CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): ii A major challenge in understanding metazoan genomes is to find and annotate the regions that control the precise spatial and temporal expression of the genes. Cis-regulatory modules (CRMs/enhancers), main players of this regulatory process, are typically short (|1kb) sequences that are embedded in non-coding regions of the genome. They harbor cis-elements (binding sites/motifs) for one or more related transcription factors (TFs) and mediate a discrete aspect of the expression pattern of their nearby gene. Although decades of research in biology have provided scientists with hundreds of such sequences, we are far from completing the search and understanding the underlying mechanisms of these regulatory regions. The goal of this thesis is to utilize computational and statistical methods to guide the search for novel CRMs, reveal the mechanisms of this regulatory action, and elucidate specific biological networks using the
Cis-regulatory modules (CRM) are segments of DNA responsible for tissue- and time- specific regulation of gene expression (1). The length of CRMs is difficult to estimate directly but it is believed to vary from several hundreds to several thousands of ba
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These graphs show the aggregated classification over three different runs, where for every category (FN, TP, TN, FP) the minimal number over the different runs is taken. For example, if 500 traces are TP in the first run, 490 in the second, and 495 in the third, then the value 490 is used as aggregated … [Read more…]. ...
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In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana ...
Before interpreting the biological results from ChIP-chip or ChIP-seq data using the Cistrome platform, researchers can upload raw data from their microarray or sequencing facilities and then preprocess those data using Cistrome peak-calling tools. Alternatively, researchers can also upload intermediate results from their own analysis tools. As illustrated in Figure 1, the peak calling step generates two types of intermediate files: peak location files (in BED format), indicating the predicted transcription factor binding sites or histone modification sites, and signal profile files (in WIGGLE format) of binding or histone modification across the genome.. Several methods can be used to import data into Cistrome. The Upload File function can import a file from the users computer or from an HTTP or FTP file server in the same manner as in Galaxy. In most cases, sequencing facilities will manage the low level base calling and read mapping processes. The least processed Cistrome data formats that ...
Traditional techniques for extracting features from images are highly structured processes which require human experts to convert their intuition and exper
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You are here: Browse: Home > Document Library > Archived Research Projects > Enrichment analysis of transcription factors binding sites in blood cells in response to ingestion of bovine milk by healthy adult humans ...
Looking for online definition of Regulatory elements in the Medical Dictionary? Regulatory elements explanation free. What is Regulatory elements? Meaning of Regulatory elements medical term. What does Regulatory elements mean?
Background. The workshop gathers authors of the LNCS Festschrift 6060 - Algorithms and Applications, Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday - to present their contribution. This festive edition of the workshop is a continuation of the local annual seminar series on string processing research (Merkkijonopäivä 2009 and Merkkijonopäivä 2008). String processing has been an active research topic in Finland since the early 80s. Some highlights over the years include first formulations of algorithms for fragment assembly, new methods for data compression, seminal results on approximate string matching and lossless filtering, string matching on compressed sequences, space-efficient full-text indexes, efficient construction algorithms for full-text indexing, bit-parallel string algorithms, two- and higher-dimensional pattern matching over different transformation classes, and motif discovery algorithms on biological sequences. The contributions from the Festschrift ...
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Perhaps the rest of you know that it is not worth engaging this Landon fellow, but here goes.. Landon - I think what you are failing to understand is something we physicists understand phenomenologically as sensitive dependence to initial conditions. Let me explain. If there exists a mutation in a gene regulatory element within the germ line of an organism (the germ line bit plays the part of the biological initial condition), then the sensitivity to that small microevolutionary event can have immense macroscopic consequence (the examples in the Post article are pretty good I thought, especially making reference to Lenskis work with his 12 bacterial cultures) - whether it be a new limb, or a macroscopically observable change in nutrient metabolism, or a macroscopically observable change in the growth rate of cells, etc. Now given that a macroscopic change has taken place, the change can help the organism produce more offspring than its fellow organisms, can hurt the organism into producing ...
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1. MEET.5.1:Motif Element Estimation Tools - MEET 5.1 is an R-package that includes a set of models, aprox. 550, and tools for the detection of cis-regulatory sequences ...
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There are many different groups that are developing software for finding transciption factor binding sites, alongside our own development of the BIFA tool which forms part of the Apples framework. ...
Welcome to the jPREdictor project. The program was developed foremost for the prediction of cis-regulatory elements. Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence. Please refer to the manual on how to use the program for the prediction of regulatory elements. With version 1.22, two new applications were incorporated into the jPREdictor: motif discovery via motif evolution and the motif clustering. Both tasks can only be started via command-line. Please refer to the manual again to get a brief description on how they function and how they are invoked. ...
Welcome to the jPREdictor project. The program was developed foremost for the prediction of cis-regulatory elements. Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence. Please refer to the manual on how to use the program for the prediction of regulatory elements. With version 1.22, two new applications were incorporated into the jPREdictor: motif discovery via motif evolution and the motif clustering. Both tasks can only be started via command-line. Please refer to the manual again to get a brief description on how they function and how they are invoked. ...
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Ng, C. [伍志祥。]. (1999). Identification of cis-regulatory sequence for the expression of epidermal growth factor (EGF) gene. (Thesis). University of Hong Kong, Pokfulam, Hong Kong SAR. Retrieved from http://dx.doi.org/10.5353/th_ ...
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