Dataset Information

Effectively utilizing publicly available databases for cancer target evaluation.

ABSTRACT: The majority of compounds designed against cancer drug targets do not progress to become approved drugs, mainly due to lack of efficacy and/or unmanageable toxicity. Robust target evaluation is therefore required before progressing through the drug discovery process to reduce the high attrition rate. There are a wealth of publicly available databases that can be mined to generate data as part of a target evaluation. It can, however, be challenging to learn what databases are available, how and when they should be used, and to understand the associated limitations. Here, we have compiled and present key, freely accessible and easy-to-use databases that house informative datasets from in vitro, in vivo and clinical studies. We also highlight comprehensive target review databases that aim to bring together information from multiple sources into one-stop portals. In the post-genomics era, a key objective is to exploit the extensive cell, animal and patient characterization datasets in order to deliver precision medicine on a patient-specific basis. Effective utilization of the highlighted databases will go some way towards supporting the cancer research community achieve these aims.

SUBMITTER: Croft D

PROVIDER: S-EPMC10346432 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Effectively utilizing publicly available databases for cancer target evaluation.

Croft Daniel D Lodhia Puja P Lourenco Sofia S MacKay Craig C

NAR cancer 20230714 3

The majority of compounds designed against cancer drug targets do not progress to become approved drugs, mainly due to lack of efficacy and/or unmanageable toxicity. Robust target evaluation is therefore required before progressing through the drug discovery process to reduce the high attrition rate. There are a wealth of publicly available databases that can be mined to generate data as part of a target evaluation. It can, however, be challenging to learn what databases are available, how and w ...[more]

PMID: 37457379

Similar Datasets

Project description:BACKGROUND: The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. RESULTS: We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. CONCLUSIONS: This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected features may allow selecting model cell lines that are more adapted and pertinent to the addressed biological question.

Project description:Conducting systematic reviews of clinical trials is arduous and resource consuming. One potential solution is to design databases that are continuously and automatically populated with clinical trial data from harmonised and structured datasets. We aimed to map publicly available, continuously updated, topic-specific databases of randomised clinical trials (RCTs). We systematically searched PubMed, Embase, the preprint servers medRxiv, ArXiv, and Open Science Framework, and Google. We described seven features (access model, database architecture, data input sources, retrieval methods, data extraction methods, trial presentation, and export options) and narratively summarised the results. We did not register a protocol for this review. We identified 14 continuously updated clinical trial databases, seven related to COVID-19 (first active in 2020) and seven non-COVID databases (first active in 2009). All databases, except one, were publicly funded and accessible without restrictions. They mainly employed methods similar to those from static article-based systematic reviews and retrieved data from journal publications and trial registries. The COVID-19 databases and some non-COVID databases implemented semi-automated features of data import, which combined automated and manual data curation, whereas the non-COVID databases mainly relied on manual workflows. Most reported information was metadata, such as author names, years of publication, and link to publication or trial registry. Two databases included trial appraisal information (risk of bias assessments). Six databases reported aggregate group level results, but only one database provided individual participant data on request. We identified few continuously updated trial databases, and existing initiatives mainly employ methods known from static article -based reviews. The main limitation to create truly live evidence synthesis is the access and import of machine-readable and harmonised clinical trial data.

Project description:Prostate cancer (PCa) is the second most common cancer in men, and the second leading cause of death from cancer in men. Many studies on PCa have been carried out, each taking much time before the data is collected and ready to be analyzed. However, on the internet there is already a wide range of PCa datasets available, which could be used for data mining, predictive modelling or other purposes, reducing the need to setup new studies to collect data. In the current scientific climate, moving more and more to the analysis of "big data" and large, international, multi-site projects using a modern IT infrastructure, these datasets could be proven extremely valuable. This review presents an overview of publicly available patient-centered PCa datasets, divided into three categories (clinical, genomics and imaging) and an "overall" section to enable researchers to select a suitable dataset for analysis, without having to go through days of work to find the right data. To acquire a list of human PCa databases, scientific literature databases and academic social network sites were searched. We also used the information from other reviews. All databases in the combined list were then checked for public availability. Only databases that were either directly publicly available or available after signing a research data agreement or retrieving a free login were selected for inclusion in this review. Data should be available to commercial parties as well. This paper focuses on patient-centered data, so the genomics data section does not include gene-centered databases or pathway-centered databases. We identified 42 publicly available, patient-centered PCa datasets. Some of these consist of different smaller datasets. Some of them contain combinations of datasets from the three data domains: clinical data, imaging data and genomics data. Only one dataset contains information from all three domains. This review presents all datasets and their characteristics: number of subjects, clinical fields, imaging modalities, expression data, mutation data, biomarker measurements, etc. Despite all the attention that has been given to making this overview of publicly available databases as extensive as possible, it is very likely not complete, and will also be outdated soon. However, this review might help many PCa researchers to find suitable datasets to answer the research question with, without the need to start a new data collection project. In the coming era of big data analysis, overviews like this are becoming more and more useful.

Dataset Information

Effectively utilizing publicly available databases for cancer target evaluation.

Publications

Effectively utilizing publicly available databases for cancer target evaluation.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets