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To interpret these lists of genes, common steps in a functional gene set analysis include the search for enrichment patterns [for a review, see (Abatangelo et al., 2009)], e.g. to identify significant signalling pathways or protein domains, and text mining in the literature [see review by (Krallinger et al., 2008)].
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Only significant signaling pathways are listed.
Further, an investigation was carried out in statistically significant signaling pathways regulated by selected miRNAs.
EGF signaling and PDGF signaling were the top two significant signaling pathways identified in high fertiliy spermatozoa.
Generally, there were 12 significant genes with dynamic regulation patterns during aging in above five truly significant signaling pathways.
Data sets were analyzed using GeneSpring GX 11.0 software for gene expression, clustering, gene ontology, and significant signaling pathways.
Importantly, we also tested whether other developmentally significant signaling pathways were similarly perturbed by changes in the dose of iRhom.
The objective of this study is to discover significant signal pathways or pathway networks from pituitary adenoma protein-mapping data, comparative proteomic data, and nitroproteomic data.
The main significant signaling pathways (p < 0.05) were related to G-protein couple receptor, hypoxia, NF-κB, VEGFα and IL6, IL10, apoptosis and leukocyte extravasation signaling.
The DEP data also clearly reveal the significant signaling pathways that include mitochondrial dysfunction, oxidative phosphorylation, and oxidative-stress response in a human pituitary adenoma.
As shown in Additional file 9: Table S6, the significant signaling pathways included steroid biosynthesis, oxidative phosphorylation, basal transcription factors, and the transcription machinery.
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