Covers mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected The Cancer Genome Atlas (TCGA) tumor samples. LinkedOmics harbors multi-omics data and clinical data for mover than 30 cancer types and of over 11 000 patients from the TCGA project. This database is available on a platform that offers three data analysis modules: LinkFinder, LinkCompare, and LinkInterpreter.
Supplies a methodology for associating gene ontology (GO) terms with protein domains. GODomainMiner consists of a simple implementation of CODAC method, permitting users to mine associations from datasets that can be represented as tripartite graphs. This tool can be used to predict GO-domain associations between each of the 3 GO ontology namespaces (biological process (BP), cellular component (CC), and molecular function (MF)) and the Pfam, CATH, and SCOP domain classifications.
Provides complex network integrating metabolic reactions, gene regulation, and signaling processes. PD Map is a knowledge repository bringing together different molecular mechanisms and pathways considered to be the key players in the disease. This method allows navigation through information on Parkinson's disease (PD) associated mechanisms. It also constitutes an interface to well-established tools and methods for updating, enriching, and analysing its contents
Allows for visualization and analysis of samples in a 2D-map that emphasizes similarities between similar samples. MEREDITH is an omic integration method which is a hybrid of an early stage (concatenation-based) and intermediate stage (transformation-based) integration approach. This resource quantifies the contribution of each molecular data-type across the genome-wide dataset. It also detects known global pan-cancer clusters as well as within-tissue-of-origin clusters.
Integrates and visualizes genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. NaDH currently hosts collections of predicted protein coding sequences of 11 plant species, including two recently sequenced Nicotiana species, and their functional annotations, 222 microarray datasets from 10 different experiments, a transcriptomic atlas based on 20 RNA-seq expression profiles and a metabolomic atlas based on 895 metabolite spectra analyzed by mass spectrometry. It allows researchers to query phylogenetic trees of 16,305 gene families and provides tools for analyzing their evolutionary history.
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