transcription factor binding site
Jaccard index based similarity measure to compare transcription factor binding site models
... In general binding site lengths and strand orientations at the DNA heteroduplex may be different. Two TFBS models can be aligned by PWM shifting and possible re- verse complement transformation. It is ...
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A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease
... SNPs are the most abundant molecular markers in the human genome. SNPs are commonly used for large-scale genetic association studies to identify genetic factors responsible for complex genetic dis- eases. Current ...
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MCOIN: a novel heuristic for determining transcription factor binding site motif width
... As noted above, results for all three classification-based measures generally decrease as mean motif conservation also decreases (Table 5). At higher levels of motif con- servation, MCOIN is shown to outperform the ...
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Improved Models for Transcription Factor Binding Site Identification Using Nonindependent Interactions
... nuclear factor 4, alpha (Hnf4a) is completely conserved between human and ...vitro binding specificity, we used this information to analyze Verzi et ...provided. Binding site location analysis ...
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An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
... have binding sequences available in the TRANSFAC database ...TF binding locations, and we randomly selected 50 sequence seg- ments from each set for our study (see additional file 3: “FASTA ...which ...
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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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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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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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Stimulation of the adenovirus major late promoter in vitro by transcription factor USF is enhanced by the adenovirus DNA binding protein.
... We and others reported previously that DBP is able to enhance the binding of the cellular transcription factor nuclear factor I NFI to its recognition site in the adenovirus auxiliary or[r] ...
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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
... NF-kB binding site, we could clearly demonstrate and partly characterize this novel upstream regulatory ...of transcription factors ...Ets transcription factor that regulates induc- ...
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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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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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Transcription factor binding sites downstream of the human immunodeficiency virus type 1 transcription start site are important for virus infectivity.
... tagenesis method (CLONTECH, Palo Alto, Calif.). Six different mutations were generated with each of the following mutagenic oligonucleotides (mutations are highlighted in bold): EV244 (DDBF), 59-CGCCCGAACAGGGACTTGCCCG ...
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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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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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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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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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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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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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