21 detection of transcription factor dna creb bss in the rat genome

... model of the sequences from A D) Information content of PWM from C Figure Clustering of information in transcription factor binding sites in TRANSFAC The information content of each position in ... on the binding specificities of transcription factors In attempting to analyze available binding matrixes in TRANSFAC [35], we were struck by how few examples there were of factors whose binding ... were inaccurate or uninformative Ninety of these factors are members of well-characterized families of transcription factors or contain well-characterized DNA binding motifs [37] We can use the...

Ngày tải lên: 14/08/2014, 14:21

... selectivity of CRM searches based on binding-site clustering The effects of integrating comparative data into searches for binding site clusters were assessed by counting the number of (a) true ... metrics were then used to rank these 929 pCRMs: the number of aligned binding sites; the density of aligned binding sites; the number of aligned plus preserved binding sites; and the density of aligned ... limitation in the widespread application of binding-site clustering methods is the absence of high-quality binding data for most Drosophila transcription factors The initial success of methods...

Ngày tải lên: 14/08/2014, 14:21

... event in determining the susceptibility to apoptosis through maintaining the integrity of the mitochondria and inhibiting activation of the caspase cascade [37] High expression levels of antiapoptotic ... expression of c-Fos and c-Jun, via the MAP kinase signaling pathway TAM67 retains the DNA binding and leucine-zipper region of c-Jun, but it lacks the transactivation domain of c-Jun (amino acids ... in the 5¢-end of the bcl-X gene [30] Because MAP kinase has been shown to regulate the transcription of c-Fos, a member of the Fos family, AP1 may be implicated in the transcription of bcl-XL induced...

Ngày tải lên: 19/02/2014, 06:20

... factor DNA binding The results of measurements of HSF1 DNA- binding activity from HeLa cells and MEFs are in line with results reported in several other papers The DNA binding is induced within minutes ... [11], exist for investigating transcription factors and transcriptional regulation, but the main purpose of using these methods is not in quantifying transcription factor DNA binding Our goal was ... without the initial incubation step was included The probe concentration was the same (working concentration of 150 nM; 0.75 nM in the well) for all of the optimizations The bars represent the mean...

Ngày tải lên: 18/02/2014, 14:20

... case of TpT, intramolecular stacking of thymine residues brings the two C(5)ẳC(6) bonds in close proximity, thereby increasing the probability of their attack by MnO4 and decreasing the effect of ... observation, conrming that the mechanism underlying the Mg2+ effect on the kinetics of nucleotide oxidation does not affect the intrinsic rate of the reaction and is due solely to the screening of the negative ... band doubling for T)11 and T+2 Therefore, the measured contribution of these forms to the integrated intensity of these two bases was used in the calculation of the contribution of individual...

Ngày tải lên: 19/02/2014, 18:20

... peaks of enrichment and call such peaks as single binding sites They not deconvolve the peaks into separate binding sites As such, they are generally incapable of identifying closely spaced binding ... Figure 3a) Then, by using MAST [31], we searched for the presence of this motif within 50 bp of the binding locations and, for 23 of the 24 binding locations, we found a matching sequence The average ... magnitudes, thereby distinguishing closely spaced transcription factorbinding sites As it is currently implemented, CSDeconv is not attractive for the study of genome- wide binding of transcription factors...

Ngày tải lên: 09/08/2014, 20:21

... relates to the index of the intensity of HPV infection This ratio of any specimen represents empirically a relative measure of the viral load in it Cut off value (RLU of specimen/ mean RLU of PC) ... deregulation of the cell cycle by inactivating p53 and pRb respectively [9] Integration often disrupts the integrity and expression of the E1 and E2 open reading frames, which may affect the transcription ... pg/ml of sample Interpretation of Cut off value (RLU of specimen/mean RLU of PC) Cut-off ratio of to 0.99 is negative for HR HPV; Cutoff ratio greater than 1.0 positive for HR HPV The cut off ratio...

Ngày tải lên: 12/08/2014, 01:22

... tion of the joint, the organism is present in the SF and synovial tissue in the intracellular, aberrant body form, which lacks a particular cell wall To determine whether the methods used for DNA ... samples of SF DNA in order to reconfirm or simply repeat results We therefore addressed the question of how detection limits of chlamydial DNA might change after storage of DNA depending on the different ... Kit® in combination with the same amplification system The same detection limits were observed using alkaline lysis in combination with the plasmid PCR and the 16s RNA PCR as well as using the...

Ngày tải lên: 12/08/2014, 11:22

... Discovery Rate [16]) explicitly incorporates the vastness of the genome in the calculation The q-value of a transcription factor binding site tells us the proportion of sites of that strength or better ... recover many of the known transcription factor binding sites that were used in the construction of the motif Conversely, the choice of a threshold for prediction that finds many of the known transcription ... binding sites Discussion Key features of PhyloScan We are able to increase the flexibility and sensitivity of scanning, without increasing the false positive rate, by incorporating the following...

Ngày tải lên: 12/08/2014, 17:20

... the elements of the PWM represent contributions to the free energy of binding for all possible bases at each position in a binding site [9] The algorithm then integrates over the affinities of ... relative affinity of binding sites, taking into account the effect of cooperative and competitive interactions Based on the binding predictions, GOMER predicts gene regulation by weighting binding sites ... model these interactions, varying the strength of the dimerization constant and the allowed distance between cooperatively interacting binding sites (Figure 2) The inclusion of homotypic cooperativity...

