Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Oncology Letters
      • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Biomedical Reports
      • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • Information for Authors
    • Information for Reviewers
    • Information for Librarians
    • Information for Advertisers
    • Conferences
  • Language Editing
Spandidos Publications Logo
  • About
    • About Spandidos
    • Aims and Scopes
    • Abstracting and Indexing
    • Editorial Policies
    • Reprints and Permissions
    • Job Opportunities
    • Terms and Conditions
    • Contact
  • Journals
    • All Journals
    • Biomedical Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Experimental and Therapeutic Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Epigenetics
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Functional Nutrition
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Molecular Medicine
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • International Journal of Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Medicine International
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular and Clinical Oncology
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Molecular Medicine Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Letters
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • Oncology Reports
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
    • World Academy of Sciences Journal
      • Information for Authors
      • Editorial Policies
      • Editorial Board
      • Aims and Scope
      • Abstracting and Indexing
      • Bibliographic Information
      • Archive
  • Articles
  • Information
    • For Authors
    • For Reviewers
    • For Librarians
    • For Advertisers
    • Conferences
  • Language Editing
Login Register Submit
  • This site uses cookies
  • You can change your cookie settings at any time by following the instructions in our Cookie Policy. To find out more, you may read our Privacy Policy.

    I agree
Search articles by DOI, keyword, author or affiliation
Search
Advanced Search
presentation
Molecular Medicine Reports
Join Editorial Board Propose a Special Issue
Print ISSN: 1791-2997 Online ISSN: 1791-3004
Journal Cover
March-2018 Volume 17 Issue 3

Full Size Image

Sign up for eToc alerts
Recommend to Library

Journals

International Journal of Molecular Medicine

International Journal of Molecular Medicine

International Journal of Molecular Medicine is an international journal devoted to molecular mechanisms of human disease.

International Journal of Oncology

International Journal of Oncology

International Journal of Oncology is an international journal devoted to oncology research and cancer treatment.

Molecular Medicine Reports

Molecular Medicine Reports

Covers molecular medicine topics such as pharmacology, pathology, genetics, neuroscience, infectious diseases, molecular cardiology, and molecular surgery.

Oncology Reports

Oncology Reports

Oncology Reports is an international journal devoted to fundamental and applied research in Oncology.

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine

Experimental and Therapeutic Medicine is an international journal devoted to laboratory and clinical medicine.

Oncology Letters

Oncology Letters

Oncology Letters is an international journal devoted to Experimental and Clinical Oncology.

Biomedical Reports

Biomedical Reports

Explores a wide range of biological and medical fields, including pharmacology, genetics, microbiology, neuroscience, and molecular cardiology.

Molecular and Clinical Oncology

Molecular and Clinical Oncology

International journal addressing all aspects of oncology research, from tumorigenesis and oncogenes to chemotherapy and metastasis.

World Academy of Sciences Journal

World Academy of Sciences Journal

Multidisciplinary open-access journal spanning biochemistry, genetics, neuroscience, environmental health, and synthetic biology.

International Journal of Functional Nutrition

International Journal of Functional Nutrition

Open-access journal combining biochemistry, pharmacology, immunology, and genetics to advance health through functional nutrition.

International Journal of Epigenetics

International Journal of Epigenetics

Publishes open-access research on using epigenetics to advance understanding and treatment of human disease.

Medicine International

Medicine International

An International Open Access Journal Devoted to General Medicine.

Journal Cover
March-2018 Volume 17 Issue 3

Full Size Image

Sign up for eToc alerts
Recommend to Library

  • Article
  • Citations
    • Cite This Article
    • Download Citation
    • Create Citation Alert
    • Remove Citation Alert
    • Cited By
  • Similar Articles
    • Related Articles (in Spandidos Publications)
    • Similar Articles (Google Scholar)
    • Similar Articles (PubMed)
  • Download PDF
  • Download XML
  • View XML
Article Open Access

Bioinformatic analysis of gene expression profiling of intracranial aneurysm

  • Authors:
    • Lijuan Bo
    • Bo Wei
    • Zhanfeng Wang
    • Chaohui Li
    • Zheng Gao
    • Zhuang Miao
  • View Affiliations / Copyright

    Affiliations: Department of Infection, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China, Department of Neurosurgery, Dandong First Hospital, Dandong, Liaoning 118000, P.R. China
    Copyright: © Bo et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 3473-3480
    |
    Published online on: December 29, 2017
       https://doi.org/10.3892/mmr.2017.8367
  • Expand metrics +
Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )
Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )
Cited By (CrossRef): 0 citations Loading Articles...

