Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods
Abstract
:1. Introduction
2. Materials and Methods
2.1. Data
2.2. Feature Ranking Algorithms
2.2.1. Last Absolute Shrinkage and Selection Operator
2.2.2. Light Gradient Boosting Machine
2.2.3. Monte Carlo Feature Selection
2.2.4. Minimum Redundancy Maximum Relevance
2.2.5. Random Forest
2.3. Incremental Feature Selection
2.4. Synthetic Minority Oversampling Technique
2.5. Classification Algorithm
2.5.1. Decision Tree
2.5.2. Random Forest
2.6. Performance Evaluation
3. Results
3.1. Dynamics of Classifier Performance
3.2. Relationships between the Most Essential Genes Extracted from Five Lists
3.3. Classification Rules
4. Discussion
4.1. T Cell Family
4.2. B Cell Family
4.3. Other Cells
4.4. Limitation of This Study
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Index | Immune Cell Subtypes | Sample Size |
---|---|---|
1 | Activated CD4 T | 1531 |
2 | B cell (cycling) | 15 |
3 | B cell (IgA Plasma) | 12,522 |
4 | B cell (IgG Plasma) | 342 |
5 | B cell (memory) | 4508 |
6 | CD8 T | 3145 |
7 | cDC1 | 38 |
8 | cDC2 | 107 |
9 | cycling DCs | 47 |
10 | cycling gd T | 25 |
11 | Follicular B cell | 2582 |
12 | gd T | 548 |
13 | ILC | 832 |
14 | Lymphoid DC | 10 |
15 | LYVE1 Macrophage | 91 |
16 | Macrophage | 268 |
17 | Mast | 1151 |
18 | Monocyte | 98 |
19 | NK | 452 |
20 | pDC | 13 |
21 | Tcm | 3042 |
22 | Tfh | 1786 |
23 | Th1 | 2833 |
24 | Th17 | 3432 |
25 | Treg | 2232 |
Feature List | Classification Algorithm | Number of Features | ACC | MCC | Macro F1 | Weighted F1 |
---|---|---|---|---|---|---|
LASSO feature list | Decision tree | 1240 | 0.823 | 0.796 | 0.775 | 0.827 |
Random forest | 1230 | 0.960 | 0.953 | 0.953 | 0.959 | |
Random forest | 50 | 0.933 | 0.923 | 0.937 | 0.933 | |
LightGBM feature list | Decision tree | 300 | 0.895 | 0.878 | 0.871 | 0.895 |
Random forest | 1200 | 0.978 | 0.974 | 0.985 | 0.978 | |
Random forest | 60 | 0.943 | 0.934 | 0.949 | 0.943 | |
MCFS feature list | Decision tree | 1620 | 0.892 | 0.875 | 0.881 | 0.893 |
Random forest | 1720 | 0.976 | 0.972 | 0.983 | 0.976 | |
Random forest | 90 | 0.944 | 0.935 | 0.954 | 0.944 | |
mRMR feature list | Decision tree | 350 | 0.873 | 0.853 | 0.855 | 0.875 |
Random forest | 560 | 0.972 | 0.968 | 0.973 | 0.972 | |
Random forest | 90 | 0.961 | 0.955 | 0.969 | 0.961 | |
RF feature list | Decision tree | 170 | 0.891 | 0.874 | 0.863 | 0.892 |
Random forest | 1510 | 0.977 | 0.974 | 0.984 | 0.978 | |
Random forest | 70 | 0.962 | 0.956 | 0.970 | 0.962 |
Category | Gene Symbol | Description |
---|---|---|
T cell family | KLRB1 | Killer Cell Lectin Like Receptor B1 |
CST3 | Cystatin C | |
AIF1 | Allograft Inflammatory Factor 1 | |
JCHAIN | Joining Chain of Multimeric IgA and IgM | |
HLA-DRA | Major Histocompatibility Complex, Class II, DR Alpha | |
TIGIT | T Cell Immunoreceptor with Ig and ITIM Domains | |
RPS12 | Ribosomal Protein S12 | |
MS4A1 | Membrane Spanning 4-Domains A1 | |
B cell family | RPL30 | Ribosomal Protein L30 |
ANXA1 | Annexin A1 | |
JCHAIN | Joining Chain of Multimeric IgA and IgM | |
ICA1 | Islet Cell Autoantigen 1 | |
TYROBP | Transmembrane Immune Signaling Adaptor TYROBP | |
RPS27 | Ribosomal Protein S27 | |
HLA-DRA | Major Histocompatibility Complex, Class II, DR Alpha | |
IFITM1 | Interferon Induced Transmembrane Protein 1 | |
IGHA1 | Immunoglobulin Heavy Constant Alpha 1 | |
CD37 | CD37 Molecule | |
Other cells | RPS13 | Ribosomal Protein S13 |
RPL34 | Ribosomal Protein L34 | |
MALAT1 | Metastasis Associated Lung Adenocarcinoma Transcript 1 | |
TMSB4X | Thymosin Beta 4 X-Linked | |
SOCS3 | Suppressor Of Cytokine Signaling 3 | |
IL7R | Interleukin 7 Receptor | |
CD-74 | CD74 Molecule | |
RPL28 | Ribosomal Protein L28 | |
ANKRD28 | Ankyrin Repeat Domain 28 | |
TYROBP | Transmembrane Immune Signaling Adaptor TYROBP |
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Yang, Y.; Zhang, Y.; Ren, J.; Feng, K.; Li, Z.; Huang, T.; Cai, Y. Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods. Life 2023, 13, 1876. https://doi.org/10.3390/life13091876
Yang Y, Zhang Y, Ren J, Feng K, Li Z, Huang T, Cai Y. Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods. Life. 2023; 13(9):1876. https://doi.org/10.3390/life13091876
Chicago/Turabian StyleYang, Yong, Yuhang Zhang, Jingxin Ren, Kaiyan Feng, Zhandong Li, Tao Huang, and Yudong Cai. 2023. "Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods" Life 13, no. 9: 1876. https://doi.org/10.3390/life13091876