
... B binding site always remained intact, and some evidence for a novel enhancer element in this region ...B site and all four Sp1 binding sites, the SIV promoter maintained about 15% of the ...
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Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers
... Oct/Sox binding sites [1] is included in the RepeatMasker library, but it does not show up ...Esrrb site (Esrrb_P2, [66], highlighted in green) is found in mammals but not in primates, in line with the ...
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A survey of motif discovery methods in an integrated framework
... the transcription factors ...the transcription level according to this information. The transcription fac- tors are proteins that bind to specific DNA ...typical binding site, although ...
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Probing protein-DNA interactions at the long terminal repeat of human immunodeficiency virus type 1 by in vivo footprinting.
... A human binding site for transcription factor USF/MLTF mimics the negative regulatory element of human immunodeficiency virus type 1.. DNA binding factors that bind to the negative regul[r] ...
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Defining the DNA Binding Site Recognized by the Fission Yeast Zn2Cys6 Transcription Factor Pho7 and Its Role in Phosphate Homeostasis
... DNA-binding domain (DBD) of Saccharomyces cerevisiae Gal4, a prototypal fungal zinc cluster transcription factor. The DBD consists of a folded zinc finger module of two ␣ -helices that recognizes the ...
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Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
... affect binding affinities remains largely unknown, preventing a rational design of PhoB- binding site mutants to investigate how the TF-binding affinity impacts gene ...PhoB-binding ...
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Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity.
... HS4 binding sites char- acterized here constitute a novel enhancer that functions in- dependently of, or in concert with, other factors binding to the HIV-1 LTR to activate HIV-1 ...NF-kB binding ...
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Evolution of transcription factor function as a mechanism for changing metazoan developmental gene regulatory networks
... alternative binding sites are not only functional in vivo, but in many cases have distinct developmental ...changing binding to one type of site are less pleiotropic than changing binding to a ...
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Temozolomide analog PMX 465 downregulates MGMT expression in HCT116 colorectal carcinoma cells
... Sp1 binding sites, and transcription factor Sp1 binding could promote MGMT expression(Bocangel et ...Sp1 binding to its consensus site in the MGMT promoter, we performed EMSA ...
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Identification of an Adeno-Associated Virus Rep Protein Binding Site in the Adenovirus E2a Promoter
... Rep68 binding to the E2a promoter region by ...the binding of purified Rep68 to the 303-bp fragment by ...the binding site in the AAV ...nucleotide binding site) bound to the ...
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The upstream factor-binding site is not essential for activation of transcription from the adenovirus major late promoter.
... Previous results 42 have suggested that the USF-binding site plays a role in the expression of the divergent IVa2 transcription unit whose start site is located 210 bases upstream from t[r] ...
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Relative importance of elements within the SL3-3 virus enhancer for T-cell specificity.
... A second region, containing sequences homologous to the binding site of factor NF-I and the glucocorticoid response element, had about a twofold effect on transcription in both T lymphoc[r] ...
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Functional Analysis of the CAAT Box in the Major Late Promoter of the Subgroup C Human Adenoviruses
... conserved transcription elements found in the putative ...of transcription and of specificity, a further set of mutations was created and examined in the context of the viral ...disrupts binding of ...
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Role of the Proximal Enhancer of the Major Immediate-Early Promoter in Human Cytomegalovirus Replication
... MIE transcription and viral replication in diverse types of cells in culture ...on transcription from the MIE promoter, but one or more cis-acting elements in the unique region repress tran- scription from ...
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