MPEA—metabolite pathway enrichment analysis
نویسندگان
چکیده
منابع مشابه
Pathway Enrichment Analysis with Networks
Detecting associations between an input gene set and annotated gene sets (e.g., pathways) is an important problem in modern molecular biology. In this paper, we propose two algorithms, termed NetPEA and NetPEA', for conducting network-based pathway enrichment analysis. Our algorithms consider not only shared genes but also gene-gene interactions. Both algorithms utilize a protein-protein intera...
متن کاملCentrality-based Pathway Enrichment
Gene set enrichment analysis is broadly used in microarray data analysis [8, 5]. It aimes to find which biological functions are affected by a group of related genes behind the massive information. The most used methotology is finding these significant gene set from a 2 × 2 contingency table, usually by Fisher’s exact test or chi-square test. This kind of analysis is known as Over-represented A...
متن کاملSEAS: A System for SEED-Based Pathway Enrichment Analysis
Pathway enrichment analysis represents a key technique for analyzing high-throughput omic data, and it can help to link individual genes or proteins found to be differentially expressed under specific conditions to well-understood biological pathways. We present here a computational tool, SEAS, for pathway enrichment analysis over a given set of genes in a specified organism against the pathway...
متن کاملNetwork-based pathway enrichment analysis with incomplete network information
MOTIVATION Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of changes in cellular activity in response to treatments and/or in disease states. Methods that use existing pathway network information have been s...
متن کاملpathDIP: an annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis
Molecular pathway data are essential in current computational and systems biology research. While there are many primary and integrated pathway databases, several challenges remain, including low proteome coverage (57%), low overlap across different databases, unavailability of direct information about underlying physical connectivity of pathway members, and high fraction of protein-coding gene...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2011
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/btr278