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For: Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet 2020;16:e1009023. [PMID: 32925947 PMCID: PMC7515200 DOI: 10.1371/journal.pgen.1009023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 09/24/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]  Open
Number Cited by Other Article(s)
1
Itai Y, Rappoport N, Shamir R. Integration of gene expression and DNA methylation data across different experiments. Nucleic Acids Res 2023;51:7762-7776. [PMID: 37395437 PMCID: PMC10450176 DOI: 10.1093/nar/gkad566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 06/04/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]  Open
2
Jung S, Arcos Hodar J, Del Sol A. Measuring biological age using a functionally interpretable multi-tissue RNA clock. Aging Cell 2023;22:e13799. [PMID: 36929664 DOI: 10.1111/acel.13799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 03/18/2023]  Open
3
Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023;13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023]  Open
4
Otálora-Otálora BA, López-Kleine L, Rojas A. Lung Cancer Gene Regulatory Network of Transcription Factors Related to the Hallmarks of Cancer. Curr Issues Mol Biol 2023;45:434-464. [PMID: 36661515 PMCID: PMC9857713 DOI: 10.3390/cimb45010029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/06/2023]  Open
5
Lee BH, Wu Z, Rhie SK. Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C. Epigenetics Chromatin 2022;15:41. [PMID: 36544209 PMCID: PMC9768916 DOI: 10.1186/s13072-022-00473-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]  Open
6
Otálora-Otálora BA, González Prieto C, Guerrero L, Bernal-Forigua C, Montecino M, Cañas A, López-Kleine L, Rojas A. Identification of the Transcriptional Regulatory Role of RUNX2 by Network Analysis in Lung Cancer Cells. Biomedicines 2022;10:biomedicines10123122. [PMID: 36551878 PMCID: PMC9775089 DOI: 10.3390/biomedicines10123122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 12/07/2022]  Open
7
Characterizing and Targeting Genes Regulated by Transcription Factor MYBL2 in Lung Adenocarcinoma Cells. Cancers (Basel) 2022;14:cancers14204979. [PMID: 36291764 PMCID: PMC9599349 DOI: 10.3390/cancers14204979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 01/16/2023]  Open
8
Wang C, Yu Q, Song T, Wang Z, Song L, Yang Y, Shao J, Li J, Ni Y, Chao N, Zhang L, Li W. The heterogeneous immune landscape between lung adenocarcinoma and squamous carcinoma revealed by single-cell RNA sequencing. Signal Transduct Target Ther 2022;7:289. [PMID: 36008393 PMCID: PMC9411197 DOI: 10.1038/s41392-022-01130-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 05/23/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]  Open
9
Yang Y, Liu X, Wang X, Zhang J, Li S, Ma X. Comprehensive Analysis of ABCA Family Members in Lung Adenocarcinoma with Prognostic Values. Mol Biotechnol 2022;64:1441-1453. [PMID: 35759117 DOI: 10.1007/s12033-022-00506-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/02/2022] [Indexed: 11/27/2022]
10
Zhuang Z, Zhong X, Chen Q, Chen H, Liu Z. Bioinformatics and System Biology Approach to Reveal the Interaction Network and the Therapeutic Implications for Non-Small Cell Lung Cancer Patients With COVID-19. Front Pharmacol 2022;13:857730. [PMID: 35721149 PMCID: PMC9201692 DOI: 10.3389/fphar.2022.857730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/28/2022] [Indexed: 01/17/2023]  Open
11
Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A. Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers. Epigenetics Chromatin 2022;15:13. [PMID: 35440061 PMCID: PMC9016969 DOI: 10.1186/s13072-022-00444-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 12/15/2022]  Open
12
Detilleux D, Spill YG, Balaramane D, Weber M, Bardet AF. Pan-cancer predictions of transcription factors mediating aberrant DNA methylation. Epigenetics Chromatin 2022;15:10. [PMID: 35331302 PMCID: PMC8944071 DOI: 10.1186/s13072-022-00443-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/04/2022] [Indexed: 12/31/2022]  Open
13
Wu Q, Jiang J. LncRNA MAFG-AS1 Promotes Lung Adenocarcinoma Cell Migration and Invasion by Targeting miR-3196 and Regulating SOX12 Expression. Mol Biotechnol 2022;64:970-983. [PMID: 35275356 DOI: 10.1007/s12033-022-00455-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/14/2022] [Indexed: 11/28/2022]
14
Cai L, Xiao G, Gerber D, D Minna J, Xie Y. Lung Cancer Computational Biology and Resources. Cold Spring Harb Perspect Med 2022;12:a038273. [PMID: 34751162 PMCID: PMC8805643 DOI: 10.1101/cshperspect.a038273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
15
Zhou B, Stueve TR, Mihalakakos EA, Miao L, Mullen D, Wang Y, Liu Y, Luo J, Tran E, Siegmund KD, Lynch SK, Ryan AL, Offringa IA, Borok Z, Marconett CN. Comprehensive epigenomic profiling of human alveolar epithelial differentiation identifies key epigenetic states and transcription factor co-regulatory networks for maintenance of distal lung identity. BMC Genomics 2021;22:906. [PMID: 34922464 PMCID: PMC8684104 DOI: 10.1186/s12864-021-08152-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/05/2021] [Indexed: 12/22/2022]  Open
16
Sano K, Hayashi T, Suehara Y, Hosoya M, Takamochi K, Kohsaka S, Kishikawa S, Kishi M, Saito S, Takahashi F, Kaneko K, Suzuki K, Yao T, Ishijima M, Saito T. Transcription start site-level expression of thyroid transcription factor 1 isoforms in lung adenocarcinoma and its clinicopathological significance. J Pathol Clin Res 2021;7:361-374. [PMID: 34014042 PMCID: PMC8185369 DOI: 10.1002/cjp2.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
17
Liu C, Barger CJ, Karpf AR. FOXM1: A Multifunctional Oncoprotein and Emerging Therapeutic Target in Ovarian Cancer. Cancers (Basel) 2021;13:3065. [PMID: 34205406 PMCID: PMC8235333 DOI: 10.3390/cancers13123065] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 02/08/2023]  Open
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