| Literature DB >> 26870179 |
Hongzhi Zhang1, Chuan Xu2, Ningyang Sun2, Yinting Zhou2, Xiaofei Yu1, Xue Yan2, Qiujuan Zhang2.
Abstract
The present study aimed to screen potential genes associated with pituitary adenomas to obtain further understanding with regard to the pathogenesis of pituitary adenomas. The microarray GSE23207 dataset, containing 16 pituitary adenoma samples from multiple endocrine neoplasia syndrome-associated rats and 5 normal pituitary tissue samples, was downloaded from Gene Expression Omnibus. The Linear Models for Microarray Data package was used to identify the differentially-expressed genes (DEGs) with the cut-off criteria of a |log2fold change (FC)|>1 and adjusted P-values of <0.05. The potential functions of the DEGs were predicted by functional and pathway enrichment analysis with the Database for Annotation, Visualization and Integrated Discovery. Furthermore, the interaction associations of the up- and downregulated DEGs obtained from the Search Tool for the Retrieval of Interacting Genes database were respectively revealed by the protein-protein interaction networks visualized with Cytoscape. A total of 391 upregulated and 238 downregulated DEGs in were screened in the pituitary adenoma samples. The upregulated DEGs with a higher degree in the protein-protein interaction network (e.g., CCNA2, CCNB1 and CDC20) were significantly involved in cell cycle and cell division. Notably, PTTG1 was enriched in every functional term. These DEGs interacted with each other. The downregulated DEGs (e.g., GABRA1, GABRA4 and GABRB1) also interacted with each other, and were relevant to neuroactive ligand-receptor interaction; the DEG POU1F1, interacting with POMC, was correlated with the development of the pituitary gland, adenohypophysis and endocrine system. Certain DEGs, including CCNB1, CCNA2, CDC20, GABRA1, GABRA4, GABRB1, POU1F1 and POMC, and particularly PTTG1, were shown to be closely involved in the pathogenesis of pituitary adenomas.Entities:
Keywords: differentially-expressed genes; pathway; pituitary adenomas; protein-protein interaction
Year: 2015 PMID: 26870179 PMCID: PMC4727179 DOI: 10.3892/ol.2015.3904
Source DB: PubMed Journal: Oncol Lett ISSN: 1792-1074 Impact factor: 2.967
Top two enriched GO biological process term clusters with the highest enrichment score for the upregulated differentially-expressed genes.
| Enrichment score | Term | Description | Count | P-value | Genes |
|---|---|---|---|---|---|
| 7.432 | GO:0007049 | Cell cycle | 31 | 1.08×10−12 | |
| GO:0022403 | Cell cycle phase | 23 | 1.10×10−12 | ||
| GO:0022402 | Cell cycle process | 27 | 3.26×10−12 | ||
| GO:0000279 | M phase | 19 | 3.09×10−11 | ||
| GO:0051301 | Cell division | 14 | 1.25×10−7 | ||
| GO:0000087 | M phase of mitotic cell cycle | 12 | 2.16×10−7 | ||
| GO:0000278 | Mitotic cell cycle | 16 | 5.40×10−7 | ||
| GO:0000280 | Nuclear division | 10 | 1.09×10−5 | ||
| GO:0007067 | Mitosis | 10 | 1.09×10−5 | ||
| GO:0048285 | Organelle fission | 10 | 1.74×10−5 | ||
| GO:0051439 | Regulation of ubiquitin-protein ligase activity during mitotic cell cycle | 4 | 4.86×10−2 | ||
| 5.335 | GO:0000279 | M phase | 19 | 3.09×10−11 | |
| GO:0051327 | M phase of meiotic cell cycle | 7 | 2.32×10−4 | ||
| GO:0007126 | Meiosis | 7 | 2.32×10−4 | ||
| GO:0051321 | Meiotic cell cycle | 7 | 2.76×10−4 |
GO, gene ontology.
