analysis of transcriptional regulatory networks in cancer research

... C-terminus of initiation factor 4E-binding protein contains multiple regulatory features that in uence its function and phosphorylation Mol Cell Biol 23, 1546–1557 Regulatory motifs in 4E-BP1 34 Gingras ... Previous work has shown that mutation of the phenylalanine to alanine in the TOS motif eliminates the binding of raptor to the C-terminal fragment of human 4E-BP1 in the overlay assay [19] (see also ... C-terminus of 4E-BP1 that are involved in its binding to raptor The data for the other truncation mutants shown in Fig 1C indicate that other regions of 4E-BP1 also contribute to stable binding...

Ngày tải lên: 16/03/2014, 06:20

... over 100 random trials, in which the interactions of both networks are reassigned while maintaining the same number of interactions per protein, resulting in a distribution of random subnetwork ... HTP networks [55] To reveal potential bias in the extent of investigation of any given node in the LC datasets, we determined the number of total interactions (that is, including redundant interactions) ... spawned a host of functional genomic tools for interrogation of gene and protein function, including DNA microarrays for global gene-expression profiling and location of DNA-binding factors, and...

Ngày tải lên: 06/08/2014, 18:21

... explainingaway effect in the Bayesian network literature [7] Selecting variables, like Xi , that take part into indirect interactions reduce the accuracy of the network inference task However, since ... “Biological network inference using redundancy analysis, ” in Proceedings of the 1st International Conference on Bioinformatics Research and Development (BIRD ’07), pp 916–927, Berlin, Germany, March ... of incoming edges per node to infer and consequently the lower the resulting complexity Note that since mutual information is a symmetric measure, it is not possible to derive the direction of...

Ngày tải lên: 22/06/2014, 19:20

... based on areas of the raw spectra, averaging of technical repeats, binning of neighboring points to reduce data complexity, removal of the spectral area below baseline and normalization of the total ... identifying subgroups of patients with different patterns of changes in intensities of spectral components in time (between samples B and C) In this analysis the procedure of unsupervised clustering ... question of detecting therapy-related changes in the mass profiles registered for blood samples collected from breast cancer patients SELDI-ToF analysis of the plasma proteome of breast cancer...

Ngày tải lên: 18/06/2014, 16:20

... evaluation of the spectrum-sharing mechanisms, but also provides a clue for future researches on strategies of primary and secondary systems in joint leasing and sensingbased CRNs The interactions ... probabilities in the NP mechanism is presented in Appendix B The main purpose of deriving the steady-state probabilities is to evaluate the performance metrics in the joint leasing and sensing-based ... delay of SU T Delay-su , mean waiting time of PU t wait-pu , and blocking probability of PU P BL-pu The expressions of these metrics are described as follows We define f(i) ≡ min(N-i, N-R) Page of...

Ngày tải lên: 20/06/2014, 22:20

... large data set involving sampling of many variables, instead of examining convergence based on [26, chapter 11.6], we adopted a more practical strategy by running a single MCMC chain for 10000 ... the corresponding elements in loading matrix must be nonzero This may overwhelmingly constrain the loading matrix, resulting the MCMC chain gets trapped in a local mode (Figure 6(c)) In the next ... noise increases, the bias of the minimum mean square estimates (MMSE) of X increases (Figure 4(a)), the mean squared error (MSE) of the MMSE of X also increases (Figure 4(b)), and the clustering...

Ngày tải lên: 21/06/2014, 16:20

... voxel of the cluster, resulting in the union of a cluster of balls in 3D In this way, we connect or attach nearby discrete voxels into a continuous boundary of the clot We then use the marching ... data points and small clusters, since filtering techniques are often effective for removing noise in images However, most filters have the undesired side-effects of changing the intensity values of certain ... purpose In different imaging settings, the users may estimate the percentage of the undesired points (the undesired points may be noise, or as in our application, scattered points of interest)...

Ngày tải lên: 21/06/2014, 19:20

... improved accuracy of Boolean network esimation Using the theoretically grounded stochastic complexity instead of ad hoc encodings genuinely reflects the intent of the MDL principle In addition, the ... Remarks Using a universal codelength when applying the MDL principle eliminates the relativity of applying ad hoc codelengths and user-defined tuning parameters In our case, this has resulted in improved ... findings, we recommend using the SF primarily for networks composed of canalizing functions and networks too large to run NML MDL with fixed K in a reasonable amount of time We also suggest using...

Ngày tải lên: 21/06/2014, 22:20

... case of order statistics has captured the attention of researchers in the area of signal processing and wireless communication systems [6, 7] The remainder of this paper is organized as follows In ... frequency-selective fading channel in the broadband OFDMA system In this case, the channel quality of each subchannel is determined by taking the average SNR over all corresponding subcarriers In the bandAMC ... must be assigned to a single user In general, the advantage of the OFDMA system is the multiuser diversity gain that can be obtained by selecting only good subcarriers for individual user, so as...

Ngày tải lên: 21/06/2014, 23:20

... testing microarray data analysis tools An artificial data generator has to be independent of the reverse engineering algorithms to avoid a bias in the test results In addition, the underlying ... Strimmer [7], the authors of the GeneNet a package including GGM, pointed out that their method is intended for analysis of small sample sizes It requires a large number of genes in the dataset to estimate ... is used for detecting statistical significant interactions This behavior is shown in Figure Increasing number of genes in the dataset decrease the distance measure dB resulting in a better performance...

