Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037.Access within the open source R statistical environment through the biomaRt bioconductor package. C – Access from Taverna workflow system. D – Access with Galaxy

Claude Chelala (3016)

Deepak Hariharan (57624)

Hannah J Whiteman (57622)

Nicholas R Lemoine (57626)

Sayka Barry (57623)

Stephan A Hahn (57621)

Tatjana Crnogorac-Jurcevic (57627)

Tomasz P Radon (57625)

Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037.lts return Ensembl Gene ID by default with a hyper-link to the Ensembl GeneView website. In the Gene DAS Report section, which can be expanded/collapsed using the "+/-" box, a list of all the DAS sources including the Pancreatic Expression database is provided. To display the Pancreatic Expression database annotations, one can simply click on the checkbox next to the Pancreatic Expression and press the Update button at the end of the DAS sources

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Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-3

Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037.s and present in plasma. 1. Filter: the query is restricted by clicking on the "" node on the left, expanding the filter section "" and selecting for genes differentially expressed in ")" as well as ")" and expanding the filter section "" and selecting for genes expressed in "". 2. Attributes: selected by clicking on the "" node on the left, choosing the "" attribute page, expanding the attribute section "" to remove ", "" and "" default options, expanding the attribute section "" and selecting "" under "". 3. Results: Clicking the "" button in the tool bar returns 37 genes satisfying the filters criteria. Clicking the "" button on the toolbar will retrieve a result table. Checking the "Unique results only" will display only the unique rows of the result table

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-4

Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037.mous, validated SNPs with frequency data associated with genes involved in pancreatic cancer. 1. Filter: one can restrict the query by clicking on the "" node on the left and selecting "" from the filter section "", "from the filter section "" and "" from the filter section "". For SNP filters, one can expand the filter section "", select "" as "coding" from its drop down menu, "" as "" from its drop down menu as well as "" and "". 2. Attributes: one can click on the "" node on the left and start choosing attributes on the right from the "" attribute page. In this example, one can expand the attribute section "" to remove "" and "" default options, expand the attribute section "" to select "" under the "Ensembl Attributes", "Synonymous SNP count" and "Non-synonymous SNP count" under "Gene SNP Attributes", expand the "" section to select the "", "" and "" under the "", ")", "", ")" and ")" under the ", and finally, ")", "" as well a "" under the "". 3. Results: one can preview the results by clicking the "" button on the toolbar. For particularly intensive queries, which is true in this example, one can use the web file options by entering an email address. An email will then be sent to the given address when the results are ready and one can click on the link in the email to download the results. In this example, results are viewed and filtered with Excel

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-9

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-13

Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037.intraepithelial neoplasias and pancreatic adenocarcinoma) and to retrieve the genes found to be de-regulated in the progression of pancreatic cancer. 1. Filter: one can choose ")", ")" and "e)" from the filter section "". 2. Attributes: one can choose the "" attribute page, expand the attribute section "" to remove ", "" and "" default options, expand the attribute section "" and select "" under "". 3. Results: Clicking the "" button in the tool bar returns 10 genes involved in the progression of pancreatic cancer

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-5

Copyright information:Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"http://www.biomedcentral.com/1471-2164/8/439BMC Genomics 2007;8():439-439.Published online 28 Nov 2007PMCID:PMC2216037. restrict the query by clicking on the "" node on the left, expanding the filter section "" using the "+" box, choosing the "" list limit simply by clicking on the left checkbox and selecting the ")" and typing in the E-cadherin gene symbol "". 2. Attributes: one can click on the "" node on the left and start choosing attributes from the "" page. In this example, one can expand the "" section, check "", "", """ and "" under "". Once can also expand the "" section to check "" under the ")" and "" to check "". 3. Results: one can click the "" button to view the results. The antibody ID for "" is displayed with a hyper-link to the Human Protein Atlas where immunohistochemistry data for normal and cancer tissues, as well as for cell lines, can be displayed

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-11

https://figshare.com/articles/Pancreatic_Expression_database:_a_generic_model_for_the_organization,_integration_and_mining_of_complex_cancer_datasets-3/69837

Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets-13

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