peptiCKDdb

Chronic kidney disease (CKD) is a global health problem. There is a need for early detection, diagnostic and progression biomarkers, which could identify the disease in its early stages, when treatments are more effective. Integration of experimental results followed by an extensive data analysis and mining could lead to the discovery of such novel biomarkers. The peptiCKDdb is a repository of manually curated peptidomics and proteomics datasets extracted from scientific publications related to CKD. It can serve as a knowledge base for scientists seeking confirmation of their findings, as well as a source of data for integrative analysis supporting biomarker research in the field of renal pathology.

DB tabs

Records

Data curated from the literature is presented on the website in the form of tables. Data is organized with regards to the type of experiment, thereofre in the navigation bar, we can find 3 separate tabs:

  1. Peptidomics - data from peptidomics studies is stored
  2. Proteomics - data from proteomics studies
  3. Healthy proteome - data from proteomics studies aiming at characterization of healthy human proteome

DB peptidomics

Browsing through records

Data extracted from peptidomics and proteomics publications can be accessed through Peptidomics/Protomics tab. Healthy proteome profiling studies are stored in Healthy proteome tab. All records are stored in the searchable table. Basic description of each entry is presented in the database, this includes: PubMedID (PMID), experimental method used (Method), number of peptides/proteins extracted from the study (# of peptides/proteins), biomarker panel name(if assigned; Biomarker), disease studied (Disease), sample type used (Source), short description or comment on a study (Comments), information if the validation was performed (Validation (Y/N)). Details button opens the detailed information about each study and the list of differentially expressed molecules.

DB peptidomics DB peptidomics

Study details

Details page of each study presents:

  1. Study details - information about the manuscript and experiment setup
  2. Validation - information on validation method (if available)
  3. Results table - differentially expressed peptides/proteins extracted from the study
Data from the results table can be filtered, ordered, columns can me hidden. Data can be copied to clipboard or exported to Excel, CSV or PDF.

DB healthy

Healthy proteome

Data extracted from proteomics publications aiming at characterization of the healthy human proteome are deposited in the Healthy protome tab. All records are stored in the searchable table. Basic description of each entry is presented in the database, this includes: PubMedID (PMID), experimental method used (Method), number of proteins extracted from the study (# of idenifications), sample type used (Source), short description or comment on a study (Comments). Details button opens the detailed information about identified molecules.

Searh results

Search results

Search results are displayed in the form of an interactive, searchable data table. Results can be easily copied or exported (CSV, Excel, PDF).

Searh results

Data visualization

Each search option returns graph summarizing data in the result tables. Each graph can be saved as a picture (PNG, JPG, PDF) or exported to data format files (Excel, CSV).

Data export

Information about records, study details and search results can be copied or exported to Excel, CSV, PDF formats. To export data from the table, use buttons located at the top of each table.

Excel, CSV, PDF export

Data export buttons

Excel, CSV, PDF export

Show/hide columns in the table

Cite us!

Krochmal, M., Fernandes, M., Filip, S., et al. (2016) PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease. Database : the journal of biological databases and curation, 2016, doi: 10.1093/database/baw128.

Pubmed

DATABASE

Contact us!

Magdalena Krochmal