Ngày tải lên: 22/06/2014, 00:20

... transmitting antenna at (interfering) node i are pointing to each other, ξi = if the receiving antenna at node is pointing to node i who is however pointing away from node or if node is pointing away ... are integers) “generally” increase as η (which is real) increases Comparing the peak value of each of the curves in Figures 4, 5, and with a corresponding value in Table 4, we see a loss of network ... for full exploitation of directional antennas in ad-hoc wireless networks, ” in Proceedings of the the 4th ACM International Symposium on Mobile Ad Hoc Networking and Computing (MobiHoc ’03), pp...

Ngày tải lên: 22/06/2014, 19:20

... particular, the triangle inequality, is essential for the problem of estimating complex networks by using simpler models This is akin to the pattern recognition problem of estimating a complex classifier ... better inference via reduction of the estimation error (so long as this reduction exceeds the projection error) [11] In the case of networks, the constraint problem becomes one of finding a projection ... constraints in the reference model The application of constraints modifies the original model, thereby obtaining a simpler one We focus on quantization of the gene expression levels (which are continuous-valued...

Ngày tải lên: 22/06/2014, 19:20

... isotropic margin of 1.0 cm for microscopic extension and set-up inaccuracies; (iii) PTVgating, consisting of the volume encompassing 3– GTVs in the gating window, plus an isotropic margin of 1.0 cm ... contouring critical structures Gross tumor volumes (GTVs) were contoured in each of the 10 phases of a 4DCT using standardized lung and mediastinal window level settings by one clinician in order ... respiratory gating, derived from calculating the displacement of the GTVgating within GTVall phases, and (iii) residual GTV mobility within gating windows, derived from displacement of the GTVsingle phase...

Ngày tải lên: 09/08/2014, 10:20

... single zinc finger motif of a small subset of WRKY proteins is distinct from that of group and members Instead of a C2H2 pattern, their WRKY domains contain a C2HC motif As a result of this distinction, ... Figure of OsWRKY genes according to their expression profile in the NIAS 22 K array Clustering Clustering of OsWRKY genes according to their expression profile in the NIAS 22 K array Clustering of ... domains of group and group members have the same type of zinc finger motif, whose pattern of potential zinc ligands CX4-5 -CX22-23 -HXH is unique among all known zinc-finger-like motifs The single...

Ngày tải lên: 12/08/2014, 03:21

... This does not appear to be the result of a higher density of TF binding sites present in the CRMs, as an analysis of the footprinted binding sites contained in the FlyReg database [41] shows that ... 20 CDS Intron Intergenic CRM Figure intergenic sequences GC content of the REDfly analysis CRMs as well as coding, intronic, and GC content of the REDfly analysis CRMs as well as coding, intronic, ... clustering SS performed the YMF analysis, oversaw the supervised clustering, and provided general input into other aspects of the analysis MSH coordinated the study, performed portions of the analysis, ...

Ngày tải lên: 14/08/2014, 07:21

... Hfe-/- D2 mice also have increased duodenal expression of mucin and spermine synthase Increased binding of Dmt1 to mucin in vesicles near the intestinal surface was observed in iron-deficient animals, ... was recently found to be involved in the control of hepcidin expression [23], in the B6 strain Finally, and worthy of note within the context of modifiers of iron loading severity, wildtype D2 ... iron ion binding category, also enriched in the liver of both strains, includes the genes for ferroportin, ferritin light chain, and heme oxygenase, which catalyzes the degradation of heme into carbon...

Ngày tải lên: 14/08/2014, 08:20

... 2002) Notch signaling inhibits the differentiation of endodermally derived cells into intestine and pancreas In mice, the activation of Notch in intestine cells leads to intestinal epithelial cells ... product by inactivating the functional domain but leaving the protein-protein interaction/dimerization domain intact Because the wildtype protein when dimerized with dominant negative protein can ... morpholinos 85 3.14 Loss of irf6 function phenotypes 86-87 3.15 Comparison of expression of molecular markers in irf6 morphants and wildtype 91-92 3.16 Hematoxylin and eosin staining of intestines...

Ngày tải lên: 14/09/2015, 12:44

... %) showing positive MT staining and only 22 cases (15.7 %) showing absence of MT staining in the nucleus The staining of MT was classified into two groups; presence or absence of MT staining and ... Tell-tale signs of breast cancer other than presence of lumps include thickening in an area of the breast, change in the size or shape of the breast, dimpling of the skin, change in shape of the nipple, ... SUMMARY Breast cancer is one of the most prevalent cancers in women worldwide The rate of breast cancer has been increasing rapidly Invasive ductal carcinoma makes up the bulk of all breast cancer cases...

Ngày tải lên: 14/09/2015, 14:08

... supported in part by Grants -in- Aid of Scientific Research, for Research in Priority Areas, for Cooperative Research, for General Science Research, and for Developmental Scientific Research from the Ministry ... order to obtain the mathematical relation of enhancing parameters of 3-chlorophenol on OH radical generation during ozonation, the initial velocities in the mixture of various amounts of ozone with ... M)]) In the drinking water treatment, 1-1.5 ppm of ozone, which are corresponding to 20-30 µM, are generally used The initial velocities of OH radical generation at the 20 µM and 30 µM of ozone...

Ngày tải lên: 05/09/2013, 08:40