Top two enriched GO biological process term clusters with the highest enrichment score for the downregulated differentially-expressed genes.
| Enrichment score | Term | Description | Count | P-value | Genes |
|---|---|---|---|---|---|
| 4.727 | GO:0006811 | Ion transport | 16 | 6.05×10−7 | |
| GO:0030001 | Metal ion transport | 12 | 3.87×10−6 | ||
| GO:0006812 | Cation transport | 12 | 2.54×10−5 | ||
| GO:0006813 | Potassium ion transport | 7 | 7.01×10−5 | ||
| GO:0015672 | Monovalent inorganic cation transport | 8 | 5.52×10−4 | ||
| 2.321 | GO:0040018 | Positive regulation of multicellular organism growth | 4 | 2.47×10−4 | |
| GO:0021983 | Pituitary gland development | 4 | 5.70×10−4 | ||
| GO:0021984 | Adenohypophysis development | 3 | 8.52×10−4 | ||
| GO:0021536 | Diencephalon development | 4 | 1.24×10−3 | ||
| GO:0043567 | Regulation of insulin-like growth factor receptor signaling pathway | 3 | 1.82×10−3 | ||
| GO:0040014 | Regulation of multicellular organism growth | 4 | 4.82×10−3 | ||
| GO:0035270 | Endocrine system development | 4 | 6.09×10−3 | ||
| GO:0030900 | Forebrain development | 5 | 9.58×10−3 | ||
| GO:0045927 | Positive regulation of growth | 4 | 9.75×10−3 | ||
| GO:0048732 | Gland development | 5 | 1.75×10−2 | ||
| GO:0045165 | Cell fate commitment | 4 | 3.22×10−2 | ||
| GO:0051240 | Positive regulation of multicellular organismal process | 5 | 3.49×10−2 | ||
| GO:0042127 | Regulation of cell proliferation | 8 | 4.55×10−2 |
GO, gene ontology.
Results of pathway enrichment analysis of the up- and downregulated differentially-expressed genes.
| Category | Term | Description | Count | P-value | Genes |
|---|---|---|---|---|---|
| Upregulated | rno04110 | Cell cycle | 14 | 5.01×10−7 | |
| rno04114 | Oocyte meiosis | 9 | 1.06×10−3 | ||
| rno00601 | Glycosphingolipid biosynthesis | 5 | 1.10×10−3 | ||
| rno04914 | Progesterone-mediated oocyte maturation | 8 | 1.15×10−3 | ||
| rno04062 | Chemokine signaling pathway | 9 | 1.46×10−2 | ||
| rno00330 | Arginine and proline metabolism | 5 | 1.70×10−2 | ||
| rno05219 | Bladder cancer | 4 | 2.94×10−2 | ||
| rno04115 | p53 signaling pathway | 5 | 3.48×10−2 | ||
| rno04610 | Complement and coagulation cascades | 5 | 4.19×10−2 | ||
| rno00510 | N-glycan biosynthesis | 4 | 4.89×10−2 | ||
| Downregulated | rno04080 | Neuroactive ligand-receptor interaction | 9 | 4.35×10−4 | |
| rno00410 | β-alanine metabolism | 3 | 1.05×10−2 | ||
| rno00340 | Histidine metabolism | 3 | 1.25×10−2 | ||
| rno00982 | Drug metabolism | 4 | 1.44×10−2 | ||
| rno00380 | Tryptophan metabolism | 3 | 3.75×10−2 | ||
| rno04020 | Calcium signaling pathway | 5 | 3.99×10−2 | ||
| rno00480 | Glutathione metabolism | 3 | 4.93×10−2 |
Figure 1.Protein-protein interaction network constructed with the upregulated differentially-expressed genes. Different shades of nodes colors represent the degree of up- or downregulation.
Figure 2.Protein-protein interaction network constructed with the downregulated differentially-expressed genes. Different shades of nodes colors represent the degree of up- or downregulation.
Upregulated DEGs with connection degrees of >30 and the downregulated DEGs with connection degrees of at least 3 in the protein-protein interaction networks.
| Category | Degree |
|---|---|
| Upregulated DEGs | |
| | 51 |
| | 47 |
| | 46 |
| | 44 |
| | 43 |
| | 42 |
| | 42 |
| | 42 |
| | 41 |
| | 41 |
| | 41 |
| | 41 |
| | 41 |
| | 41 |
| | 40 |
| | 40 |
| | 40 |
| | 40 |
| | 39 |
| | 38 |
| | 38 |
| | 38 |
| | 38 |
| | 37 |
| | 36 |
| | 36 |
| | 36 |
| | 35 |
| | 35 |
| | 34 |
| | 34 |
| | 33 |
| | 33 |
| | 32 |
| | 32 |
| Downregulated DEGs | |
| | 6 |
| | 5 |
| | 5 |
| | 4 |
| | 4 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
| | 3 |
DEGs, differentially-expressed genes.