Chemical Similarity Enrichment analysis of metabolomics datasets. Assuming a statistical independence among metabolites is incorrect for metabolomics datasets because of the existence of 1) metabolic pathways 2) same origin 3) genetic regulation of metabolism and 4) chemical similarity among metabolites. The...
ChemRICH utilizes structure similarity and chemical ontologies to map all known metabolites and name metabolic modules. Unlike pathway mapping, this strategy yields study-specific, non-overlapping sets of all identified metabolites. Subsequent enrichment statistics is superior to pathway enrichments because ...
Overall, it should be clear that while many attempts have been made to create chemical taxonomies or ontologies, many are proprietary or “closed source”, most require manual analysis or annotation, most are limited in scope and many do not provide meaningful names, definitions or descriptors. T...
we first assessed the profiling similarity among different compounds. In Fig.5a, we calculated the PCC within a group of sensitive compounds (denoted as Sensitive), as well as the PCC between sensitive and resistant compounds (denoted as Sensitive...
Identification and enrichment analysis of DEGs First, to determine the consistency of the repeats, we performed intersample principal component analysis (PCA) (Fig. 3), and the results revealed high similarity between the wild-type and grafted repeats, which ensured the robustness and reliability of...
This was done by assigning one or more synonyms to each ChemOnt category, and specifying the corresponding level or scope of term similarity. For any ChemOnt term, a synonym can have the identical meaning (exact scope), a more specific meaning (narrow scope), or a less specific meaning (...
extending the concept of chemical similarity to similarity between bioactivity signatures. We show how CC signatures can aid drug discovery tasks, including target identification and library characterization. We also demonstrate the discovery of compounds that reverse and mimic biological signatures of diseas...
Highly significant chemical prediction p-values for the prostate, lung, and breast cancer datasets (p = 0.001, 0.001, 0.01, for the prostate, lung, and breast cancer datasets) are reordered by their BioActivity similarity computed by PubChem. A column represents the cancer analyzed and each ...
The resulting cosine similarity heatmap (Supplementary Fig. 6g) shows that most cell lines from the same tissue exhibit higher similarity in the latent space compared to those from different tissues. Human cancer cell lines have facilitated drug discoveries in cancer biology, but they are neither ...
In purple, we report ROC analysis of KEGG functional enrichment without accounting for operon structure. D) Each corresponds to a KEGG metabolic pathway and the respective AUC values estimated from gene-gene similarity. Only KEGG pathways with an AUC ≥ 0.6 are reported. Source data Extended...