Cargando…
Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation
The objective of this study was to reveal hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia (BPD) based on the pathway enrichment analysis and Monte Carlo Cross-Validation (MCCV) method. The inference of key pathway cross-talk consisted of four parts: i) Identifying diffe...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
D.A. Spandidos
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425286/ https://www.ncbi.nlm.nih.gov/pubmed/30930971 http://dx.doi.org/10.3892/etm.2019.7257 |
_version_ | 1783404812243566592 |
---|---|
author | Wang, Chengbin Zhu, Bin Chen, Ming Chen, Gaoyan Xu, Muzhen Pan, Rui |
author_facet | Wang, Chengbin Zhu, Bin Chen, Ming Chen, Gaoyan Xu, Muzhen Pan, Rui |
author_sort | Wang, Chengbin |
collection | PubMed |
description | The objective of this study was to reveal hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia (BPD) based on the pathway enrichment analysis and Monte Carlo Cross-Validation (MCCV) method. The inference of key pathway cross-talk consisted of four parts: i) Identifying differentially expressed genes (DEGs); ii) detecting differentially expressed pathways (DEPs); iii) computing discriminating score (DS) for each pair of DEPs or cross-talk and investigating seed cross-talk through the random forest (RF) algorithm and iv) extracting hub cross-talk dependent on the MCCV method. The results showed that a total of 132 DEGs and 137 DEPs were obtained across BPD patients and normal controls. Using the DS and RF algorithm, 10 seed DEP cross-talk were detected. By conducting the MCCV on seed cross-talk, 3 hub cross-talk for BPD were uncovered: i) The pair of pathways role of interleukin-17F (IL-17F) in allergic inflammatory airway diseases and role of IL-17A in psoriasis; ii) the pair of pathways role of IL random forest 17A in psoriasis and IL-17A signaling in fibroblasts and ii) the pair of pathways IL-17A signaling in airway cells and role of hypercytokinemia/hyperchemokinemia in the pathogenesis of influenza. These 3 hub cross-talk among DEPs might give an insight to reveal the molecular mechanism underlying the premature newborns with BPD. |
format | Online Article Text |
id | pubmed-6425286 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | D.A. Spandidos |
record_format | MEDLINE/PubMed |
spelling | pubmed-64252862019-03-29 Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation Wang, Chengbin Zhu, Bin Chen, Ming Chen, Gaoyan Xu, Muzhen Pan, Rui Exp Ther Med Articles The objective of this study was to reveal hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia (BPD) based on the pathway enrichment analysis and Monte Carlo Cross-Validation (MCCV) method. The inference of key pathway cross-talk consisted of four parts: i) Identifying differentially expressed genes (DEGs); ii) detecting differentially expressed pathways (DEPs); iii) computing discriminating score (DS) for each pair of DEPs or cross-talk and investigating seed cross-talk through the random forest (RF) algorithm and iv) extracting hub cross-talk dependent on the MCCV method. The results showed that a total of 132 DEGs and 137 DEPs were obtained across BPD patients and normal controls. Using the DS and RF algorithm, 10 seed DEP cross-talk were detected. By conducting the MCCV on seed cross-talk, 3 hub cross-talk for BPD were uncovered: i) The pair of pathways role of interleukin-17F (IL-17F) in allergic inflammatory airway diseases and role of IL-17A in psoriasis; ii) the pair of pathways role of IL random forest 17A in psoriasis and IL-17A signaling in fibroblasts and ii) the pair of pathways IL-17A signaling in airway cells and role of hypercytokinemia/hyperchemokinemia in the pathogenesis of influenza. These 3 hub cross-talk among DEPs might give an insight to reveal the molecular mechanism underlying the premature newborns with BPD. D.A. Spandidos 2019-04 2019-02-12 /pmc/articles/PMC6425286/ /pubmed/30930971 http://dx.doi.org/10.3892/etm.2019.7257 Text en Copyright: © Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
spellingShingle | Articles Wang, Chengbin Zhu, Bin Chen, Ming Chen, Gaoyan Xu, Muzhen Pan, Rui Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title | Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title_full | Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title_fullStr | Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title_full_unstemmed | Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title_short | Revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and Monte Carlo Cross-Validation |
title_sort | revealing hub pathway cross-talk for premature newborns with bronchopulmonary dysplasia by the integration of pathway analysis and monte carlo cross-validation |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425286/ https://www.ncbi.nlm.nih.gov/pubmed/30930971 http://dx.doi.org/10.3892/etm.2019.7257 |
work_keys_str_mv | AT wangchengbin revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation AT zhubin revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation AT chenming revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation AT chengaoyan revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation AT xumuzhen revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation AT panrui revealinghubpathwaycrosstalkforprematurenewbornswithbronchopulmonarydysplasiabytheintegrationofpathwayanalysisandmontecarlocrossvalidation |