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For: Jin N, Wu H, Miao Z, Huang Y, Hu Y, Bi X, Wu D, Qian K, Wang L, Wang C, Wang H, Li K, Li X, Wang D. Network-based survival-associated module biomarker and its crosstalk with cell death genes in ovarian cancer. Sci Rep 2015;5:11566. [PMID: 26099452 DOI: 10.1038/srep11566] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/28/2015] [Indexed: 12/27/2022]  Open
Number Cited by Other Article(s)
1
Tombaz M, Yanyatan C, Keskus AG, Konu O. Extraction and Prioritization of a Gene-Cancer-By-Survival Network Involved in Homeostasis of Intracellular Calcium Concentrations Using TCGA PANCAN Data. Bioelectricity 2022. [DOI: 10.1089/bioe.2022.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
2
Survival-Based Biomarker Module Identification Associated with Oral Squamous Cell Carcinoma (OSCC). BIOLOGY 2021;10:biology10080760. [PMID: 34439992 PMCID: PMC8389591 DOI: 10.3390/biology10080760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 12/28/2022]
3
Savino A, Provero P, Poli V. Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. Int J Mol Sci 2020;21:E9461. [PMID: 33322692 PMCID: PMC7764314 DOI: 10.3390/ijms21249461] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 02/02/2023]  Open
4
Sun Y, Li C, Pang S, Yao Q, Chen L, Li Y, Zeng R. Kinase-substrate Edge Biomarkers Provide a More Accurate Prognostic Prediction in ER-negative Breast Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2020;18:525-538. [PMID: 33450402 PMCID: PMC8377385 DOI: 10.1016/j.gpb.2019.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 08/27/2019] [Accepted: 11/11/2019] [Indexed: 11/19/2022]
5
Bashiri H, Rahmani H, Bashiri V, Módos D, Bender A. EMDIP: An Entropy Measure to Discover Important Proteins in PPI networks. Comput Biol Med 2020;120:103740. [PMID: 32421645 DOI: 10.1016/j.compbiomed.2020.103740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/24/2022]
6
Lalremmawia H, Tiwary BK. Identification of molecular biomarkers for ovarian cancer using computational approaches. Carcinogenesis 2020;40:742-748. [PMID: 30753333 DOI: 10.1093/carcin/bgz025] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/26/2019] [Accepted: 02/01/2019] [Indexed: 12/31/2022]  Open
7
Lei H, Liu W, Si J, Wang J, Zhang T. Analyzing the regulation of miRNAs on protein-protein interaction network in Hodgkin lymphoma. BMC Bioinformatics 2019;20:449. [PMID: 31477006 PMCID: PMC6720096 DOI: 10.1186/s12859-019-3041-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 08/21/2019] [Indexed: 12/28/2022]  Open
8
Zhang W, Ma J, Ideker T. Classifying tumors by supervised network propagation. Bioinformatics 2019;34:i484-i493. [PMID: 29949979 PMCID: PMC6022559 DOI: 10.1093/bioinformatics/bty247] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
9
Shafi A, Nguyen T, Peyvandipour A, Nguyen H, Draghici S. A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. Front Genet 2019;10:159. [PMID: 30941158 PMCID: PMC6434849 DOI: 10.3389/fgene.2019.00159] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/14/2019] [Indexed: 12/20/2022]  Open
10
Shao B, Bjaanæs MM, Helland Å, Schütte C, Conrad T. EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS One 2019;14:e0204186. [PMID: 30703089 PMCID: PMC6354965 DOI: 10.1371/journal.pone.0204186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 12/25/2018] [Indexed: 12/16/2022]  Open
11
Yu L, Qian S, Wei S. Identification of a noncoding RNA‑mediated gene pair‑based regulatory module in Alzheimer's disease. Mol Med Rep 2018;18:2164-2170. [PMID: 29956760 PMCID: PMC6072230 DOI: 10.3892/mmr.2018.9190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/22/2018] [Indexed: 12/13/2022]  Open
12
Optimizing miRNA-module diagnostic biomarkers of gastric carcinoma via integrated network analysis. PLoS One 2018;13:e0198445. [PMID: 29879180 PMCID: PMC5991748 DOI: 10.1371/journal.pone.0198445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/18/2018] [Indexed: 12/17/2022]  Open
13
De Meulder B, Lefaudeux D, Bansal AT, Mazein A, Chaiboonchoe A, Ahmed H, Balaur I, Saqi M, Pellet J, Ballereau S, Lemonnier N, Sun K, Pandis I, Yang X, Batuwitage M, Kretsos K, van Eyll J, Bedding A, Davison T, Dodson P, Larminie C, Postle A, Corfield J, Djukanovic R, Chung KF, Adcock IM, Guo YK, Sterk PJ, Manta A, Rowe A, Baribaud F, Auffray C. A computational framework for complex disease stratification from multiple large-scale datasets. BMC SYSTEMS BIOLOGY 2018;12:60. [PMID: 29843806 PMCID: PMC5975674 DOI: 10.1186/s12918-018-0556-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/21/2018] [Indexed: 01/05/2023]
14