Ngày tải lên: 14/08/2014, 14:22

... number of binding sites in its interactions Figure 'Fuzziness' of Reb1 binding sites 'Fuzziness' of Reb1 binding sites Average fit of Reb1 binding sites to the consensus matrix, as a function of the ... of bindingmotifs the function ofexactly average promoterfactors/binding sitesregion a A figure depicting theof thebinding sitespromoters between toto the Additionalthe file onebinding sites,ofand ... http://genomebiology.com/2005/6/12/R103 lobs be the linear line that best fits the points (in the sense that it minimizes the sum of squares of the distances) The sign of the slope of lobs defines the correlation as positive...

Ngày tải lên: 14/08/2014, 15:20

... sequence logos BSs We find no obvious dependence of the error rate on the number of BSs and on the BS length Comparing the GC content of the BSs, we find that the GC content of the BSs of all but ... NarL and the Comparison of binding-sitelogos for the data sets of the TFs CpxR, Crp, logos, the consensus sequences for the TFs obtained from the literature [56-61], Comparison of binding-site ... verified" data, the calculation of P values for the occurrence of BSs, the detection of putative BSs in genome- wide scans and their experimental validation, or the reconstruction of transcriptional...

Ngày tải lên: 14/08/2014, 21:20

... one another in the genome In these cases, when scoring the negative binding site, a true binding site for the transcription factor of interest is present; thus these corresponding binding sites ... particular transcription factor and those of other proteins While there may be some overlap between the binding domains for different transcription factors, the known DNA binding sites for the transcription ... complexes The majority of binding sites are located in close proximity to the transcription start site, upstream of it relative to the direction of transcription The region of DNA containing these...

Ngày tải lên: 13/11/2014, 09:10

Ngày tải lên: 14/11/2014, 08:21

... domain and the POU homeodomain The two subdomains can cooperatively bind DNA even when they are not joined by the linker53,57-60 Certain transcription factors containing the POU-homeodomain are ... regulatory chain motifs48 The 12 Figure Functional domains of a transcription factor The amino acid sequence of a prototypical transcription factor is illustrated, containing a DNA- binding domain (DBD), ... 1.4.1 The Zic gene family The Zic proteins (Zinc finger protein of the cerebellum) belong to the GLI superfamily of transcription factors and are vertebrate homologues of the Drosophila zinc finger...

Ngày tải lên: 11/09/2015, 09:02

... rRNA termini are present in both the 50S and the 70S fractions We then investigated whether the observed extended termini present in the 23S processing stem mutants were incorporated into the 50S ... [29–32] Taking these findings together, we suggest that the R69L mutant of IF1 allows premature subunit joining by either failing to discriminate between certain TIR elements in mRNA, or inducing a ... imbalances of the 30S and 50S subunits The same analysis revealed that there was a general decrease in the amount of 50S subunits in the sucrose gradient in the case of the suppressor plasmid pD3 In...

Ngày tải lên: 06/03/2014, 00:21

... determination of the exact position of the two introns which were 780- and 630-bp long (Fig 1B) These introns contained the typical GT/AG consensus splicing signal The excision of the two introns from the ... TgDRE cDNA is estimated at 40% less than that of the wild-type bacteria in the presence of mitomycin C In addition, we also investigated whether TgDRE is capable of correcting the DNA- damaging sensitive ... other DNA- binding proteins [11,20], whereas RRM (RNA recognition motif) was already described in numerous proteins [21, 22] Further analyses of the N-terminal moiety of the TgDRE sequence using...

Ngày tải lên: 08/03/2014, 22:20

... Downstream of PI3 kinase, a transcription factor of the cAMP response element (CRE)binding protein (CREB) ⁄ activating transcription factor (ATF) family, ATF-1, was suggested to take part in the induction ... reported the involvement of ATF-1, a transcription factor of the CREB ⁄ ATF family, in the up-regulation of NOX1 expression in VSMC [8] ATF-1 elicits transcriptional activation by binding to the cAMP ... structure of the NOX1 gene and its splicing pathway Open boxes indicate exons Numbers in the box denote the size of each exon (bp) The size of the intron is indicated under the broken lines (bp)...

Ngày tải lên: 30/03/2014, 03:20

... obtained by Elliphant using the training data randomly ordered The performance reaches its plateau using 90% of the training instances Using different ordering of the training set we obtain the ... Omission of all but one of the “simple” features led to a reduction in accuracy, justifying their inclusion in the training instances Nevertheless, the majority of features present low informativeness ... to the great variety of subjects occurring in the training data In addition, reaching a precision of 92.0% for explicit subjects using just 20% of the training data is far more expensive in terms...

Ngày tải lên: 31/03/2014, 21:20

... %; These rates increases with aging of animal - The Infection rate of T evansi in buffaloes and catle is the highest in Autumn (26,16 %) and the lowest is in Spring (5,61 %) The percentage of ... causing trypanosomiasis in cattle and buffaloes in northern mountainous provinces 3.1.2 Trypanosoma infection in cattle and buffaloes in four of Northern mountainous provinces 3.1.2.1 Infection rates ... Infection rates of trypanosomes in buffaloes and cattle were illustrated by the line graph in figure 3.2 Infection rates of trypanosomes in cattle and buffaloes in mountainous provinces tended to increase...

Ngày tải lên: 28/04/2014, 13:08