This article is mentioned in:



Abstract

Intracranial aneurysm (IA) is a severe clinical condition of primary concern and currently, there is no effective therapeutic reagent. The present study aimed to investigate the molecular mechanism of IA via bioinformatic analysis. Various gene expression profiles (GSE26969) were downloaded from the Gene Expression Omnibus database, including 3 IA and 3 normal superficial temporal artery samples. Firstly, the limma package in R language was used to identify differentially expressed genes (DEGs; P‑value <0.01 and |log2 FC|≥1). Secondly, the database for annotation, visualization and integrated discovery software was utilized to perform pathway and functional enrichment analyses (false discovery rate ≤0.05). Finally, protein‑protein interaction (PPI) network and sub‑network clustering analyses were performed using the biomolecular interaction network database and ClusterONE software, respectively. Following this, a transcription factor regulatory network was identified from the PPI network. A total of 1,124 DEGs were identified, of which 989 were upregulated and 135 downregulated. Pathway and functional enrichment analyses revealed that the DEGs primarily participated in RNA splicing, functioning of the spliceosome, RNA processing and the mRNA metabolic process. Following PPI network analysis, 1 hepatocyte nuclear factor (HNF) 4A (transcription factor)‑centered regulatory network and 5 DEG‑centered sub‑networks were identified. On analysis of the transcription factor regulatory network, 6 transcription factors (HNF6, HNF4A, E2F4, YY1, H4 and H31T) and a regulatory pathway (HNF6‑HNF4‑E2F4) were identified. The results of the present study suggest that activating transcription factor‑5, Jun proto‑oncogene, activator protein‑1 transcription factor subunit, HNF6, HNF4 and E2F4 may participate in IA progression via vascular smooth muscle cell apoptosis, inflammation, vessel wall remodeling and damage and the tumor necrosis factor‑β signaling pathway. However, further experimental studies are required to validate these predictions.
View Figures

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

View References

1 

Alg VS, Sofat R, Houlden H and Werring DJ: Genetic risk factors for intracranial aneurysms: A meta-analysis in more than 116,000 individuals. Neurology. 80:2154–2165. 2013. View Article : Google Scholar : PubMed/NCBI

2 

Bakke SJ and Lindegaard KF: Subarachnoid haemorrhage-diagnosis and management. Tidsskr Nor Laegeforen. 127:1074–1078. 2007.(In Norwegian). PubMed/NCBI

3 

Li L, Yang X, Jiang F, Dusting GJ and Wu Z: Transcriptome-wide characterization of gene expression associated with unruptured intracranial aneurysms. Eur Neurol. 62:330–337. 2009. View Article : Google Scholar : PubMed/NCBI

4 

Pera J, Korostynski M, Krzyszkowski T, Czopek J, Slowik A, Dziedzic T, Piechota M, Stachura K, Moskala M, Przewlocki R and Szczudlik A: Gene expression profiles in human ruptured and unruptured intracranial aneurysms: What is the role of inflammation? Stroke. 41:224–231. 2010. View Article : Google Scholar : PubMed/NCBI

5 

Kurki MI, Hakkinen SK, Frosen J, Tulamo R, von und zu Fraunberg M, Wong G, Tromp G, Niemelä M, Hernesniemi J, Jääskeläinen JE and Ylä-Herttuala S: Upregulated signaling pathways in ruptured human saccular intracranial aneurysm wall: An emerging regulative role of Toll-like receptor signaling and nuclear factor-κB, hypoxia-inducible factor-1A and ETS transcription factors. Neurosurgery. 68:1666–1675. 2011. View Article : Google Scholar

6 

Yagi K, Tada Y, Kitazato KT, Tamura T, Satomi J and Nagahiro S: Ibudilast inhibits cerebral aneurysms by down-regulating inflammation-related molecules in the vascular wall of rats. Neurosurgery. 66:551–559. 2010. View Article : Google Scholar : PubMed/NCBI

