dna protein interaction analysis chip seq

... next-generation sequencing (NGS) technologies, ChIP- Seq has come into a wide use for transcription factor binding sites analysis By directly sequencing the DNA fragments immunoprecipitated in a ChIP experiments, ... Time Series Analysis Cambridge University Press; 2000 doi: 10.1186/1742-4682-7-18 Cite this article as: Wu et al., ChIP- PaM: an algorithm to identify protein -DNA interaction using ChIP- Seq data ... genomewide coverage for the ChIP sample is 0.015 read/nt This low sequencing coverage is typical of ChIP- Seq data because the high-affinity of TF -DNA binding averts the need for deep sequencing on the...

Ngày tải lên: 13/08/2014, 16:20

... motions of biological molecules such as DNA and proteins, and DNA- protein interaction in nanometer scale In particular, the interaction between DNA and proteins has been receiving a lot of research ... (c-d) DNA- protein complexes respond to pH in 50 mM KCl and 100 nM protein concentrations Folding is much stronger at lower pH (6.5) and the DNA is hardly unfolded at this condition (e-f) DNA- protein ... to DNA and introduce strong bending to DNA which supplies the tension needed for DNA supercoiling IHF can specifically bind to certain sequences of DNA and introduce additional bending to DNA...

Ngày tải lên: 12/10/2015, 17:34

... used IMaps is a manually curated database with more than 200 000 protein- protein, proteinRNA, protein- small molecule, and protein -DNA interactions from 17 different organisms The curated data from ... further analysis Guidelines followed for capturing interactions manually and validating interactions derived from NLP tools (i) To consider an interaction complete, information on source protein ... to distinguish between protein and protein reagents that lead to generation of wrong interactions (Table 4) Another instance was where an interaction is drawn between protein and its corresponding...

Ngày tải lên: 22/06/2014, 19:20

... applied in ChIP- PET data analysis [4] In considering the ChIP enrichment score of a binding site, the number of ChIP fragments at a binding site is counted This is similar to the existing ChIP enrichment ... using ChIP- qPCR [9] Chromatin interaction identification is done in two steps: first, define the ChIP enriched interaction anchor regions from inter-ligation PETs and then quantify the interaction ... reflect the relative interaction frequency As each interaction involves two anchors and one loop, it is called a 'duplex interaction' Similar to the binding site analysis, a real interaction is expected...

Ngày tải lên: 09/08/2014, 20:21

... classification methods for use in protein interaction prediction Proteins 2006, 63:490-500 57 Ben-Hur A, Noble WS: Choosing negative examples for the predication of protein- protein interactions BMC bioinformatics ... direct interactions with one or more of the proteins in the hand-curated GBM pathway In this way we were able to extend the hand-curated pathway from 73 proteins and 187 interactions to 181 proteins ... the KEGG human p53 sig- Table 3: Protein identifiers and functional interactions in the extended FI network Source type Proteins SwissProt proteins (coverage) Interaction 6,316 5,496 (27%) 98,590...

Ngày tải lên: 09/08/2014, 20:22

... differences in ChIP -DNA library fragment size (Figure 5), MM -ChIP first models the characteristic fragment size of the sequenced ChIP -DNA library for each individual data source The ChIP- seq tags are ... for the joint analysis of one ChIP- chip and one ChIP- seq dataset, using a Bayesian inference procedure [25] However, HHMM does not effectively support the joint analysis of ChIPchip datasets ... for the detailed proof) Integrative analysis of ChIP- seq data Model building and tag shifting for individual ChIP- seq datasets The Model-based Analysis of ChIP- Seq data (MACS) algorithm [12] was...

Ngày tải lên: 09/08/2014, 22:23

... consideration relative protein abundance when assaying protein interactions Besides this, the GO category analysis for under-representation shows certain proteins and protein complexes that not ... assessment of large-scale data sets of proteinprotein interactions Nature 2002, 417:399-403 Thomas A, Cannings R, Monk N, Cannings C: On the structure of protein- protein interactions networks Biochem ... been made to probe membrane-bound proteins deposited research Figure Measured protein interaction data are represented by a directed graph Measured protein interaction data are represented by...

