Estimation of prognostic marker genes by public microarray data in patients with ovarian serous cystadenocarcinoma

San Duk Yang; Se Song Jang; Jeong A. Han; Hyun Seok Park; Jong Il Kim

doi:10.3349/ymj.2016.57.4.872

Estimation of prognostic marker genes by public microarray data in patients with ovarian serous cystadenocarcinoma

San Duk Yang, Se Song Jang, Jeong A. Han, Hyun Seok Park, Jong Il Kim

Department of Computer Science & Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

Purpose: Lymphatic invasion (LI) is regarded as a predictor of the aggressiveness of ovarian cancer (OC). However, LI is not always the major determinant of long-term patient survival. To establish proper diagnosis and treatment for OC, we analyzed differentially expressed genes (DEGs) for patients with serous epithelial OC, with or without LI, who did or did not survive for 5 years. Materials and Methods: Gene expression data from 63 patients with OC and LI, and 35 patients with OC but without LI, were investigated using an Affymetrix Human Genome U133 Array and analyzed using The Cancer Genome Atlas (TCGA) database. Among these 98 patients, 16 survived for 5 years or more. DEGs were identified using the Bioconductor R package, and their functions were analyzed using the DAVID web tool. Results: We found 55 significant DEGs (p<0.01) from the patients with LI and 20 highly significant DEGs (p<0.001) from those without it. Pathway analysis showed that DEGs associated with carbohydrate metabolism or with renal cell carcinoma pathways were enriched in the patients with and without LI, respectively. Using the top five prognostic marker genes, we generated survival scores that could be used to predict the 5-year survival of patients with OC without LI. Conclusion: The DEGs identified in this study could be used to elucidate the mechanism of tumor progression and to guide the prognosis and treatment of patients with serous OC but without LI.

Original language	English
Pages (from-to)	872-878
Number of pages	7
Journal	Yonsei Medical Journal
Volume	57
Issue number	4
DOIs	https://doi.org/10.3349/ymj.2016.57.4.872
State	Published - Jul 2016

Bibliographical note

Funding Information:
This study was supported by the Research Grant from Seoul National University Hospital (No. 04-2009-0780). This research was supported by a grant of the Korean Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI13C2148). The study resources were provided by TCGA.

Publisher Copyright:
© Yonsei University College of Medicine 2016.

Keywords

Gene expression
Microarray analysis
Ovarian cancer
Prognosis

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.3349/ymj.2016.57.4.872

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title = "Estimation of prognostic marker genes by public microarray data in patients with ovarian serous cystadenocarcinoma",

abstract = "Purpose: Lymphatic invasion (LI) is regarded as a predictor of the aggressiveness of ovarian cancer (OC). However, LI is not always the major determinant of long-term patient survival. To establish proper diagnosis and treatment for OC, we analyzed differentially expressed genes (DEGs) for patients with serous epithelial OC, with or without LI, who did or did not survive for 5 years. Materials and Methods: Gene expression data from 63 patients with OC and LI, and 35 patients with OC but without LI, were investigated using an Affymetrix Human Genome U133 Array and analyzed using The Cancer Genome Atlas (TCGA) database. Among these 98 patients, 16 survived for 5 years or more. DEGs were identified using the Bioconductor R package, and their functions were analyzed using the DAVID web tool. Results: We found 55 significant DEGs (p<0.01) from the patients with LI and 20 highly significant DEGs (p<0.001) from those without it. Pathway analysis showed that DEGs associated with carbohydrate metabolism or with renal cell carcinoma pathways were enriched in the patients with and without LI, respectively. Using the top five prognostic marker genes, we generated survival scores that could be used to predict the 5-year survival of patients with OC without LI. Conclusion: The DEGs identified in this study could be used to elucidate the mechanism of tumor progression and to guide the prognosis and treatment of patients with serous OC but without LI.",

