publication . Article . Other literature type . 2018

Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor

Wang, Guang-Yu; Li, Ling; Liu, Bo; Han, Xiao; Wang, Chunhua; Wang, Jiwen;
Open Access English
  • Published: 01 Apr 2018 Journal: OncoTargets and therapy, volume 11, pages 1,849-1,859 (eissn: 1178-6930, Copyright policy)
  • Publisher: Dove Medical Press
Abstract
Guang-Yu Wang,1,* Ling Li,2,* Bo Liu,1 Xiao Han,1 Chun-Hua Wang,1 Ji-Wen Wang3 1Department of Neurosurgery, 2Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Jinan, Shandong, 3Department of Neurology, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Pudong New District, Shanghai, People’s Republic of China *These authors contributed equally to this work Purpose: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET). Materials and methods: Gene expression profile of GSE1429...
Subjects
free text keywords: OncoTargets and Therapy, Original Research, primitive neuroectodermal tumor, microarray analysis, protein-protein interaction, transcription factors, Supratentorial primitive neuroectodermal tumor, Differentially expressed genes, Pathway enrichment analysis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282, Pharmacology (medical), Oncology, Pathology, medicine.medical_specialty, medicine, Gene, Pathogenesis, business.industry, business
39 references, page 1 of 3

1. Jones DTW, Korshunov A, Pfister SM, Taylor MD, Northcott PA. Medulloblastoma and CNS primitive neuroectodermal tumors. In: Karajannis M, Zagzag D, editors. Molecular Pathology of Nervous System Tumors. Molecular Pathology Library, Vol 8. New York, NY: Springer; 2015:121-142.

2. Vermeulen JF, Hecke WV, Spliet WGM, et al. Pediatric primitive neuroectodermal tumors of the central nervous system differentially express granzyme inhibitors. PLoS One. 2016;11(3):e0151465.

3. Sturm D, Orr B, Toprak U, et al. New brain tumor entities emerge from molecular classification of CNS-PNETs. Cell. 2016;164(5): 1060-1072.

4. Miller S, Ward JH, Rogers HA, Lowe J, Grundy RG. Loss of INI1 protein expression denfies a subgroup of aggressive central nervous system primitive neuroectodermal tumors. Brain Pathol. 2012;23(1):19-27.

5. Koch A, Waha A, Tonn JC, et al. Somatic mutations of WNT/wingless signaling pathway components in primitive neuroectodermal tumors. Int J Cancer. 2001;93(3):445-449.

6. Phi JH, Kim JH, Eun KM, et al. Upregulation of SOX2, NOTCH1, and ID1 in supratentorial primitive neuroectodermal tumors: a distinct differentiation pattern from that of medulloblastomas. J Neurosurg Pediatr. 2010;5(6):608-614.

7. Rogers HA, Ward JH, Miller S, Lowe J, Coyle B, Grundy RG. The role of the WNT/β-catenin pathway in central nervous system primitive neuroectodermal tumours (CNS PNETs). Br J Cancer. 2013;108(10): 2130-2141. [OpenAIRE]

8. Li M, Lee KF, Lu Y, et al. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell. 2009;16(6):533-546.

9. Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res. 2013;41(Database issue):991-995.

10. Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.

11. Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc. 1995; 57(57):289-300.

12. Reiner-Benaim A. FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis. Biom J. 2007;49(1):107-126. [OpenAIRE]

13. Huang DW, Sherman BT, Tan Q, et al. DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007;35 (Web Server issue):169-175.

14. Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucl Acids Res. 2015;43(Database issue):447-452. [OpenAIRE]

15. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431-432. [OpenAIRE]

39 references, page 1 of 3
Abstract
Guang-Yu Wang,1,* Ling Li,2,* Bo Liu,1 Xiao Han,1 Chun-Hua Wang,1 Ji-Wen Wang3 1Department of Neurosurgery, 2Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Jinan, Shandong, 3Department of Neurology, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Pudong New District, Shanghai, People’s Republic of China *These authors contributed equally to this work Purpose: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET). Materials and methods: Gene expression profile of GSE1429...
Subjects
free text keywords: OncoTargets and Therapy, Original Research, primitive neuroectodermal tumor, microarray analysis, protein-protein interaction, transcription factors, Supratentorial primitive neuroectodermal tumor, Differentially expressed genes, Pathway enrichment analysis, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282, Pharmacology (medical), Oncology, Pathology, medicine.medical_specialty, medicine, Gene, Pathogenesis, business.industry, business
39 references, page 1 of 3

1. Jones DTW, Korshunov A, Pfister SM, Taylor MD, Northcott PA. Medulloblastoma and CNS primitive neuroectodermal tumors. In: Karajannis M, Zagzag D, editors. Molecular Pathology of Nervous System Tumors. Molecular Pathology Library, Vol 8. New York, NY: Springer; 2015:121-142.

2. Vermeulen JF, Hecke WV, Spliet WGM, et al. Pediatric primitive neuroectodermal tumors of the central nervous system differentially express granzyme inhibitors. PLoS One. 2016;11(3):e0151465.

3. Sturm D, Orr B, Toprak U, et al. New brain tumor entities emerge from molecular classification of CNS-PNETs. Cell. 2016;164(5): 1060-1072.

4. Miller S, Ward JH, Rogers HA, Lowe J, Grundy RG. Loss of INI1 protein expression denfies a subgroup of aggressive central nervous system primitive neuroectodermal tumors. Brain Pathol. 2012;23(1):19-27.

5. Koch A, Waha A, Tonn JC, et al. Somatic mutations of WNT/wingless signaling pathway components in primitive neuroectodermal tumors. Int J Cancer. 2001;93(3):445-449.

6. Phi JH, Kim JH, Eun KM, et al. Upregulation of SOX2, NOTCH1, and ID1 in supratentorial primitive neuroectodermal tumors: a distinct differentiation pattern from that of medulloblastomas. J Neurosurg Pediatr. 2010;5(6):608-614.

7. Rogers HA, Ward JH, Miller S, Lowe J, Coyle B, Grundy RG. The role of the WNT/β-catenin pathway in central nervous system primitive neuroectodermal tumours (CNS PNETs). Br J Cancer. 2013;108(10): 2130-2141. [OpenAIRE]

8. Li M, Lee KF, Lu Y, et al. Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. Cancer Cell. 2009;16(6):533-546.

9. Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res. 2013;41(Database issue):991-995.

10. Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.

11. Benjamini Y, Hochberg Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J R Stat Soc. 1995; 57(57):289-300.

12. Reiner-Benaim A. FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis. Biom J. 2007;49(1):107-126. [OpenAIRE]

13. Huang DW, Sherman BT, Tan Q, et al. DAVID bioinformatics resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 2007;35 (Web Server issue):169-175.

14. Szklarczyk D, Franceschini A, Wyder S, et al. STRING v10: proteinprotein interaction networks, integrated over the tree of life. Nucl Acids Res. 2015;43(Database issue):447-452. [OpenAIRE]

15. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431-432. [OpenAIRE]

39 references, page 1 of 3
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publication . Article . Other literature type . 2018

Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor

Wang, Guang-Yu; Li, Ling; Liu, Bo; Han, Xiao; Wang, Chunhua; Wang, Jiwen;