Dataset Information

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

ABSTRACT: Protein quantification at proteome-wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome-wide quantification is not yet fully routine, many datasets approaching proteome-wide coverage are becoming available through biophysical and MS techniques. Data of this type can be accessed via a variety of sources, including publication supplements and online data repositories. However, access to the data is still fragmentary, and comparisons across experiments and organisms are not straightforward. Here, we describe recent updates to our database resource "PaxDb" (Protein Abundances Across Organisms). PaxDb focuses on protein abundance information at proteome-wide scope, irrespective of the underlying measurement technique. Quantification data is reprocessed, unified, and quality-scored, and then integrated to build a meta-resource. PaxDb also allows evolutionary comparisons through precomputed gene orthology relations. Recently, we have expanded the scope of the database to include cell-line samples, and more systematically scan the literature for suitable datasets. We report that a significant fraction of published experiments cannot readily be accessed and/or parsed for quantitative information, requiring additional steps and efforts. The current update brings PaxDb to 414 datasets in 53 organisms, with (semi-) quantitative abundance information covering more than 300,000 proteins.

SUBMITTER: Wang M

PROVIDER: S-EPMC6680238 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Wang Mingcong M Herrmann Christina J CJ Simonovic Milan M Szklarczyk Damian D von Mering Christian C

Proteomics 20150312 18

Protein quantification at proteome-wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome-wide quantification is not yet fully routine, many datasets approaching proteome-wide coverage are becoming available through biophysical and MS techniques. Data of this type can be accessed via a variety of sources, including publication supplements and online data repositories. However, access to the d ...[more]

PMID: 25656970

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Project description:BACKGROUND: Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-scale experiments have enabled the discovery of thousands of previously unknown linkages among proteins in many organisms, the high-throughput interaction data is often associated with high error rates. Since protein interaction networks have been utilized in numerous biological inferences, the inclusive experimental errors inevitably affect the quality of such prediction. Thus, it is essential to assess the quality of the protein interaction data. RESULTS: In this paper, a novel Bayesian network-based integrative framework is proposed to assess the reliability of protein-protein interactions. We develop a cross-species in silico model that assigns likelihood scores to individual protein pairs based on the information entirely extracted from model organisms. Our proposed approach integrates multiple microarray datasets and novel features derived from gene ontology. Furthermore, the confidence scores for cross-species protein mappings are explicitly incorporated into our model. Applying our model to predict protein interactions in the human genome, we are able to achieve 80% in sensitivity and 70% in specificity. Finally, we assess the overall quality of the experimentally determined yeast protein-protein interaction dataset. We observe that the more high-throughput experiments confirming an interaction, the higher the likelihood score, which confirms the effectiveness of our approach. CONCLUSION: This study demonstrates that model organisms certainly provide important information for protein-protein interaction inference and assessment. The proposed method is able to assess not only the overall quality of an interaction dataset, but also the quality of individual protein-protein interactions. We expect the method to continually improve as more high quality interaction data from more model organisms becomes available and is readily scalable to a genome-wide application.

Project description:The Pediatric Quality of Life InventoryTM Version 4.0 Short Form Generic Core Scale (PedsQLTM) is a validated and widely used tool assessing the quality of life (QoL) of children and youth. It has been used extensively across healthy populations as well as those with chronic and acute illnesses, allowing for comparison of the psychosocial impact of chronic illness between pediatric disease cohorts. As part of the QoL initiative undertaken at the British Columbia Children's Hospital (BCCH) Inflammatory Bowel Disease (IBD) program and published in the Journal of Pediatrics titled "Cross-Sectional Analysis of Quality of Life in Pediatric Patients with IBD in British Columbia, Canada," a limited literature review was conducted using Embasse and Ovid. Studies using the English version of the PedsQLTM short form generic scale (not a disease specific scale) were identified. Studies with populations greater than 50 patients with robust subgroup sample size were included, with an emphasis on studies with well-defined patients with chronic disease. These data were compared to the BCCH population, as discussed in the aforementioned journal article. Analysis within the BCCH cohort is described separately. Comparison between different populations from the existing literature was qualitative only, with no statistical analysis done given the heterogeneity of populations and studies. In a study of patients from the emergency department at BCCH (n=178), the mean (SD) QoL scores of the healthy patients was 89.2 (10.3). In a group of self-identified healthy patients in California (n=5079), their mean QoL score was 83.9 (12.5). Separating the BCCH IBD population by disease activity, those in remission (n=220, 84.4 (12.8)) have similar QoL scores to these healthy cohorts, though their scores remain slightly below the previously published BCCH cohort. For children with any degree of active IBD (n=98, 75.6 (15.8)), their QoL scores are below the healthy means and are lower than other groups with self-identified "chronic illnesses" (n=367, 77.2 (15.5)), diabetes (n=418, 82.3 (13.5)), mild asthma (n=281, 85.5 (13.3)), or Canadian patients 4 weeks post-concussion (n=1157, 80.3). BCCH IBD patients with moderately to severely active disease have QoL scores well below the other disease groups (n=33, 63.1 (18.8)); lower than oncology patients on induction chemotherapy regimens (n=105, 68.9 (16.0)), acute inpatients (n=359, 63.9 (20.3)), and asthmatics with moderate-severe, persistent asthma (n=86, 67.1 (18.6)). This data is useful for clinicians treating pediatric patients looking at how QoL is influenced by chronic illness and by factors such as disease type and severity.

