dbDEPC 2.0: updated database of differentially expressed proteins in human cancers.

A large amount of differentially expressed proteins (DEPs) have been identified in various cancer proteomics experiments, curation and annotation of these proteins are important in deciphering their roles in oncogenesis and tumor progression, and may further help to discover potential protein biomarkers for clinical applications. In 2009, we published the first database of DEPs in human cancers (dbDEPCs). In this updated version of 2011, dbDEPC 2.0 has more than doubly expanded to over 4000 protein entries, curated from 331 experiments across 20 types of human cancers. This resource allows researchers to search whether their interested proteins have been reported changing in certain cancers, to compare their own proteomic discovery with previous studies, to picture selected protein expression heatmap across multiple cancers and to relate protein expression changes with aberrance in other genetic level. New important developments include addition of experiment design information, advanced filter tools for customer-specified analysis and a network analysis tool. We expect dbDEPC 2.0 to be a much more powerful tool than it was in its first release and can serve as reference to both proteomics and cancer researchers. dbDEPC 2.0 is available at http://lifecenter.sgst.cn/dbdepc/index.do.

SAS: A Platform of Spike Antigenicity for SARS-CoV-2.

Since the outbreak of SARS-CoV-2, antigenicity concerns continue to linger with emerging mutants. As recent variants have shown decreased reactivity to previously determined monoclonal antibodies (mAbs) or sera, monitoring the antigenicity change of circulating mutants is urgently needed for vaccine effectiveness. Currently, antigenic comparison is mainly carried out by immuno-binding assays. Yet, an online predicting system is highly desirable to complement the targeted experimental tests from the perspective of time and cost. Here, we provided a platform of SAS (Spike protein Antigenicity for SARS-CoV-2), enabling predicting the resistant effect of emerging variants and the dynamic coverage of SARS-CoV-2 antibodies among circulating strains. When being compared to experimental results, SAS prediction obtained the consistency of 100% on 8 mAb-binding tests with detailed epitope covering mutational sites, and 80.3% on 223 anti-serum tests. Moreover, on the latest South Africa escaping strain (B.1.351), SAS predicted a significant resistance to reference strain at multiple mutated epitopes, agreeing well with the vaccine evaluation results. SAS enables auto-updating from GISAID, and the current version collects 867K GISAID strains, 15.4K unique spike (S) variants, and 28 validated and predicted epitope regions that include 339 antigenic sites. Together with the targeted immune-binding experiments, SAS may be helpful to reduce the experimental searching space, indicate the emergence and expansion of antigenic variants, and suggest the dynamic coverage of representative mAbs/vaccines among the latest circulating strains. SAS can be accessed at https://www.biosino.org/sas.

Putative Familial Transmissible Bacteria of Various Body Niches Link with Home Environment and Children's Immune Health.

Owing to their significant impact on children's long-term health, familial factors in the microbiomes of children have attracted increasing attention. However, the mechanism underlying microbiome transmission across generations remains unclear. A significantly lower alpha diversity was observed in the gut flora of children than in the gut flora of parents and grandparents; the alpha diversity of oral and skin microbiota was relatively higher in children than in their predecessors. Gut, oral, and skin microbiome was more similar between family members than between unrelated individuals. Meanwhile, 55.05%, 61.09%, and 76.73% of amplicon sequence variants (ASVs) in children's gut, oral, and skin microbiomes, respectively, were transmitted from all family members. Among these, the most transmissible ASVs belonged to Methylophilaceae, Solimonadaceae, Neisseriaceae, and Burkholderiaceae, which were defined as "putative familial transmissible bacteria." Furthermore, we found that the time spent with parents/grandparents and children's dietary preferences were important factors that influenced the proportion of the transmissible microbiome. Moreover, the majority of transmissible ASVs (85.06%), especially those of Ruminococcaceae and Lachnospiraceae, were significantly associated with the immune indices, such as CD3+, CD4+, CD8+, IgG, and IgA. IMPORTANCE Our study revealed that the children's microbiota was partially transmitted from their family members and specific putative transmissible ASVs were associated with the immune system of children. These findings suggest that home life plays a key role in the shaping of young children's microbiomes and has long-term health benefits.

SysPTM 2.0: an updated systematic resource for post-translational modification.

Post-translational modifications (PTMs) of proteins play essential roles in almost all cellular processes, and are closely related to physiological activity and disease development of living organisms. The development of tandem mass spectrometry (MS/MS) has resulted in a rapid increase of PTMs identified on proteins from different species. The collection and systematic ordering of PTM data should provide invaluable information for understanding cellular processes and signaling pathways regulated by PTMs. For this original purpose we developed SysPTM, a systematic resource installed with comprehensive PTM data and a suite of web tools for annotation of PTMs in 2009. Four years later, there has been a significant advance with the generation of PTM data and, consequently, more sophisticated analysis requirements have to be met. Here we submit an updated version of SysPTM 2.0 (http://lifecenter.sgst.cn/SysPTM/), with almost doubled data content, enhanced web-based analysis tools of PTMBlast, PTMPathway, PTMPhylog, PTMCluster. Moreover, a new session SysPTM-H is constructed to graphically represent the combinatorial histone PTMs and dynamic regulation of histone modifying enzymes, and a new tool PTMGO is added for functional annotation and enrichment analysis. SysPTM 2.0 not only facilitates resourceful annotation of PTM sites but allows systematic investigation of PTM functions by the user. Database URL: http://lifecenter.sgst.cn/SysPTM/.