[PDF] Top 20 Computational analysis in vivo p53 binding sites in the context of chromatin and repeat regions
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Computational analysis in vivo p53 binding sites in the context of chromatin and repeat regions
... binding sites can be ...of P53 Binding Sites The chromatin context provides another perspective to see the regulation of p53-DNA ...that p53 genomic ... See full document
42
c-Myb Binding Sites in Haematopoietic Chromatin Landscapes
... c-Myb binding in six different cell-types using digital DNase I footprints, from the haematopoietic progenitor CD34+ to the more differenti- ated cell-types GM12865, CD20+ and Th1 and the cancerous cell-types K562 ... See full document
25
Inhibition of p53 expression modifies the specificity of chromatin binding by the androgen receptor
... (PC). p53 likely also plays a role given that p53 mutations are commonly found in advanced PC, and loss of wild-type protein function contributes to the phenotype of castration- resistant prostate cancer ... See full document
12
Site specific chromatin immunoprecipitation: a selective method to individually analyze neighboring transcription factor binding sites in vivo
... functional analysis of a complex regulation scheme of a single gene in a systems biology view - ...new binding sites in combination with a preceded con- sensus analysis and b) the individual ... See full document
9
SATB1-Binding Sequences and Alu-Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites
... active regions of ...integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist ... See full document
11
In vivo chromatin organization on native yeast telomeric regions is independent of a cis-telomere loopback conformation
... 5 Chromatin organization of the X element on TEL05R (XY’ ...In vivo ChEC experiments with GBD-MN, NLS-MN and MN-RAP1 analyzed on the TEL05R X–Y’ junction ...potential binding sites) is ... See full document
22
Integrating Epigenetic Priors For Improving Computational Identification of Transcription Factor Binding Sites
... Interpreting chromatin states While chromatin states are defined based on a statistical model using chromatin modification data alone, they are useful if there exists meaningful functionality and ... See full document
108
In Vivo Protein Binding and Functional Analysis ofcis-Acting Elements in the U3 Region of the Bovine Leukemia Virus Long Terminal Repeat
... protein binding elements by in vivo footprinting and analyzed their function by site- directed ...in vivo dimethyl sulfate footprinting by ligation-mediated PCR to detect con- stitutive in ... See full document
10
In Vivo and In Vitro Analysis of Factor Binding Sites in Jaagsiekte Sheep Retrovirus Long Terminal Repeat Enhancer Sequences: Roles of HNF-3, NF-I, and C/EBP for Activity in Lung Epithelial Cells
... and binding sites that are responsible for the lung epithelial cell specificity of the JSRV ...factor binding sites in the LTR, our approach was first to identify sites that show ... See full document
10
Enhanced maps of transcription factor binding sites improve regulatory networks learned from accessible chromatin data
... in Vivo Binding Events A wide variety of tools are used in the plant research community to map TF motifs (Supplemental Table ...protein- binding microarrays and DAP-Seq, were selected based on the ... See full document
14
A computational approach to discovering p53 binding sites in the human genome
... the binding of other proteins which are required to loose the tightly packed chromatin structure to facilitate the binding of several activators to their binding ...contain binding ... See full document
155
Models incorporating chromatin modification data identify functionally important p53 binding sites
... of binding sites that establish the chro- matin ...of analysis on their experimentally defined p53 binding sites and identified enrichment for the REs of eight transcription ... See full document
12
Computational DIO2 rSNP Analysis, Transcriptional Factor Binding Sites and Disease
... promoter regions but in the introns, exons and the UTRs of a gene ...TF binding and have been associated with ...by computational analyses need to be verified by future protein/DNA electrophoretic ... See full document
24
Impact of Alu repeats on the evolution of human p53 binding sites
... the p53 binding affi- nity, of these sites are largely ...are p53 ChIP fragments - DNA sequence intervals experimentally characterized to be bound by p53 gen- ...These sites are ... See full document
20
Multiple protein-binding sites in an intracisternal A particle long terminal repeat.
... Symbols: 0, 0, exo III contact points (0, noncoding strand; 0, coding strand) (w, weak exo III stop site); *+ - - - -*, boundaries of the protein-DNA interactions as determined by DNase [r] ... See full document
8
Computational Methods for Predicting Protein-protein Interactions and Binding Sites
... This chapter introduces our recent publication DELPHI [80, 79], a deep learning based program for protein-protein interaction site prediction. We first describe the deep learn- ing prerequisites used in DELPHI and the ... See full document
138
Preferred binding of gain-of-function mutant p53 to bidirectional promoters with coordinated binding of ETS1 and GABPA to multiple binding sites
... or p53 R273H binding for promoters with more ETS motifs, yet the probability of binding went up ...and p53 R273H bound per promoter, which could be as few as one, that this binding ... See full document
11
Computational Analysis of Functional Sites in Proteins
... Firstly, a Web-based tool has been developed which can autom atically annotate a protein sequence or an alignment of protein sequences by colouring residues with useful d ata from structural analyses such as secondary ... See full document
197
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 ... See full document
64
Analysis of transcriptional regulatory regions in vivo
... The problems in comparing the transcriptional activity of differ- ent transgenes due to multiple transgene copies integrated at random sites with variable amounts of silencing can be overcome by the site-specific ... See full document
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