An open-access database of quantitative mRNA and protein profiles specifically for immune cells and tissues. The database currently contains: (i) quantitative mRNA profiles for human and mouse immune cells/tissues obtained using Affymetrix GeneChip technology; (ii) quantitative protein profiles for mouse immune cells obtained using two-dimensional gel electrophoresis (2-DE) followed by image analysis and mass spectrometry and (iii) various visualization tools to cross-reference the mRNA and protein profiles of immune cells.
A database designed to collect the published data regarding the nonspecific immunological effects of reagents (e.g., siRNAs, shRNAs, sh-miRs, and anti-miRs) observed in investigated cell lines and model organisms. RNAimmuno is also designed to be the comprehensive source of knowledge regarding different aspects of these immunological off-target effects. Currently, the database contains more than 2000 records, most of which describe the effects caused by various siRNA reagents.
Facilitates the reutilization of immune-related scRNA-seq datasets ready for analysis and visualization of reads at the single-cell level. JingleBells provides data of publicly available immune-related scRNA-seq datasets. It contains alignments between the reads to the relevant genome and conserved them in a uniform format, annotated for cell of origin. The database can help the user to estimate cell-specific preferences for splicing, mutation load, or alleles in a gene thank to the visualization of the reads aligned to this gene.
Supplies information about mutations reported in the F9 gene prior. FACTORIX is a repository that permits users to find data for all the sequence, structural and statistical information for the mutations. The online interface of this database allows researchers to submit new mutations and also to contribute to the genetic services provided.
Covers a set of about 1 000 previously identified human immunosuppression genes using text mining and manual curation. HisgAtlas supplies information about human immunosuppression genes and their related drugs and diseases. It was constructed thanks to a self-developed ontology-based bio-entity recognizer. This database gives an overview of human immunosuppression genes’ protein classes and their related biological pathways.
Allows users to investigate phenotype and genotype relationships in FXI gene (F11) mutations. FactorXI is an online database that includes several features for: (1) searching information; (2) obtaining information about mutation data; or (3) displaying patient data. It can be used to retrieve data on mutations for a specific codon number. This platform also provides an amino acid sequences map.
A freely available database on gene plasticity and electronic sorting for immune cells. Gene plasticity is defined as the extent of the change in a gene’s expression in response to various environmental or genetic influences.
This data repository bridges the gap between immunological and computer science/machine learning communities by providing preprocessed and scaled immunological data sets suitable for use in machine learning applications.
Gathers information about CHO protein impurities (CHOPs). CHOPPI provides a resource for assessing impurity risks related to CHOPs and their immunogenicity. The database provides an entry for each specific CHO or an entire subset of the CHO genome. Searches can be made by using the “CHOP query” mode which permits to select a specific protein or by the “genome filter” which allows filtering from a targeted CHO genome.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.
Dong Li Bioinformatics
Beijing Proteome Research Center