A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Dataset
2.2. Feature Ranking and Selection
2.3. Classification Algorithm
2.4. Measurements
3. Results
3.1. Results of Feature Ranking
3.2. Results of Feature Selection
3.3. Comparison of SVM Model with Tissue Enriched Genes
3.4. Performance of the Optimal SVM Classification Model on Test Dataset
3.5. Comparison of SVM Model with t-Test Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Tag | Tissue | Number of Samples | Tag | Tissue | Number of Samples | ||
---|---|---|---|---|---|---|---|
Training Dataset | Test Dataset | Training Dataset | Test Dataset | ||||
T1 | Adipose tissue | 577 | 237 | T2 | Adrenal gland | 145 | 50 |
T3 | Blood | 511 | 54 | T4 | Blood vessel | 689 | 242 |
T5 | Brain | 1259 | 455 | T6 | Breast | 214 | 84 |
T7 | Colon | 345 | 169 | T8 | Esophagus | 686 | 348 |
T9 | Heart | 412 | 201 | T10 | Liver | 119 | 58 |
T11 | Lung | 320 | 123 | T12 | Muscle | 430 | 155 |
T13 | Nerve | 304 | 122 | T14 | Ovary | 97 | 39 |
T15 | Pancreas | 171 | 82 | T16 | Pituitary | 103 | 82 |
T17 | Prostate | 106 | 48 | T18 | Skin | 890 | 342 |
T19 | Small intestine | 88 | 52 | T20 | Spleen | 104 | 60 |
T21 | Stomach | 192 | 75 | T22 | Testis | 172 | 91 |
T23 | Thyroid | 323 | 139 | T24 | Uterus | 83 | 32 |
T25 | Vagina | 96 | 27 | Total | - | 8436 | 3367 |
Rank | Gene | Description | The Human Protein Atlas [8] | Expression Atlas of EMBL-EBI [37] |
---|---|---|---|---|
1 | ARAF | A-Raf Proto-Oncogene, Serine/Threonine Kinase | Expressed in all | Multiple tissues |
2 | ITGA3 | Integrin Subunit Alpha 3 | Mixed | Multiple tissues |
3 | SLAIN2 | SLAIN Motif Family Member 2 | Expressed in all | Multiple tissues |
4 | ZNF532 | Zinc Finger Protein 532 | Mixed | Multiple tissues |
5 | PPIC | Peptidylprolyl Isomerase C | Mixed | Multiple tissues |
6 | KDELR1 | KDEL Endoplasmic Reticulum Protein Retention Receptor 1 | Expressed in all | Multiple tissues |
7 | NBL1 | Neuroblastoma 1, DAN Family BMP Antagonist | Expressed in all | Multiple tissues |
8 | PLP2 | Proteolipid Protein 2 | Expressed in all | Multiple tissues |
9 | STAT6 | Signal Transducer and Activator of Transcription 6 | Expressed in all | Multiple tissues |
10 | ARHGAP23 | Rho GTPase Activating Protein 23 | Mixed | Multiple tissues |
11 | LRIG3 | Leucine Rich Repeats And Immunoglobulin Like Domains 3 | Tissue enhanced (thyroid gland) | Multiple tissues |
12 | MANBAL | Mannosidase Beta Like | Expressed in all | Multiple tissues |
13 | PTPRA | Protein Tyrosine Phosphatase, Receptor Type A | Expressed in all | Multiple tissues |
14 | YAP1 | Yes Associated Protein 1 | Mixed | Multiple tissues |
15 | CLIC1 | Chloride Intracellular Channel 1 | Expressed in all | Multiple tissues |
16 | TMEM109 | Transmembrane Protein 109 | Expressed in all | Multiple tissues |
17 | MOCS2 | Molybdenum Cofactor Synthesis 2 | Expressed in all | Multiple tissues |
18 | PTPRF | Protein Tyrosine Phosphatase, Receptor Type F | Mixed | Multiple tissues |
19 | MYO1C | Myosin IC | Expressed in all | Multiple tissues |
20 | FAM127B | Family with Sequence Similarity 127 Member B | Expressed in all | Multiple tissues |
21 | TRIP10 | Thyroid Hormone Receptor Interactor 10 | Expressed in all | Multiple tissues |
22 | SERPING1 | Serpin Family G Member 1 | Expressed in all | Multiple tissues |
23 | TOM1L2 | Target of Myb1 Like 2 Membrane Trafficking Protein | Expressed in all | Multiple tissues |
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Li, J.; Chen, L.; Zhang, Y.-H.; Kong, X.; Huang, T.; Cai, Y.-D. A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes. Genes 2018, 9, 449. https://doi.org/10.3390/genes9090449
Li J, Chen L, Zhang Y-H, Kong X, Huang T, Cai Y-D. A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes. Genes. 2018; 9(9):449. https://doi.org/10.3390/genes9090449
Chicago/Turabian StyleLi, JiaRui, Lei Chen, Yu-Hang Zhang, XiangYin Kong, Tao Huang, and Yu-Dong Cai. 2018. "A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes" Genes 9, no. 9: 449. https://doi.org/10.3390/genes9090449