7 

Aoki T, Kataoka H, Nishimura M, Ishibashi R, Morishita R and Miyamoto S: Ets-1 promotes the progression of cerebral aneurysm by inducing the expression of MCP-1 in vascular smooth muscle cells. Gene Ther. 17:1117–1123. 2010. View Article : Google Scholar : PubMed/NCBI

8 

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U and Speed TP: Exploration, normalization and summaries of high density oligonucleotide array probe level data. Biostatistics. 4:249–264. 2003. View Article : Google Scholar : PubMed/NCBI

9 

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 5:R802004. View Article : Google Scholar : PubMed/NCBI

10 

Reiner A, Yekutieli D and Benjamini Y: Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 19:368–375. 2003. View Article : Google Scholar : PubMed/NCBI

11 

Kolde R: Pheatmap: Pretty heatmaps. R package version 0.6. 1:2012.

12 

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al: Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25–29. 2000. View Article : Google Scholar : PubMed/NCBI

13 

Kanehisa M and Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27–30. 2000. View Article : Google Scholar : PubMed/NCBI

14 

Huang da W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar : PubMed/NCBI

15 

Bader GD, Betel D and Hogue CW: BIND: The biomolecular interaction network database. Nucleic Acids Res. 31:248–250. 2003. View Article : Google Scholar : PubMed/NCBI

16 

Nepusz T, Yu H and Paccanaro A: Detecting overlapping protein complexes in protein-protein interaction networks. Nat Methods. 9:471–472. 2012. View Article : Google Scholar : PubMed/NCBI

17 

Greene LA, Lee HY and Angelastro JM: The transcription factor ATF5: Role in neurodevelopment and neural tumors. J Neurochem. 108:11–22. 2009. View Article : Google Scholar : PubMed/NCBI

18 

Schoenen H, Huber A, Sonda N, Zimmermann S, Jantsch J, Lepenies B, Bronte V and Lang R: Differential control of mincle-dependent cord factor recognition and macrophage responses by the transcription factors C/EBPβ and HIF1α. J Immunol. 2014. View Article : Google Scholar : PubMed/NCBI

19 

Chalouhi N, Ali MS, Jabbour PM, Tjoumakaris SI, Gonzalez LF, Rosenwasser RH, Koch WJ and Dumont AS: Biology of intracranial aneurysms: Role of inflammation. J Cereb Blood Flow Metab. 32:1659–1676. 2012. View Article : Google Scholar : PubMed/NCBI

20 

Wisdom R, Johnson RS and Moore C: c-Jun regulates cell cycle progression and apoptosis by distinct mechanisms. EMBO J. 18:188–197. 1999. View Article : Google Scholar : PubMed/NCBI

21 

Brenner DA, O'Hara M, Angel P, Chojkier M and Karin M: Prolonged activation of jun and collagenase genes by tumour necrosis factor-alpha. Nature. 337:661–663. 1989. View Article : Google Scholar : PubMed/NCBI

22 

Polavarapu R, Gongora MC, Winkles JA and Yepes M: Tumor necrosis factor-like weak inducer of apoptosis increases the permeability of the neurovascular unit through nuclear factor-kappa B pathway activation. J Neurosci. 25:10094–10100. 2005. View Article : Google Scholar : PubMed/NCBI

23 

Thomson EM, Williams A, Yauk CL and Vincent R: Overexpression of tumor necrosis factor-α in the lungs alters immune response, matrix remodeling and repair and maintenance pathways. Am J Pathol. 180:1413–1430. 2012. View Article : Google Scholar : PubMed/NCBI

24 

Moriwaki T, Takagi Y, Sadamasa N, Aoki T, Nozaki K and Hashimoto N: Impaired progression of cerebral aneurysms in interleukin-1beta-deficient mice. Stroke. 37:900–905. 2006. View Article : Google Scholar : PubMed/NCBI

25 

Wang K and Holterman AX: Pathophysiologic role of hepatocyte nuclear factor 6. Cell Signal. 24:9–16. 2012. View Article : Google Scholar : PubMed/NCBI

26 

Jayaraman T, Paget A, Shin YS, Li X, Mayer J, Chaudhry H, Niimi Y, Silane M and Berenstein A: TNF-alpha-mediated inflammation in cerebral aneurysms: A potential link to growth and rupture. Vasc Health Risk Manag. 4:805–817. 2008. View Article : Google Scholar : PubMed/NCBI

