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发布于:2018-10-11 20:17:08  访问:65 次 回复:0 篇
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Ease 27) (see More File 2). The network model of "ErbB signalling" developed
[35] was CS-1774 web pubmed ID:http://www.ncbi.nlm.nih.gov/pubmed/25746230 downloaded in SBML format from BioModels http:// www.ebi.ac.uk/biomodels-main/publmodel.do?mid=BIOMD0000000175. The network model of "ErbB signalling" developed by Birthwistle et al. [35] was PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/25746230 downloaded in SBML format from BioModels http:// www.ebi.ac.uk/biomodels-main/publmodel.do?mid=BIOMD0000000175. This model was utilized for the visualization in Cytoscape [28] plus the network modelling. Cytoscape version 2.six.0 supports SBML Level two Version 1 (SBML L2 V1). As the model downloaded from BioModels is in SBML L2 V3 format, it had to be modified for visualization in Cytoscape (see Added File 3). Because the model downloaded from the original publication [35] doesn‘t include a mapping to UniProt identifiers, the mapping among all proteins appearing inside the ErbB signalling network and UniProt was obtained from the annotations in the BioModels database and is supplied as a mapping file as part of the supplementary supplies (see Additional File 4). Information integration We extracted the details of mutagenesis experiments and organic variants for all human entries of your manuallyPage 10 of(page number not for citation purposes)BMC Bioinformatics 2009, ten(Suppl 8):Shttp://www.biomedcentral.com/1471-2105/10/S8/SABFigure eight Dynamic and dose response on the ErbB signalling pathway within the presence of mutated MEK1 Dynamic and dose response from the ErbB signalling pathway within the presence of mutated MEK1. Simulation of Akt activation in response to simulatenous EGF and HGR stimulation. (A) EGF: ten nM, HGR rising. (B) HGR ten n M, EGF growing. Responses were obtained and normalized as described in [35].Page 11 of(page number not for citation purposes)BMC Bioinformatics 2009, ten(Suppl 8):Shttp://www.biomedcentral.com/1471-2105/10/S8/Suniprot_sprot.datahumsavar.txt1) get mutagenesis and natural variant information2) get illness mapping to OMIM EntrezGene 3) get uniProt-Entrez Gene mappingSQL DB4) get annotation to dbSNP dbSNP6) create node attribute files5) get annotation to GO, UniProt GO UniProtCytoscape node attriute file7) annotated network visualizationFigure 10-fold ErbB2 overexpession Effect of9 Effect of 10-fold ErbB2 overexpession. Simulations of EGF- and HRG-induced Akt activation under wild-type (WT) and ErbB2 overexpression conditions (ErbB2 up). (A) Stimulation with EGFR. (B) Stimulation with HRG. The figure and legends are in the original publication [35].Figure 10 Workflow with the information integration procedure Workflow of the data integration procedure. 1) Data on mutations and sequence variants is gathered from UniProt. 2) The illness association mapping to OMIM is obtained from UniProt, if accessible. 3) A mapping of UniProt and Entrez Gene ids is made. 4) The annotation to dbSNP, that is in portion offered by UniProt is extended. 5) Additional annotations to GO ontology are obtained by NER. 6) Cytoscape node attribute files are made from the integrated data that‘s PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/25580570 stored in a SQL database. 7) The annotated network is visualized in Cytoscape.curated part of UniProt resulting in 11806 entries (Figure 10). For this objective, we parsed the flat file ftp://ftp.uni prot.org/pub/databases/uniprot/current_release/knowl edgebase/complete/uniprot_sprot.dat.gz with the UniProtKB/Swiss-Prot database employing Swissknife [39], an object-oriented Perl library to manage Swiss-Prot entries.
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