Ngày tải lên: 14/08/2014, 08:20

... identity for each protein pair Protein- protein interaction dataset The protein- protein interaction dataset we investigated contains a total of 4,143 selected interactions involving 2,643 proteins We ... classification of proteins solely on the basis of protein- protein interaction data, independently of sequence data It clusters proteins with respect to their common interactors and defines classes of proteins ... Vespignani A: Global protein function prediction from protein- protein interaction networks Nat Biotechnol 2003, 21:697-700 Schwikowski B, Uetz P, Fields S: A network of protein- protein interactions in...

Ngày tải lên: 14/08/2014, 14:21

... interaction with importin-b [6] In the nucleus, SREBPs detach from importin-b, and their transcription factor activities are regulated through interaction with a variety of nuclear proteins Interaction ... 2008 FEBS 625 Protein interaction and SREBPs R Sato ing proteins, SCAP and importin-b, play an important role in determining the fate of SREBPs In the nucleus, multiple nuclear proteins form ... R Sato Protein interaction and SREBPs Fig SREBPs interact with SCAP or importin-b in the cytoplasm SREBPs localized on the ER membrane associate with another ER membrane protein, SCAP...

Ngày tải lên: 18/02/2014, 13:20

... Proteins 41, 47–57 16 Valdar, W.S.J & Thornton, J.M (2001) Protein protein interfaces: analysis of amino acid conservation in homodimers Proteins 42, 108–124 Ó FEBS 2002 Predicting protein protein ... Chothia, C & Janin, J (1975) Principles of protein- protein recognition Nature 256, 705–708 13 Jones, S & Thornton, J.M (1997) Analysis of protein protein interaction sites using surface patches ... (1999) Detecting protein function and protein protein interactions from genome sequences Science 285, 751–753 Eisenberg, D., Marcotte, E.M., Xenarios, I & Yeates, T.O (2000) Protein function...

Ngày tải lên: 21/02/2014, 15:20

... clones and the cDNAs were identified by DNA sequencing Ten cDNAs from the 88 positive clones encoded catalytic subunits of the type 2A phosphatases PP2Aca (one cDNA), PP2Acb (three cDNAs), the C-terminal ... PP2Aca ⁄ b (one cDNA), PP4c (three cDNAs) and PP6c (two cDNAs) Initial mapping of the region of PP2Ac involved in TIPRL binding was obtained from the cDNAs that showed positive interaction with ... immunoblot analysis to exclude those that did not express the fulllength lexA–TIPRL fusion protein Using these criteria, clones of 65 transformants tested were selected for DNA sequencing analysis...

Ngày tải lên: 07/03/2014, 05:20

... 2005 FEBS A K Dunker et al derived protein protein interaction network (Fig 1C) suggests a similar underlying architecture The scale-free nature of protein protein interaction networks gives them ... observations, analysis of the S cerevisiae protein protein interaction network revealed that although proteins with five or fewer links constitute about 93% of the total number of proteins, only ... proof that biological protein protein interaction networks maintain a scale-free nature throughout full interactomes remains to be verified Secondly, experimental protein protein interaction data contains...

Ngày tải lên: 07/03/2014, 21:20

... investigating the molecular mechanism involved in protein protein interaction and for screening novel molecules that might enhance or block the protein protein interactions of molecules of interest In ... results indicate that protein protein interaction did not occur between GFP and EYFP, GFP and GnRH-R, or EYFP and GnRH-R FRET observed in Fig 4D was a result of specific interaction between GnRH-R ... efficient and convenient method for measuring protein protein interaction The same insect cell line can be routinely used to express any recombinant proteins of interest, allowing various combinations...

Ngày tải lên: 30/03/2014, 20:20

... of protein- protein interaction information from immunology literature Proc of IPSJSIG-NL,150: 15-20 Jenssen, Tor-Kristian, et al 2001 A literature network of human genes for high-throughput analysis ... References Blaschke, Christian and Valencia, Alfonso 2001 The potential use of SUISEKI as a protein interaction discovery tool Genome Informatics, 12: 123-134 Carletta, Jean, et al 1997 The reliability ... biologist a list of words denoting interactions and 1000 abstracts retrieved from Medline using the PubMed These abstracts are related to Interleukin-6, a secreted protein whose main function is...

