Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma
There are lots of studies attempting to identify the expression changes in oral squamous cell carcinoma. Most studies include insufficient samples to apply statistical methods for detecting significant gene sets. This study combined two small microarray datasets from a public database and identified...
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BioMed Central
2012-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-10-23.pdf |
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| author | Ki-Yeol Kim In-Ho Cha |
| author_facet | Ki-Yeol Kim In-Ho Cha |
| author_sort | Ki-Yeol Kim |
| collection | DOAJ |
| description | There are lots of studies attempting to identify the expression changes in oral squamous cell carcinoma. Most studies include insufficient samples to apply statistical methods for detecting significant gene sets. This study combined two small microarray datasets from a public database and identified significant genes associated with the progress of oral squamous cell carcinoma. There were different expression scales between the two datasets, even though these datasets were generated under the same platforms - Affymetrix U133A gene chips. We discretized gene expressions of the two datasets by adjusting the differences between the datasets for detecting the more reliable information. From the combination of the two datasets, we detected 51 significant genes that were upregulated in oral squamous cell carcinoma. Most of them were published in previous studies as cancer-related genes. From these selected genes, significant genetic pathways associated with expression changes were identified. By combining several datasets from the public database, sufficient samples can be obtained for detecting reliable information. Most of the selected genes were known as cancer-related genes, including oral squamous cell carcinoma. Several unknown genes can be biologically evaluated in further studies. |
| format | Article |
| id | doaj-art-4bc74cff0ce34eb698c95f763d24a810 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2012-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-4bc74cff0ce34eb698c95f763d24a8102025-02-02T20:27:29ZengBioMed CentralGenomics & Informatics1598-866X2234-07422012-03-01101233210.5808/GI.2012.10.1.2328Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell CarcinomaKi-Yeol Kim0In-Ho Cha1Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul 120-752, Korea.Oral Cancer Research Institute, College of Dentistry, Yonsei University, Seoul 120-752, Korea.There are lots of studies attempting to identify the expression changes in oral squamous cell carcinoma. Most studies include insufficient samples to apply statistical methods for detecting significant gene sets. This study combined two small microarray datasets from a public database and identified significant genes associated with the progress of oral squamous cell carcinoma. There were different expression scales between the two datasets, even though these datasets were generated under the same platforms - Affymetrix U133A gene chips. We discretized gene expressions of the two datasets by adjusting the differences between the datasets for detecting the more reliable information. From the combination of the two datasets, we detected 51 significant genes that were upregulated in oral squamous cell carcinoma. Most of them were published in previous studies as cancer-related genes. From these selected genes, significant genetic pathways associated with expression changes were identified. By combining several datasets from the public database, sufficient samples can be obtained for detecting reliable information. Most of the selected genes were known as cancer-related genes, including oral squamous cell carcinoma. Several unknown genes can be biologically evaluated in further studies.http://genominfo.org/upload/pdf/gni-10-23.pdfcombined datasetgenetic pathwayoral squamous cell carcinomapublic microarray databasesignificant gene |
| spellingShingle | Ki-Yeol Kim In-Ho Cha Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma Genomics & Informatics combined dataset genetic pathway oral squamous cell carcinoma public microarray database significant gene |
| title | Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma |
| title_full | Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma |
| title_fullStr | Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma |
| title_full_unstemmed | Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma |
| title_short | Possibility of the Use of Public Microarray Database for Identifying Significant Genes Associated with Oral Squamous Cell Carcinoma |
| title_sort | possibility of the use of public microarray database for identifying significant genes associated with oral squamous cell carcinoma |
| topic | combined dataset genetic pathway oral squamous cell carcinoma public microarray database significant gene |
| url | http://genominfo.org/upload/pdf/gni-10-23.pdf |
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