dbDEPC 3.0 provides four query methods, namely, protein query, cancer type query, multi-level annotations of proteins and network based drug indication. An online enrichment analysis tool also has been developed.
Proteins page allows users to extract summarized information of a protein, and draw a cancer profile heatmap with protein lists.Protein query
User can easily use accession from UniProt, Entrez, RefSeq, Ensembl, gene name or gene symbol in the protein search page. Firstly, users fill the input data corresponding to your interesting fields and then click on the button to query the matching proteins.
a. The general information (protein description, chromosome location, GO, KEGG pathway and drug annotation) of the protein matching the query keywords are retrieved from our database. Moreover, differentially expressed protein (DEP) related experiments will be shown in a table. To view the detailed information about the experiment, users just click on the link of EXPID.
b. The detailed information about experiment is displayed in this page.
Select a design type of your interested experiment first, input protein IDs or names and then select cancers to draw a DEPs profile heatmap in cancers.
Heatmap of differentially expressed proteins across multiple cancers is visualized(A). If the number of experiments in a specific cancer type is clicked, the detailed information of these DEPs can be displayed(B).
Cancers Page allows users to browse experiments information and DEPs of queried cancers.Cancers query
Users can select the cancer type, experimental design and sample type of interest.
The related MS experiment results of queries will be displayed(A), select interested experiments and click the button of “View” to have an overview of the DEPs(B).
Annotations Page allows users to browse multi-level annotation of interested proteins, including cancer-related variations, post-translational modifications (PTMs), and protein related drug information.Annotations query
Users can input the protein list to browse multi-level annotation of queried proteins.
The result shows that whether the queried proteins have multi-level annotations(A), and detailed information of the proteins can be retrieved with a further click(B).
Networks Page allows users to integrated targeting drug information with different biological networks (KEGG Pathway, Protein-Protein Interaction and PhoSigNet).KEGG Pathway query
First, input the candidate proteins and select the KEGG pathway.
A colored KEGG pathway will be drawn with drug targets highlighted(A), and detailed protein information can be achieved with a further click(B). The “PhoSigNet” query result is similar with “Protein–Protein Interaction” query result.
Users should input an interested protein first, set an score (0-1000) (which is the confidence provided by STRING database) threshold of network edge, select one or more cancer types and then select annotation types of network node.
The query result shows a network of the first-layer-associated proteins of the interested protein node in dbDEPC(A). Detailed multi-level annotation information can be achieved with a further click(B).
Tools Page provides a visualization solution to characterize the differentially expressed proteins in the pathway.Enrichment analysis
Input the queried protein list to see the distribution in KEGG pathway.
A heatmap to show the distribution in pathways will be displayed(A), and the enriched pathways with a threshold of p-value <= 0.05 are listed(B). With a further click on the specific pathway, the distribution of queried proteins in KEGG pathways will be shown, with differential expression information highlighted(C).