Continuing our series looking at recent publications citing products from QIAGEN Bioinformatics, today we recap several fascinating papers from customers who made use of Ingenuity® Pathway Analysis™ to understand the meaning of changes in gene expression.
Long-Term Mild, rather than Intense, Exercise Enhances Adult Hippocampal Neurogenesis and Greatly Changes the Transcriptomic Profile of the Hippocampus
First author: Koshiro Inoue
In this PLoS One publication, scientists from the University of Tsukuba and other institutes in Japan used rats to understand why mild exercise shows benefits to spatial memory while intense exercise does not. Focusing on a stress biomarker, they performed microarray analysis and found that mild exercise regulated more genes. IPA reported that genes influenced by mild exercise were mostly connected to lipid metabolism and protein synthesis, while intense exercise was linked to a negative effect on hippocampal neuroadaptation.
Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction
First author: Cielito Reyes-Gibby
MD Anderson Cancer Center scientists report in this BMC Systems Biology paper a study of the genetic basis for alcohol, smoking, and opioid addiction. Using IPA, they found candidate genes as well as common pathways; for example, ERK1/2 was connected in all of the addiction networks.
Targeting of multiple oncogenic signaling pathways by Hsp90 inhibitor alone or in combination with berberine for treatment of colorectal cancer
First author: Yen-Hao Su
Published in Biochimica et Biophysica Acta – Molecular Cell Research, this paper demonstrates the use of heat shock protein 90 inhibitors to treat colorectal cancer, also finding that herbal medicine berberine can improve drug sensitivity. A separate data supplement shows results from IPA that contributed to a global molecular network of the significant genes studied.
Macrophage Gene Expression Associated with Remodeling of the Prepartum Rat Cervix: Microarray and Pathway Analyses
First author: Abigail Dobyns
Scientists from Loma Linda University School of Medicine and the University of Edinburgh describe in this PLoS One paper a study of differences in cervical physiology between pregnant and nonpregnant rats. IPA was used to determine that changes in resident macrophages indicate networks of genes that are collectively up- or down-regulated prior to birth. Associated pathways were linked to wound healing and inflammation.
Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and response
First authors: Mark Jesus M. Magbanua, Denise M. Wolf, Christina Yau
Scientists from the University of California, San Francisco, published in Breast Cancer Research the results of a breast cancer transcriptome study designed to elucidate response to neoadjuvant chemotherapy. Gene expression data were analyzed with IPA to map genes to pathways and gene ontology groups, revealing that poor response was linked to lower expression of cell cycle inhibitors.
(1) Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing and (2) Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency
First authors: Marie Mutryn and Nan Zhou
This pair of papers from scientists at the University of Delaware and Maple Leaf Farms are both highly accessed publications in BMC Genomics. The first uses RNA-seq to study an emerging muscle disorder seen recently in chickens. IPA was used to interpret the 1,500 genes differentially expressed between affected and unaffected chickens and resulted in new leads about the biological mechanism behind the disorder. In the second paper, RNA-seq data was generated to help explain the differences between chickens with high or low feed efficiency. The team used IPA for functional and canonical pathways, molecule activity prediction, and analysis of upstream regulators.
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