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Efficient proximal gradient algorithm for inference of differential gene networks

Published on Dec 1, 2019in BMC Bioinformatics2.51
· DOI :10.1186/s12859-019-2749-x
Chen Wang (UM: University of Miami), Feng Gao (UM: University of Miami)+ 2 AuthorsXiaodong Cai24
Estimated H-index: 24
(UM: University of Miami)
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Abstract
Background Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in gene networks is very important to understand molecular basis of various biological process. While existing algorithms can be used to infer two gene networks separately from gene expression data under two different conditions, and then to identify network changes, such an approach does not exploit the similarity between two gene networks, and it is thus suboptimal. A desirable approach would be clearly to infer two gene networks jointly, which can yield improved estimates of network changes.
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Published on Nov 17, 2017in PeerJ2.35
Lei Wang9
Estimated H-index: 9
(Capital Medical University),
Zhiqiang Peng4
Estimated H-index: 4
(Capital Medical University)
+ 6 AuthorsJunfang Zheng6
Estimated H-index: 6
(Capital Medical University)
Published on May 1, 2017in Nephrology Dialysis Transplantation4.20
Francesco Trevisani6
Estimated H-index: 6
,
Alessandro Larcher21
Estimated H-index: 21
+ 12 AuthorsCristina Carenzi6
Estimated H-index: 6
Dong Dong2
Estimated H-index: 2
(TMUCIH: Tianjin Medical University Cancer Institute and Hospital),
Li Jia1
Estimated H-index: 1
(TMUCIH: Tianjin Medical University Cancer Institute and Hospital)
+ 3 AuthorsJun Zhang1
Estimated H-index: 1
(PKU: Peking University)
Abstract Objectives This study aimed to determine the serum levels of angiopoietin-like 4 (ANGPTL4) in patients with renal cell carcinoma (RCC) and explore its potential as a biomarker. Materials and methods Blood samples were taken from 110 patients with RCC, 66 healthy controls, and patients with other solid tumors. Serum ANGPTL4 levels were measured using the enzyme-linked immunosorbent assay, and their correlation with clinical characteristics was further analyzed. Received operating charact...
Published on Nov 1, 2016in Scandinavian Journal of Urology and Nephrology1.40
Øystein Solberg Eikrem3
Estimated H-index: 3
(Haukeland University Hospital),
Strauss P1
Estimated H-index: 1
(Haukeland University Hospital)
+ 9 AuthorsKarin M. Hjelle7
Estimated H-index: 7
(Haukeland University Hospital)
AbstractObjective: A previous study by this group demonstrated the feasibility of RNA sequencing (RNAseq) technology for capturing disease biology of clear cell renal cell carcinoma (ccRCC), and presented initial results for carbonic anhydrase-9 (CA9) and tumor necrosis factor-α-induced protein-6 (TNFAIP6) as possible biomarkers of ccRCC (discovery set) [Eikrem et al. PLoS One 2016;11:e0149743]. To confirm these results, the previous study is expanded, and RNAseq data from additional matched ccR...
Published on Sep 13, 2016in Renal Failure1.69
Lei Liu2
Estimated H-index: 2
(CSU: Central South University),
Gongbin Lan7
Estimated H-index: 7
(CSU: Central South University)
+ 5 AuthorsXiaotian Tang1
Estimated H-index: 1
(CSU: Central South University)
AbstractBackground: NDUFA4L2 is overexpressed in VHL-deficient cell lines and neuroblastoma. The clinical significance of NDUFA4L2 in clear cell renal cell carcinoma (ccRCC) has not been well studied. Therefore, we evaluated the prognostic value of NDUFA4L2 in ccRCC patients.Methods: In our study, NDUFA4L2 expression in 86 cases of ccRCC and adjacent normal tissues was monitored by immunohistochemistry, semi-quantitative RT-PCR, and Western blot analyses. The relationship between NDUFA4L2 expres...
Published on Jul 29, 2016in Briefings in Bioinformatics9.10
Yvonne Lichtblau2
Estimated H-index: 2
(Humboldt University of Berlin),
Karin Zimmermann8
Estimated H-index: 8
(Charité)
+ 3 AuthorsUlf Leser30
Estimated H-index: 30
(Humboldt University of Berlin)
Published on Jun 1, 2016in Clinical Cancer Research8.91
Denise R. Minton5
Estimated H-index: 5
(NYU: New York University),
Leiping Fu6
Estimated H-index: 6
(Cornell University)
+ 3 AuthorsLorraine J. Gudas48
Estimated H-index: 48
(Cornell University)
Purpose: We delineated the functions of the hypoxia-inducible factor-1α (HIF1α) target NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) in clear cell renal cell carcinoma (ccRCC) and characterized NDUFA4L2 as a novel molecular target for ccRCC treatment. Experimental Design: We evaluated normal kidney and ccRCC patient microarray and RNAseq data from Oncomine and The Cancer Genome Atlas for NDUFA4L2 mRNA levels and the clinical implications of high NDUFA4L2 expression. In a...
Published on Apr 1, 2016in Scientific Reports4.01
Nooshin Omranian7
Estimated H-index: 7
(MPG: Max Planck Society),
Jeanne M. O. Eloundou-Mbebi2
Estimated H-index: 2
(MPG: Max Planck Society)
+ 1 AuthorsZoran Nikoloski30
Estimated H-index: 30
(MPG: Max Planck Society)
Devising computational methods to accurately reconstruct gene regulatory networks given gene expression data is key to systems biology applications. Here we propose a method for reconstructing gene regulatory networks by simultaneous consideration of data sets from different perturbation experiments and corresponding controls. The method imposes three biologically meaningful constraints: (1) expression levels of each gene should be explained by the expression levels of a small number of transcri...
Vanessa Sandim7
Estimated H-index: 7
,
Denise de Abreu Pereira9
Estimated H-index: 9
+ 5 AuthorsRussolina B. Zingali33
Estimated H-index: 33
(UFRJ: Federal University of Rio de Janeiro)
Objective The aim of this study was to evaluate the differentially secreted protein profile in the urine from patients with clear cell renal cell carcinoma (ccRCC) using mass spectrometry–based methods. Urine composition can reflect kidney physiology and can be used to detect markers for renal diseases. Moreover, characterization of the secretome is likely to assist in the investigation of new drugs for biological targets and diagnose the ccRCC at an early stage. Methods and materials Urine samp...
Published on Dec 1, 2015in Cell systems8.64
Arthur Liberzon11
Estimated H-index: 11
(Broad Institute),
Chet Birger5
Estimated H-index: 5
(Broad Institute)
+ 3 AuthorsPablo Tamayo56
Estimated H-index: 56
(UCSD: University of California, San Diego)
Summary The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, he...
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