Cluster and Principal Component Analysis of Human Glioblastoma Multiforme (GBM) Tumor Proteome

Mehdi  Pooladi; Mostafa Rezaei-Tavirani; Mehrdad Hashemi; Saeed Hesami-Tackallou; Solmaz Khaghani-Razi-Abad; Afshin Moradi; Ali Reza Zali; Masoumeh Mousavi; Leila  Firozi Dalvand; Azadeh Rakhshan; Mona Zamanian Azodi

International Journal of Cancer Management

The Official Journal of Cancer Research Center (CRC), Shahid Beheshti University of Medical Sciences

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Abstract
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Cluster and Principal Component Analysis of Human Glioblastoma Multiforme (GBM) Tumor Proteome

Author(s):

Mehdi Pooladi^1,*,

Mostafa Rezaei-Tavirani²,

Mehrdad Hashemi³,

Saeed Hesami-Tackallou⁴,

Solmaz Khaghani-Razi-Abad¹,

Afshin Moradi⁵,

Ali Reza Zali⁶,

Masoumeh Mousavi²,

Leila Firozi Dalvand⁷,

Azadeh Rakhshan⁵,

Mona Zamanian Azodi²

1Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Dept. of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran

2Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran

3Dept. Of Molecular Genetics, Tehran Medical Branch, Islamic Azad University Tehran, Iran

4Dept. of Biology, Garmsar Branch, Islamic Azad University, Garmsar, Iran

5Dept. Of Pathology, Shohada Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran

6Dept. of Neurosurgery, Shohada Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran

7Dept. of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran

International Journal of Cancer Management:Vol. 7, issue 2; e80525

Published online:Jun 30, 2014

Article type:Research Article

Received:Jan 27, 2014

Accepted:Apr 26, 2014

How to Cite:Pooladi M, Rezaei-Tavirani M, Hashemi M, Hesami-Tackallou S, Khaghani-Razi-Abad S, et al. Cluster and Principal Component Analysis of Human Glioblastoma Multiforme (GBM) Tumor Proteome.Int J Cancer Manag.2014;7(2):e80525.

Abstract

Background: Glioblastoma Multiforme (GBM) or grade IV astrocytoma is the most common and lethal adult malignant brain tumor. Several of the molecular alterations detected in gliomas may have diagnostic and/or prognostic implications. Proteomics has been widely applied in various areas of science, ranging from the deciphering of molecular pathogen nests of discuses.

Methods: In this study proteins were extracted from the tumor and normal brain tissues and then the protein purity was evaluated by Bradford test and spectrophotometry. In this study, proteins were separated by 2-Dimensional Gel (2DG) electrophoresis method and the spots were then analyzed and compared using statistical data and specific software. Protein clustering analysis was performed on the list of proteins deemed significantly altered in glioblastoma tumors (t-test and one-way ANOVA; P< 0.05).

Results: The 2D gel showed totally 876 spots. We reported, 172 spots were exhibited differently in expression level (fold > 2) for glioblastoma. On each analytical 2D gel, an average of 876 spots was observed. In this study, 188 spots exhibited up regulation of expression level, whereas the remaining 232 spots were decreased in glioblastoma tumor relative to normal tissue. Results demonstrate that functional clustering (up and down regulated) and Principal Component Analysis (PCA) has considerable merits in aiding the interpretation of proteomic data.

Conclusion: 2D gel electrophoresis is the core of proteomics which permitted the separation of thousands of proteins. High resolution 2DE can resolve up to 5,000 proteins simultaneously. Using cluster analysis, we can also form groups of related variables, similar to what is practiced in factor analysis.

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