Project description:: (1) Motivation: The exponential increase in multilayered data, including omics, pathways, chemicals, and experimental models, requires innovative strategies to identify new linkages between drug response information and omics features. Despite the availability of databases such as the Cancer Cell Line Encyclopedia (CCLE), the Cancer Therapeutics Response Portal (CTRP), and The Cancer Genome Atlas (TCGA), it is still challenging for biologists to explore the relationship between drug response and underlying genomic features due to the heterogeneity of the data. In light of this, the Integrated Pharmacogenomic Database of Cancer Cell Lines and Tissues (IPCT) has been developed as a user-friendly way to identify new linkages between drug responses and genomic features, as these findings can lead not only to new biological discoveries but also to new clinical trials. (2) Results: The IPCT allows biologists to compare the genomic features of sensitive cell lines or small molecules with the genomic features of tumor tissues by integrating the CTRP and CCLE databases with the REACTOME, cBioPortal, and Expression Atlas databases. The input consists of a list of small molecules, cell lines, or genes, and the output is a graph containing data entities connected with the queried input. Users can apply filters to the databases, pathways, and genes as well as select computed sensitivity values and mutation frequency scores to generate a relevant graph. Different objects are differentiated based on the background color of the nodes. Moreover, when multiple small molecules, cell lines, or genes are input, users can see their shared connections to explore the data entities common between them. Finally, users can view the resulting graphs in the online interface or download them in multiple image or graph formats. (3) Availability and Implementation: The IPCT is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on the Tomcat server. The user interface was developed using HTML5, JQuery v.3.1.0 , and the Cytoscape Graph API v.1.0.4. The IPCT can be accessed at http://ipct.ewostech.net. The source code is available at https://github.com/muhammadshoaib/ipct.

Project description:BackgroundThe Chicago Classification version 4.0 (CCv4.0) of ineffective esophageal motility (IEM) is more stringent than the Chicago Classification version 3.0 (CCv3.0) definition. We aimed to compare the clinical and manometric features of patients meeting CCv4.0 IEM criteria (group 1) versus patients meeting CCv3.0 IEM but not CCv4.0 criteria (group 2).MethodsWe collected retrospective clinical, manometric, endoscopic, and radiographic data on 174 adults diagnosed with IEM from 2011 to 2019. Complete bolus clearance was defined as evidence of exit of the bolus by impedance measurement at all distal recording sites. Barium studies included barium swallow, modified barium swallow, and barium upper gastrointestinal series studies, and collected data from these reports include abnormal motility and delay in the passage of liquid barium or barium tablet. These data along with other clinical and manometric data were analyzed using comparison and correlation tests. All records were reviewed for repeated studies and the stability of the manometric diagnoses.ResultsMost demographic and clinical variables were not different between the groups. A lower mean lower esophageal sphincter pressure was correlated with greater percent of ineffective swallows in group 1 (n = 128) (r = -0.2495, P = 0.0050) and not in group 2. In group 1, increased percent of failed contractions on manometry was associated with increased incomplete bolus clearance (r = 0.3689, P = 0.0001). No such association was observed in group 2. A lower median integrated relaxation pressure was correlated with greater percent of ineffective contractions in group 1 (r = -0.1825, P = 0.0407) and not group 2. Symptom of dysphagia was more prevalent (51.6% versus 69.6%, P = 0.0347) in group 2. Dysphagia was not associated with intrabolus pressure, bolus clearance, barium delay, or weak or failed contractions in either group. In the small number of subjects with repeated studies, a CCv4.0 diagnosis appeared more stable over time.ConclusionsCCv4.0 IEM was associated with worse esophageal function indicated by reduced bolus clearance. Most other features studied did not differ. Symptom presentation cannot predict if patients are likely to have IEM by CCv4.0. Dysphagia was not associated with worse motility, suggesting it may not be primarily dependent on bolus transit.

Dataset Information

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

Publications

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.

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