DbDEPC 3.0:the Database Of Differentially Expressed Proteins In Human Cancer With Multi-level Annotation And Drug Indication

Cancer characteristic with multi-factor participation and staged recurrence is one of the main causes of human death.Differentially expressed proteins(DEPs)are widely used as important biomarkers in pathological mechanism,prognosis prediction as well as treatment targeting in cancer research.With the rapid application of mass spectrometry(MS)technology,large amounts of DEPs have been identified in various human cancers,which are scattered in a wealth of peer reviewed MS/MS literatures.It is an urgent issue to properly organize these data for the use of cancer researchers.Therefore,we established the database of differentially expressed proteins in human cancer(dbDEPC)for the first time to provide a systematic resource for the storage and query of the DEPs generated by MS.It was updated to dbDEPC 2.0 in 2012.In recent years,high-throughput technology of MS combined with computer has contributed to the rapid growth of DEPs and it is extremely necessary to update dbDEPC in time.Therefore,here we provide another updated version of dbDEPC 3.0,not only with the data updated,but also with the function expanded.Through rigorous screening criteria of literatures,data content has expanded to 11669 unique DEPs covering 26 different cancer types,extracted from 779 MS experiments and all the data types have been increased more than twice compared to the previous version.Also,the web interface has been greatly refined and enhanced.On the one hand,to characterize the proteomic alterations in different aspects will promote a better understanding of molecular drivers of cancers,so we introduced multi-level annotation on DEPs,including peptide amino acid variation and protein post-translational modifications(PTMs)information.On the other hand,to allow for the advantage of network approaches in the identification of drug target,we integrated targeting drug information with different biological networks,expecting to shed light on network-based drug discovery.Finally,an online enrichment analysis tool has been developed to help access molecular interaction and reaction networks for DEPs in KEGG pathway.dbDEPC 3.0 is available at https://www.scbit.org/dbdepc3/index.php.Based on the current data and enrichment analysis tool,we provide two practical demonstrations of the use of dbDEPC 3.0 in cancer research,to help illustrate the foreseeable application in the future.Firstly,for the guidance of experiments on specific subjects,users can predict the key proteins and guide their biological experiments by utilizing our database.Secondly,for the consistency analysis of DEPs,users can find the preferred behavior of specific proteins and the common characteristics of DEPs in human cancers.At the same time,researchers can also do some pan-cancer analysis similarly.Overall,dbDEPC 3.0 aims to serve as a systematic resource,with comprehensive data amount and data analysis tool to facilitate study of DEPs in human cancer.We believe that the development of dbDEPC database can help accelerate the integration between proteomic and cancer studies.