Ngày tải lên: 31/03/2014, 20:20

... the case of DNAprotein interactions, the problem of quantity and hence of detection is often offset by the high degree of selectivity and stability of DNA protein interactions DNAprotein binding ... Preface by the protein identified At the protein level, the protein species binding a given DNA sequence can be identified The amino acids contacting DNA and the protein surface facing the DNA may be ... 465 33 Analysis of DNAProtein Interactions by Intrinsic Fluorescence Mark L Carpenter, Anthony W Oliver, and G Geoff Kneale 491 34 Circular Dichroism for the Analysis of ProteinDNA Interactions...

Ngày tải lên: 08/04/2014, 12:51

... ordered series of samples (DNA, RNA, protein, tissue) The type of microarray depends upon the material placed onto the slide: DNA, DNA microarray; RNA, RNA microarray; protein, protein microarray; tissue, ... Picaset Oy Helsinki 2003 DNA microarray data analysis Preface This is the first edition of the DNA microarray data analysis guidebook Although invented in the mid-90s, DNA microarrays are still ... that help to stabilize the DNA 16 DNA microarray data analysis onto the slide, either by covalent bonds or electrostatic interactions An alternative technology allows the DNA to be synthesized directly...

Ngày tải lên: 11/04/2014, 09:40

... in three stages: binding of the protein to the DNA, partial digestion of the protein -DNA complex with DNase I, and separation of the digestion fragments on a DNA sequencing gel 1, The binding reaction ... available proteins with too much DNA This limitation can in part be overcome when a protein also generates a gel-shift It is then feasible to fractionate the partially DNase digested protein -DNA complex ... end-labeling allows both DNA strands to be analyzed side by side from the same end of the DNA duplex DNase I footprinting requires an excess of DNA- binding protein over the DNA fragment used The...

Ngày tải lên: 11/04/2014, 09:40

... RNA -Protein Interaction Protocols Edited by: S Haynes © Humana Press Inc., Totowa, NJ 21 22 Hanna, Bentsen, Lucido, and Sapre Fig Nucleotide analogs for analysis of protein nucleic acid interactions ... RNA protein interactions (see, e.g., Fig 2) We originally demonstrated that MB crosslinking could be used to detect interactions of dsRNA with either purified proteins or with dsRNA binding proteins ... deaminase, and a GST fusion protein with a dsRNA binding domain from the Drosophila staufen protein (22,25) Both proteins show sequence nonspecific binding to dsRNA The proteins were MB crosslinked...

Ngày tải lên: 11/04/2014, 10:31

... comprehensive analysis of protein- protein interactions in Saccharomyces cerevisiae,” Nature, vol 403, no 6770, pp 623–627, 2000 [11] R M Kini and J H Evans, “Prediction of potential proteinprotein interaction ... “Prediction of protein interaction sites from sequence profile and residue neighbor list,” Proteins, vol 44, no 3, pp 336–343, 2001 [24] J R Bock and D A Gough, “Predicting protein- protein interactions ... the basic units of protein interactions, proteins without domain information cannot provide Evaluation criteria (5) Predicting PPI Training In order to predict protein- protein interactions, our...

Ngày tải lên: 22/06/2014, 23:20

... “Missing value estimation methods for DNA microarrays,” Bioinformatics, vol 17, no 6, pp 520–525, 2001 [13] A H Tewfik and A B Tchagang, “Biclustering of DNA microarray data with early pruning,” ... Acids Research, vol 33, Database issue, pp D364–D368, 2005 [18] Munich Information Center for Protein Sequences (MIPS) and GSF-National Research Center for Environment and Health, “Comprehensive ... transport processes, and medical imaging; (B) mathematical modeling and analysis of biological systems and data (genomics, proteomics, DNA microarray, gene expression, gene regulatory networks, and computational...

Ngày tải lên: 22/06/2014, 23:20