GOMA: functional enrichment analysis tool based on GO modules

GOMA: functional enrichment analysis tool based on GO modules

Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel...

SciMiner: Web-based literature mining tool for target identification and functional enrichment analysis SciMiner: Web-based literature mining tool for target identification and functional enrichment analysis

Extracellular exosomes and preeclampsia: a microarray-based study and functional enrichment analysis

Background:  Preeclampsia (PE) is a heterogeneous pregnancy disease which the exact pathophysiology of it is unknown. Recently exosomes have been indicated as a causative factor in the pathogenesis of PE. The aim of the study was to investigate in microarray library data to extract the differentially expressed genes (DEGs) in PE and to perform a functional enrichment analysis to predict the rol...

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis

UNLABELLED SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multi...

Identifying functional miRNA-mRNA modules based on hypergraph-based learning

1 Background and problem Analyzing functional relationships between microRNAs (miRNAs) and mRNAs is an important issue in biological process because it can give new insights into the pathogenesis mechanism of complex diseases including various cancers. Especially, miRNAs emerge recently as one of crucial molecules in post-transcriptional regulation and play critical roles in diverse processes s...