Cheng L, Leung KS. Quantification of non-coding RNA target localization diversity and its application in cancers. J Mol Cell Biol 2018;10:130-138. [DOI: 10.1093/jmcb/mjy006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/24/2018] [Indexed: 12/13/2022]  Open
15
Yu G, Li N, Zhao Y, Wang W, Feng XL. Salidroside induces apoptosis in human ovarian cancer SKOV3 and A2780 cells through the p53 signaling pathway. Oncol Lett 2018;15:6513-6518. [PMID: 29616120 DOI: 10.3892/ol.2018.8090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]  Open
16
Omony J, de Jong A, Krawczyk AO, Eijlander RT, Kuipers OP. Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens: a transcriptomic model. Microb Genom 2018;4. [PMID: 29424683 PMCID: PMC5857382 DOI: 10.1099/mgen.0.000157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
17
Comprehensive analysis of lncRNA expression profiles reveals a novel lncRNA signature to discriminate nonequivalent outcomes in patients with ovarian cancer. Oncotarget 2018;7:32433-48. [PMID: 27074572 PMCID: PMC5078024 DOI: 10.18632/oncotarget.8653] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 02/01/2023]  Open
18
Cheng L, Han Y, Zhao X, Xu X, Wang J. Identifying pathway modules of tuberculosis in children by analyzing multiple different networks. Exp Ther Med 2017;15:755-760. [PMID: 29399082 PMCID: PMC5769296 DOI: 10.3892/etm.2017.5434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/13/2017] [Indexed: 02/02/2023]  Open
19
Gov E, Kori M, Arga KY. RNA-based ovarian cancer research from 'a gene to systems biomedicine' perspective. Syst Biol Reprod Med 2017;63:219-238. [PMID: 28574782 DOI: 10.1080/19396368.2017.1330368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
20
Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry. Sci Rep 2017;7:2472. [PMID: 28559546 PMCID: PMC5449392 DOI: 10.1038/s41598-017-02522-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/10/2017] [Indexed: 12/12/2022]  Open
21
A powerful weighted statistic for detecting group differences of directed biological networks. Sci Rep 2016;6:34159. [PMID: 27686331 PMCID: PMC5054825 DOI: 10.1038/srep34159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/08/2016] [Indexed: 12/15/2022]  Open
22
Cao Z, Zhang S. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures. Sci Rep 2016;6:33398. [PMID: 27633916 PMCID: PMC5025752 DOI: 10.1038/srep33398] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022]  Open
23
Differential Regulatory Analysis Based on Coexpression Network in Cancer Research. BIOMED RESEARCH INTERNATIONAL 2016;2016:4241293. [PMID: 27597964 PMCID: PMC4997028 DOI: 10.1155/2016/4241293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/09/2016] [Accepted: 06/12/2016] [Indexed: 12/15/2022]
24
Yin X, Wang X, Shen B, Jing Y, Li Q, Cai MC, Gu Z, Yang Q, Zhang Z, Liu J, Li H, Di W, Zhuang G. A VEGF-dependent gene signature enriched in mesenchymal ovarian cancer predicts patient prognosis. Sci Rep 2016;6:31079. [PMID: 27498762 PMCID: PMC4976329 DOI: 10.1038/srep31079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022]  Open
25
A Five-Gene Expression Signature Predicts Clinical Outcome of Ovarian Serous Cystadenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2016;2016:6945304. [PMID: 27478834 PMCID: PMC4949334 DOI: 10.1155/2016/6945304] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/25/2016] [Indexed: 12/28/2022]
26
Feng L, Tong R, Liu X, Zhang K, Wang G, Zhang L, An N, Cheng S. A network-based method for identifying prognostic gene modules in lung squamous carcinoma. Oncotarget 2016;7:18006-20. [PMID: 26919109 PMCID: PMC4951267 DOI: 10.18632/oncotarget.7632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/13/2016] [Indexed: 12/23/2022]  Open
27
Predicting cancerlectins by the optimal g-gap dipeptides. Sci Rep 2015;5:16964. [PMID: 26648527 PMCID: PMC4673586 DOI: 10.1038/srep16964] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 10/22/2015] [Indexed: 12/14/2022]  Open
28
Guan X, Yi Y, Huang Y, Hu Y, Li X, Wang X, Fan H, Wang G, Wang D. Revealing potential molecular targets bridging colitis and colorectal cancer based on multidimensional integration strategy. Oncotarget 2015;6:37600-12. [PMID: 26461477 PMCID: PMC4741951 DOI: 10.18632/oncotarget.6067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 09/24/2015] [Indexed: 02/05/2023]  Open
29
Zhang S, Jing Y, Zhang M, Zhang Z, Ma P, Peng H, Shi K, Gao WQ, Zhuang G. Stroma-associated master regulators of molecular subtypes predict patient prognosis in ovarian cancer. Sci Rep 2015;5:16066. [PMID: 26530441 PMCID: PMC4632004 DOI: 10.1038/srep16066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/06/2015] [Indexed: 02/06/2023]  Open
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