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

<p>Abstract</p> <p>Background</p> <p>Pancreatic cancer is the 5th leading cause of cancer death in both males and females. In recent years, a wealth of gene and protein expression studies have been published broadening our understanding of pancreatic cancer biology. Due to the explosive growth in publicly available data from multiple different sources it is becoming increasingly difficult for individual researchers to integrate these into their current research programmes. The Pancreatic Expression database, a generic web-based system, is aiming to close this gap by providing the research community with an open access tool, not only to mine currently available pancreatic cancer data sets but also to include their own data in the database.</p> <p>Description</p> <p>Currently, the database holds 32 datasets comprising 7636 gene expression measurements extracted from 20 different published gene or protein expression studies from various pancreatic cancer types, pancreatic precursor lesions (PanINs) and chronic pancreatitis. The pancreatic data are stored in a data management system based on the BioMart technology alongside the human genome gene and protein annotations, sequence, homologue, SNP and antibody data. Interrogation of the database can be achieved through both a web-based query interface and through web services using combined criteria from pancreatic (disease stages, regulation, differential expression, expression, platform technology, publication) and/or public data (antibodies, genomic region, gene-related accessions, ontology, expression patterns, multi-species comparisons, protein data, SNPs). Thus, our database enables connections between otherwise disparate data sources and allows relatively simple navigation between all data types and annotations.</p> <p>Conclusion</p> <p>The database structure and content provides a powerful and high-speed data-mining tool for cancer research. It can be used for target discovery i.e. of biomarkers from body fluids, identification and analysis of genes associated with the progression of cancer, cross-platform meta-analysis, SNP selection for pancreatic cancer association studies, cancer gene promoter analysis as well as mining cancer ontology information. The data model is generic and can be easily extended and applied to other types of cancer. The database is available online with no restrictions for the scientific community at <url>http://www.pancreasexpression.org/</url>.</p

Discovery of novel small molecule inhibitors of S100P, with in vitro anti-metastatic effects on pancreatic cancer cells

© 2020 The Author(s). This is an open access article published under the terms of the Creative Commons Attribution 4.0 International licence (CC BY 4.0). For further details please see https://creativecommons.org/licenses/by/4.0/.S100P, a calcium- binding protein, is known to advance tumor progression and metastasis in pancreatic and several other cancers. Herein is described the in silico identification of a putative binding pocket of S100P to identify, synthesize and evaluate novel small molecules with the potential to selectively bind S100P and inhibit its activation of cell survival and metastatic pathways. The virtual screening of a drug-like database against the S100P model led to the identification of over 100 clusters of diverse scaffolds. A representative test set identified a number of structurally unrelated hits that inhibit S100P-RAGE interaction, measured by ELISA, and reduce in vitro cell invasion selectively in S100P-expressing pancreatic cancer cells at 10 µM. This study establishes a proof of concept in the potential for rational design of small molecule S100P inhibitors for drug candidate development.Peer reviewe

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

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

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

<p><b>Copyright information:</b></p><p>Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"</p><p>http://www.biomedcentral.com/1471-2164/8/439</p><p>BMC Genomics 2007;8():439-439.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2216037.</p><p></p>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-3

<p><b>Copyright information:</b></p><p>Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"</p><p>http://www.biomedcentral.com/1471-2164/8/439</p><p>BMC Genomics 2007;8():439-439.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2216037.</p><p></p>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

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

<p><b>Copyright information:</b></p><p>Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"</p><p>http://www.biomedcentral.com/1471-2164/8/439</p><p>BMC Genomics 2007;8():439-439.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2216037.</p><p></p>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-10

<p><b>Copyright information:</b></p><p>Taken from "Pancreatic Expression database: a generic model for the organization, integration and mining of complex cancer datasets"</p><p>http://www.biomedcentral.com/1471-2164/8/439</p><p>BMC Genomics 2007;8():439-439.</p><p>Published online 28 Nov 2007</p><p>PMCID:PMC2216037.</p><p></p>ally regulated in neuroendocrine tumours (PEN). 1. Filter: one can restrict the query by clicking on the "" node on the left, expanding the filter section "" to restricted the query for genes differentially expressed in "". Next, one can expand the filter section "" and restrict the query further to genes having expression profiles in pancreas and tumour by selecting. "" for "" () and the "" for "" (). 2. Attributes: one can click on the "" node on the left and start choosing attributes on the right. In this example, one can choose the "" attribute page, expand the attribute section "" to remove "" and "" options selected by default, expand the attribute section "" and select the "" under the ". 3. Results: one can preview the results by clicking the Results button on the toolbar