In this work, we presented RPS, a comprehensive database of LLPS-related RNAs in 20 distinct biomolecular condensates from eukaryotes and viruses. Currently, RPS contains 21,613 LLPS-related RNAs with three different evidence types, including ‘Reviewed’, ‘High-throughput’ and ‘Predicted’. RPS provides extensive annotations of LLPS-associated RNA properties, including sequence features, RNA structures, RNA–protein/RNA–RNA interactions, and RNA modifications. Moreover, RPS also provides comprehensive disease annotations to help users to explore the relationship between LLPS and disease. The user-friendly web interface of RPS allows users to access the data efficiently. The RPS database is freely available for academic researchers at: http://rps.renlab.org/

In this work, we present SPENCER, collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. The SPENCER database is freely available for academic researchers at: http://spencer.renlab.org

In this study, we present RMVar, collected functional variants, and aimed at providing potential help for revealing the functional roles of RNA modification variants. RMVar contains several most common RNA modifications, including N6-methyladenosine (m6A), N6-dimethyladenosine (m6Am), N1-methyladenosine (m1A), pseudouridine (ψ), 5-methylcytosine (m5C), ribose methylations (2′-O-Me) and 7-Methylguanosine (m7G), 5-methyluridine (m5U), Adenosine-to-inosine (A-to-I). So far, 1,457,898 germline mutations from dbSNP, HGVD, and 220,228 somatic mutations from TCGA, ICGC and COSMIC has been included in RMVar. The RMVar database is freely available for academic researchers at: http://rmvar.renlab.org/

In this study, we present BBCancer (http://bbcancer.renlab.org/), a web-accessible and comprehensive open resource for providing the expression landscape of six types of RNAs, including messenger RNAs (mRNAs), long noncoding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), tRNA-derived fragments (tRFRNAs) and Piwi-interacting RNAs (piRNAs) in blood samples, including plasma, CTCs and EVs, from cancer patients with various cancer types. Currently, BBCancer contains expression data of the six RNA types from 5040 normal and tumor blood samples across 15 cancer types. We believe this database will serve as a powerful platform for developing blood biomarkers. The BBCancer database is freely available for academic researchers at: http://bbcancer.renlab.org/

In this work, we present lnCAR, a comprehensive open resource for providing expression profiles and prognostic landscape of lncRNAs derived from re-annotation of public microarray data. Currently, lnCAR contains 52,300 samples for differential expression analysis and 12,883 samples for survival analysis from 10 cancer types. lnCAR allows users to interactively explore any annotated or novel lncRNAs. We believe lnCAR will serve as a valuable resource for the community focused on lncRNA research in cancer. The lnCAR database is freely available for academic researchers at: https://lncar.renlab.org/

In this work, you can search or browse: m6A-associated genetics mutations(dbsnp), m6A-associated cancer somatic mutations(TCGA), disease related m6A-associated variants(GWAS and ClinVar), Splicing sites affected by m6A-associated variants, RNA binding protein affected by m6A associated variants, and miRNA targeting and processing affected by m6A-associated variants. The m6AVar database is freely available for academic researchers at: http://m6avar.renlab.org/

In this work, we performed a genome-wide analysis of genetic polymorphisms that influence protein phosphorylation in H. Sapiens.And we proposed that our results could be a useful resource for future disease diagnostics and provide basis for better and individualized. The PhosSNP 1.0 database is freely available for academic researchers at: http://phossnp.biocuckoo.org/

In this work, we report a visualization database called VirusMap for investigating the epidemiological and geographical distribution of influenza A viruses. The VirusMap database is freely available at: http://virusmap.renlab.org/

In this work, we have collected all experimental enzymes of the ubiquitin and ubiquitin-like conjugation systems from all the related literature of PubMed and predicted all the potential E3s or subunits of complex E3s in 70 species.The Ubiquitin and Ubiquitin-like Conjugation Database (UUCD) is the most integrative and comprehensive resource for users to systematically search for each enzyme and generate a integrative view of enzyme cascades in ubiquitin and ubiquitin-like conjugation systems. The UUCD database is freely available at: http://uucd.biocuckoo.org/

In this work, we have collected 347 protein phosphatase data from literatures, integrated and curated five protein kinase complements of H. sapiens, M. musculus, D. melanogaster, C. elegans and S. cerevisiae from KinBase with a total number of 1,855.Currently, the Eukaryotic Kinase and Phosphatase Database -- EKPD is the most comprehensive resource to get protein kinases and protein phosphatases information in eukaryotic organisms. The EKPD database is freely available at: http://epkm.biocuckoo.org/

Spermatogenesis, the sperm-generating process, is a complex process involving mitosis of spermatogonia, meiosis of spermatocytes and spermiogenesis of spermatids.In this study, the phosphoproteome in testis was greatly expanded and carefully analyzed. To share the results with the community, the database of pTestis was constructed. All the identified phosphorylation sites in this study were included in the database with detailed annotation from UniProt database. Furthermore, the testis phosphorylation sites from Huttlin et al. were also included. All the information was available in the pTestis database at http://ptestis.biocuckoo.org/

In this work, we develop a database of dbPPT 1.0 (database of Phospho-sites in PlanTs), which contains large-scale phosphorylation sites (p-sites) based on mass spectrometry across 20 plant species. Moreover, we also integrated other phosphorylation resource into this database including PhosPhAt (Durek et al., 2010) and P3DB (Yao et al., 2014). Currently, dbPPT contains 82,175 p-sites in 31,012 proteins for 20 plant species. The dbPPT database is freely available at: http://dbppt.biocuckoo.org/

Phosphorylation regulates a wide variety of biological processes, including signal transduction events. However, Previous studies about constructing database of prokaryotic phosphorylation sites negelect some unusual residues.To make up this shortage, we provide a comprehensive database of Prokaryotic Protein Phosphorylation Sites for 7 types of residues, including 7,391 phosphorylation sites in 3,750 proteins The dbPSP database is freely available at: http://dbpsp.biocuckoo.org/

The dbPAF (database of Phospho-sites in Animals and Fungi) is an online data resource specifically designed for protein phosphorylation in seven eukaryotic species, including H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature, we collected 294,370 non-redundant phosphorylation sites of 40,432 proteins. We also integrated known phosphorylation sites from a number of public databases.In total, dbPAF 1.0 contained 483,001 known phosphorylation sites of 54,148 protein substrates, as a comprehensive data resource for human, animals and fungi. The dbPAF database is freely available at: http://dbpaf.biocuckoo.org/

Ribosome profiling is a technique that provides genome wide information of translated mRNA based on deep sequencing of ribosome protected mRNA fragments (RPF). The current version of database contains 777 samples from 82 studies in eight species, processed and reanalyzed by a unified pipeline.To explore the rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. RPFdb is a comprehensive resource for hosting, analyzing and visualizing RPF data, available at: http://www.rpfdb.org/.

In this work, we have collected all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi and five animals.The database will be updated routinely as new microkits proteins are reported. The MiCroKit databaseis freely available at: http://microkit.biocuckoo.org/

CPLM (Compendium of Protein Lysine Modifications) is an online data resource specifically designed for protein lysine modifications (PLMs). The CPLM database was extended and adapted from our CPLA 1.0 (Compendium of Protein Lysine Acetylation) database (Liu et al., 2011), and the 2.0 release contains 203,972 modification events on 189,919 modified lysines in 45,748 proteins for 12 types of PLMs, including ubiquitination,methylation and etc. The CPLM database is freely available at: http://cplm.biocuckoo.org/