keywords = "Gene expression, Microarray analysis, Ovarian cancer, Prognosis",

author = "Yang, {San Duk} and Jang, {Se Song} and Han, {Jeong A.} and Park, {Hyun Seok} and Kim, {Jong Il}",

note = "Funding Information: This study was supported by the Research Grant from Seoul National University Hospital (No. 04-2009-0780). This research was supported by a grant of the Korean Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI13C2148). The study resources were provided by TCGA. Publisher Copyright: {\textcopyright} Yonsei University College of Medicine 2016.",

year = "2016",

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doi = "10.3349/ymj.2016.57.4.872",

language = "English",

volume = "57",

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AU - Yang, San Duk

AU - Jang, Se Song

AU - Han, Jeong A.

AU - Park, Hyun Seok

AU - Kim, Jong Il

N1 - Funding Information: This study was supported by the Research Grant from Seoul National University Hospital (No. 04-2009-0780). This research was supported by a grant of the Korean Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (grant number: HI13C2148). The study resources were provided by TCGA. Publisher Copyright: © Yonsei University College of Medicine 2016.

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Y1 - 2016/7

N2 - Purpose: Lymphatic invasion (LI) is regarded as a predictor of the aggressiveness of ovarian cancer (OC). However, LI is not always the major determinant of long-term patient survival. To establish proper diagnosis and treatment for OC, we analyzed differentially expressed genes (DEGs) for patients with serous epithelial OC, with or without LI, who did or did not survive for 5 years. Materials and Methods: Gene expression data from 63 patients with OC and LI, and 35 patients with OC but without LI, were investigated using an Affymetrix Human Genome U133 Array and analyzed using The Cancer Genome Atlas (TCGA) database. Among these 98 patients, 16 survived for 5 years or more. DEGs were identified using the Bioconductor R package, and their functions were analyzed using the DAVID web tool. Results: We found 55 significant DEGs (p<0.01) from the patients with LI and 20 highly significant DEGs (p<0.001) from those without it. Pathway analysis showed that DEGs associated with carbohydrate metabolism or with renal cell carcinoma pathways were enriched in the patients with and without LI, respectively. Using the top five prognostic marker genes, we generated survival scores that could be used to predict the 5-year survival of patients with OC without LI. Conclusion: The DEGs identified in this study could be used to elucidate the mechanism of tumor progression and to guide the prognosis and treatment of patients with serous OC but without LI.

AB - Purpose: Lymphatic invasion (LI) is regarded as a predictor of the aggressiveness of ovarian cancer (OC). However, LI is not always the major determinant of long-term patient survival. To establish proper diagnosis and treatment for OC, we analyzed differentially expressed genes (DEGs) for patients with serous epithelial OC, with or without LI, who did or did not survive for 5 years. Materials and Methods: Gene expression data from 63 patients with OC and LI, and 35 patients with OC but without LI, were investigated using an Affymetrix Human Genome U133 Array and analyzed using The Cancer Genome Atlas (TCGA) database. Among these 98 patients, 16 survived for 5 years or more. DEGs were identified using the Bioconductor R package, and their functions were analyzed using the DAVID web tool. Results: We found 55 significant DEGs (p<0.01) from the patients with LI and 20 highly significant DEGs (p<0.001) from those without it. Pathway analysis showed that DEGs associated with carbohydrate metabolism or with renal cell carcinoma pathways were enriched in the patients with and without LI, respectively. Using the top five prognostic marker genes, we generated survival scores that could be used to predict the 5-year survival of patients with OC without LI. Conclusion: The DEGs identified in this study could be used to elucidate the mechanism of tumor progression and to guide the prognosis and treatment of patients with serous OC but without LI.

KW - Gene expression

KW - Microarray analysis

KW - Ovarian cancer

KW - Prognosis

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IS - 4

ER -

Estimation of prognostic marker genes by public microarray data in patients with ovarian serous cystadenocarcinoma

Abstract

Bibliographical note

Keywords

UN SDGs

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