27 

Frösen J, Tulamo R, Heikura T, Sammalkorpi S, Niemelä M, Hernesniemi J, Levonen AL, Hörkkö S and Ylä-Herttuala S: Lipid accumulation, lipid oxidation and low plasma levels of acquired antibodies against oxidized lipids associate with degeneration and rupture of the intracranial aneurysm wall. Acta Neuropathol Commun. 1:712013. View Article : Google Scholar : PubMed/NCBI

28 

Ruigrok YM, Tan S, Medic J, Rinkel GJ and Wijmenga C: Genes involved in the transforming growth factor beta signalling pathway and the risk of intracranial aneurysms. J Neurol Neurosurg Psychiatry. 79:722–724. 2008. View Article : Google Scholar : PubMed/NCBI

29 

Tan F, Morris PW, Skidgel RA and Erdos EG: Sequencing and cloning of human prolylcarboxypeptidase (angiotensinase C). Similarity to both serine carboxypeptidase and prolylendopeptidase families. J Biol Chem. 268:16631–16638. 1993.PubMed/NCBI

30 

Shoja MM, Agutter PS, Tubbs RS, Payner TD, Ghabili K and Cohen-Gadol AA: The role of the renin-angiotensin system in the pathogenesis of intracranial aneurysms. J Renin Angiotensin Aldosterone Syst. 12:262–273. 2011. View Article : Google Scholar : PubMed/NCBI

31 

Dutton A, Young LS and Murray PG: The role of cellular FLICE inhibitory protein (c-FLIP) in the pathogenesis and treatment of cancer. Expert Opin Ther Targets. 10:27–35. 2006. View Article : Google Scholar : PubMed/NCBI

32 

Aoki T, Kataoka H, Morimoto M, Nozaki K and Hashimoto N: Macrophage-derived matrix metalloproteinase-2 and −9 promote the progression of cerebral aneurysms in rats. Stroke. 38:162–169. 2007. View Article : Google Scholar : PubMed/NCBI

Related Articles

  • Abstract
  • View
  • Download
  • Twitter
Copy and paste a formatted citation
Spandidos Publications style
Bo L, Wei B, Wang Z, Li C, Gao Z and Miao Z: Bioinformatic analysis of gene expression profiling of intracranial aneurysm. Mol Med Rep 17: 3473-3480, 2018.
APA
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., & Miao, Z. (2018). Bioinformatic analysis of gene expression profiling of intracranial aneurysm. Molecular Medicine Reports, 17, 3473-3480. https://doi.org/10.3892/mmr.2017.8367
MLA
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., Miao, Z."Bioinformatic analysis of gene expression profiling of intracranial aneurysm". Molecular Medicine Reports 17.3 (2018): 3473-3480.
Chicago
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., Miao, Z."Bioinformatic analysis of gene expression profiling of intracranial aneurysm". Molecular Medicine Reports 17, no. 3 (2018): 3473-3480. https://doi.org/10.3892/mmr.2017.8367
Copy and paste a formatted citation
x
Spandidos Publications style
Bo L, Wei B, Wang Z, Li C, Gao Z and Miao Z: Bioinformatic analysis of gene expression profiling of intracranial aneurysm. Mol Med Rep 17: 3473-3480, 2018.
APA
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., & Miao, Z. (2018). Bioinformatic analysis of gene expression profiling of intracranial aneurysm. Molecular Medicine Reports, 17, 3473-3480. https://doi.org/10.3892/mmr.2017.8367
MLA
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., Miao, Z."Bioinformatic analysis of gene expression profiling of intracranial aneurysm". Molecular Medicine Reports 17.3 (2018): 3473-3480.
Chicago
Bo, L., Wei, B., Wang, Z., Li, C., Gao, Z., Miao, Z."Bioinformatic analysis of gene expression profiling of intracranial aneurysm". Molecular Medicine Reports 17, no. 3 (2018): 3473-3480. https://doi.org/10.3892/mmr.2017.8367
Follow us
  • Twitter
  • LinkedIn
  • Facebook
About
  • Spandidos Publications
  • Careers
  • Cookie Policy
  • Privacy Policy
How can we help?
  • Help
  • Live Chat
  • Contact
  • Email to our Support Team