Classification of Genes Based on Age-Related Differential Expression in Breast Cancer
Transcriptome analysis has been widely used to make biomarker panels to diagnose cancers. In breast cancer, the age of the patient has been known to be associated with clinical features. As clinical transcriptome data have accumulated significantly, we classified all human genes based on age-specifi...
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BioMed Central
2017-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2017-15-4-156.pdf |
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| author | Gunhee Lee Minho Lee |
| author_facet | Gunhee Lee Minho Lee |
| author_sort | Gunhee Lee |
| collection | DOAJ |
| description | Transcriptome analysis has been widely used to make biomarker panels to diagnose cancers. In breast cancer, the age of the patient has been known to be associated with clinical features. As clinical transcriptome data have accumulated significantly, we classified all human genes based on age-specific differential expression between normal and breast cancer cells using public data. We retrieved the values for gene expression levels in breast cancer and matched normal cells from The Cancer Genome Atlas. We divided genes into two classes by paired t test without considering age in the first classification. We carried out a secondary classification of genes for each class into eight groups, based on the patterns of the p-values, which were calculated for each of the three age groups we defined. Through this two-step classification, gene expression was eventually grouped into 16 classes. We showed that this classification method could be applied to establish a more accurate prediction model to diagnose breast cancer by comparing the performance of prediction models with different combinations of genes. We expect that our scheme of classification could be used for other types of cancer data. |
| format | Article |
| id | doaj-art-21aba19caef0494e88aedced95417fd9 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2017-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-21aba19caef0494e88aedced95417fd92025-02-02T09:35:11ZengBioMed CentralGenomics & Informatics2234-07422017-12-0115415616110.5808/GI.2017.15.4.156499Classification of Genes Based on Age-Related Differential Expression in Breast CancerGunhee Lee0Minho Lee1 Department of Biological Science, Sangji University, Wonju 26339, Korea Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, KoreaTranscriptome analysis has been widely used to make biomarker panels to diagnose cancers. In breast cancer, the age of the patient has been known to be associated with clinical features. As clinical transcriptome data have accumulated significantly, we classified all human genes based on age-specific differential expression between normal and breast cancer cells using public data. We retrieved the values for gene expression levels in breast cancer and matched normal cells from The Cancer Genome Atlas. We divided genes into two classes by paired t test without considering age in the first classification. We carried out a secondary classification of genes for each class into eight groups, based on the patterns of the p-values, which were calculated for each of the three age groups we defined. Through this two-step classification, gene expression was eventually grouped into 16 classes. We showed that this classification method could be applied to establish a more accurate prediction model to diagnose breast cancer by comparing the performance of prediction models with different combinations of genes. We expect that our scheme of classification could be used for other types of cancer data.http://genominfo.org/upload/pdf/gi-2017-15-4-156.pdfbiomarkersbreast cancerdifferentially expressed genesgene classification |
| spellingShingle | Gunhee Lee Minho Lee Classification of Genes Based on Age-Related Differential Expression in Breast Cancer Genomics & Informatics biomarkers breast cancer differentially expressed genes gene classification |
| title | Classification of Genes Based on Age-Related Differential Expression in Breast Cancer |
| title_full | Classification of Genes Based on Age-Related Differential Expression in Breast Cancer |
| title_fullStr | Classification of Genes Based on Age-Related Differential Expression in Breast Cancer |
| title_full_unstemmed | Classification of Genes Based on Age-Related Differential Expression in Breast Cancer |
| title_short | Classification of Genes Based on Age-Related Differential Expression in Breast Cancer |
| title_sort | classification of genes based on age related differential expression in breast cancer |
| topic | biomarkers breast cancer differentially expressed genes gene classification |
| url | http://genominfo.org/upload/pdf/gi-2017-15-4-156.pdf |
| work_keys_str_mv | AT gunheelee classificationofgenesbasedonagerelateddifferentialexpressioninbreastcancer AT minholee classificationofgenesbasedonagerelateddifferentialexpressioninbreastcancer |