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Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system
OBJECTIVES: Immune microenvironment was closely related to the occurrence and progression of colorectal cancer (CRC). The objective of the current research was to develop and verify a Machine learning survival predictive system for CRC based on immune gene expression data and machine learning algori...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8991575/ https://www.ncbi.nlm.nih.gov/pubmed/35395711 http://dx.doi.org/10.1186/s12859-022-04657-3 |
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author | Zhang, Zhiqiao Huang, Liwen Li, Jing Wang, Peng |
author_facet | Zhang, Zhiqiao Huang, Liwen Li, Jing Wang, Peng |
author_sort | Zhang, Zhiqiao |
collection | PubMed |
description | OBJECTIVES: Immune microenvironment was closely related to the occurrence and progression of colorectal cancer (CRC). The objective of the current research was to develop and verify a Machine learning survival predictive system for CRC based on immune gene expression data and machine learning algorithms. METHODS: The current study performed differentially expressed analyses between normal tissues and tumor tissues. Univariate Cox regression was used to screen prognostic markers for CRC. Prognostic immune genes and transcription factors were used to construct an immune-related regulatory network. Three machine learning algorithms were used to create an Machine learning survival predictive system for CRC. Concordance indexes, calibration curves, and Brier scores were used to evaluate the performance of prognostic model. RESULTS: Twenty immune genes (BCL2L12, FKBP10, XKRX, WFS1, TESC, CCR7, SPACA3, LY6G6C, L1CAM, OSM, EXTL1, LY6D, FCRL5, MYEOV, FOXD1, REG3G, HAPLN1, MAOB, TNFSF11, and AMIGO3) were recognized as independent risk factors for CRC. A prognostic nomogram was developed based on the previous immune genes. Concordance indexes were 0.852, 0.778, and 0.818 for 1-, 3- and 5-year survival. This prognostic model could discriminate high risk patients with poor prognosis from low risk patients with favorable prognosis. CONCLUSIONS: The current study identified twenty prognostic immune genes for CRC patients and constructed an immune-related regulatory network. Based on three machine learning algorithms, the current research provided three individual mortality predictive curves. The Machine learning survival predictive system was available at: https://zhangzhiqiao8.shinyapps.io/Artificial_Intelligence_Survival_Prediction_for_CRC_B1005_1/, which was valuable for individualized treatment decision before surgery. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04657-3. |
format | Online Article Text |
id | pubmed-8991575 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-89915752022-04-09 Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system Zhang, Zhiqiao Huang, Liwen Li, Jing Wang, Peng BMC Bioinformatics Research OBJECTIVES: Immune microenvironment was closely related to the occurrence and progression of colorectal cancer (CRC). The objective of the current research was to develop and verify a Machine learning survival predictive system for CRC based on immune gene expression data and machine learning algorithms. METHODS: The current study performed differentially expressed analyses between normal tissues and tumor tissues. Univariate Cox regression was used to screen prognostic markers for CRC. Prognostic immune genes and transcription factors were used to construct an immune-related regulatory network. Three machine learning algorithms were used to create an Machine learning survival predictive system for CRC. Concordance indexes, calibration curves, and Brier scores were used to evaluate the performance of prognostic model. RESULTS: Twenty immune genes (BCL2L12, FKBP10, XKRX, WFS1, TESC, CCR7, SPACA3, LY6G6C, L1CAM, OSM, EXTL1, LY6D, FCRL5, MYEOV, FOXD1, REG3G, HAPLN1, MAOB, TNFSF11, and AMIGO3) were recognized as independent risk factors for CRC. A prognostic nomogram was developed based on the previous immune genes. Concordance indexes were 0.852, 0.778, and 0.818 for 1-, 3- and 5-year survival. This prognostic model could discriminate high risk patients with poor prognosis from low risk patients with favorable prognosis. CONCLUSIONS: The current study identified twenty prognostic immune genes for CRC patients and constructed an immune-related regulatory network. Based on three machine learning algorithms, the current research provided three individual mortality predictive curves. The Machine learning survival predictive system was available at: https://zhangzhiqiao8.shinyapps.io/Artificial_Intelligence_Survival_Prediction_for_CRC_B1005_1/, which was valuable for individualized treatment decision before surgery. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04657-3. BioMed Central 2022-04-08 /pmc/articles/PMC8991575/ /pubmed/35395711 http://dx.doi.org/10.1186/s12859-022-04657-3 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Zhang, Zhiqiao Huang, Liwen Li, Jing Wang, Peng Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title | Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title_full | Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title_fullStr | Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title_full_unstemmed | Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title_short | Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
title_sort | bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8991575/ https://www.ncbi.nlm.nih.gov/pubmed/35395711 http://dx.doi.org/10.1186/s12859-022-04657-3 |
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