cran: WGCNA | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-85020-z

Systems-wide effects of short-term feed deprivation in obese mice
Cited by: 2
Author(s): Daniel S. Andersen, Henrik Munch Roager, Li Zhang, Janne Marie Moll, Henrik Lauritz Frandsen, Niels Banhos Danneskiold‐Samsøe, Axel Kornerup Hansen, Karsten Kristiansen, Tine Rask Licht, Susanne Brix
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2015.00301

Moving from capstones toward cornerstones: successes and challenges in applying systems biology to identify mechanisms of autism spectrum disorders
Cited by: 14
Author(s): Nathan Kopp, Sharlee Climer, Joseph D. Dougherty
Software Mentions: 1
Published: almost 11 years ago

10.7150/ijbs.51309

CDH1 is Identified as A Therapeutic Target for Skin Regeneration after Mechanical Loading
Cited by: 9
Author(s): Xiaolu Huang, Xiao Liang, Yiwen Zhou, Haizhou Li, Hengyu Du, Yinjun Suo, Wenhui Liu, Rui Jin, Bangda Chai, Ran Duan, Qingfeng Li
Software Mentions: 1
Published: over 5 years ago

10.7150/ijbs.59559

Upregulation of ATP Binding Cassette Subfamily C Member 5 facilitates Prostate Cancer progression and Enzalutamide resistance via the CDK1-mediated AR Ser81 Phosphorylation Pathway
Cited by: 7
Author(s): Guangjie Ji, Shiming He, Cong Huang, Yanqing Gong, Xuesong Li, Liqun Zhou
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2019.00964

Transcriptomic and Functional Analyses of Phenotypic Plasticity in a Higher Termite, Macrotermes barneyi Light
Cited by: 10
Author(s): Pengdong Sun, Ganghua Li, Jianbo Jian, Long Liu, Junhui Chen, Shuxin Yu, Huan Xu, Chaoliang Lei, Xuguo Zhou, Qiuying Huang
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13046-018-1002-1

Classification of triple-negative breast cancers based on Immunogenomic profiling
Cited by: 274
Author(s): Hanlin Yin, Zhongshan Jiang, Chen Cai, Xiaosheng Wang
Software Mentions: 1
Published: almost 8 years ago

10.3390/metabo9070145

Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)
Cited by: 27
Author(s): Mary C. Playdon, Amit D. Joshi, Fred K. Tabung, Susan Cheng, Mir Henglin, Andy Kim, Tengda Lin, Eline H. van Roekel, Jiaqi Huang, Jan Krumsiek, Ying Wang, Ewy A. Mathé, Marinella Temprosa, Steven C. Moore, Bo Chawes, A. Heather Eliassen, Andrea Gsur, Marc J. Gunter, Sei Harada, Claudia Langenberg, Matej Orešič, Wei Perng, Wei Jie Seow, Oana A. Zeleznik
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2019.00037

Co-expression Network Analysis Identifies Four Hub Genes Associated With Prognosis in Soft Tissue Sarcoma
Cited by: 29
Author(s): Zhifeng Zhu, Zheng Jin, Yuyou Deng, Lai Wei, Xiaowei Yuan, Mei Zhang, Dahui Sun
Software Mentions: 1
Published: over 7 years ago

10.1186/s13046-020-01803-8

Hepatitis B virus P protein initiates glycolytic bypass in HBV-related hepatocellular carcinoma via a FOXO3/miRNA-30b-5p/MINPP1 axis
Cited by: 47
Author(s): Wenbiao Chen, Jingjing Jiang, Lan Gong, Zheyue Shu, Da‐Xiong Xiang, Xujun Zhang, Kefan Bi, Hongyan Diao
Software Mentions: 1
Published: over 5 years ago

10.1186/s13046-020-01782-w

Alcoholic fatty liver disease inhibited the co-expression of Fmo5 and PPARα to activate the NF-κB signaling pathway, thereby reducing liver injury via inducing gut microbiota disturbance
Cited by: 27
Author(s): Ling Kong, Jing Chen, Xiao li Ji, Qian Qin, Hui Yang, Dan Liú, De liang Li, Mei ling Sun
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.650102

Identification of a MicroRNA Signature Associated With Lymph Node Metastasis in Endometrial Endometrioid Cancer
Cited by: 3
Author(s): Kaiyou Fu, Yanrui Li, Junxian Song, Weixiong Cai, Wei Wu, Xiaohang Ye, Jian Xu
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2021.685341

Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep
Cited by: 3
Author(s): P. K. Chitneedi, Rosemarie Weikard, Juan José Arranz, María Martínez‐Valladares, Christa Küehn, Beatriz Gutiérrez-Gil
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2016.00218

A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal
Cited by: 5
Author(s): Nicole A.R. Walter, De Aunne L. Denmark, Laura B. Kozell, Kari J. Buck
Software Mentions: 1
Published: over 9 years ago

10.3390/jof6030108

Modeling Approaches Reveal New Regulatory Networks in Aspergillus fumigatus Metabolism
Cited by: 2
Author(s): Enzo Acerbi, Marcela Hortová-Kohoutková, Tsokyi Choera, Nancy P. Keller, Jan Frič, Fabio Stella, Luigina Romani, Teresa Zelante
Software Mentions: 1
Published: about 6 years ago

10.3390/jof7040270

Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics
Cited by: 4
Author(s): Tim J. H. Baltussen, Jordy P. M. Coolen, Paul E. Verweij, Jan Dijksterhuis, Willem J. G. Melchers
Software Mentions: 1
Published: over 5 years ago

10.3389/fgene.2020.597888

Identifying Biomarkers to Predict the Progression and Prognosis of Breast Cancer by Weighted Gene Co-expression Network Analysis
Cited by: 6
Author(s): Gengsheng Shi, Zhenru Shen, Yi Liu, Wenqin Yin
Software Mentions: 1
Published: over 5 years ago

10.1155/2020/9827349

The Effect of Inflammation on the Formation of Thyroid Nodules
Cited by: 4
Author(s): Zexin Li, Yiteng Huang, Xiang Cheng, Chiju Wei, Peixuan Yang, Weilai Xu
Software Mentions: 1
Published: about 6 years ago

10.3389/fgene.2019.01323

An Integrated Model Based on a Six-Gene Signature Predicts Overall Survival in Patients With Hepatocellular Carcinoma
Cited by: 40
Author(s): Wenli Li, Jianjun Lu, Zhu Ma, Jia-feng Zhao, Jun Li
Software Mentions: 1
Published: over 6 years ago

10.1186/s12967-015-0383-6

Berberine ameliorates nonalcoholic fatty liver disease by a global modulation of hepatic mRNA and lncRNA expression profiles
Cited by: 86
Author(s): Xinlu Yuan, Jie Wang, Xiaoyan Tang, Yixue Li, Pu Xia, Xin Gao
Software Mentions: 1
Published: over 11 years ago

10.3389/fgene.2019.01258

Candidate Regulators of Dyslipidemia in Chromosome 1 Substitution Lines Using Liver Co-Expression Profiling Analysis
Cited by: 1
Author(s): Fuyi Xu, Maochun Wang, Shixian Hu, Yuxun Zhou, John Collyer, Kai Li, Hongyan Xu, Junhua Xiao
Software Mentions: 1
Published: over 6 years ago

10.1007/s10585-020-10062-y

Correlation of exosomal microRNA clusters with bone metastasis in non-small cell lung cancer
Cited by: 20
Author(s): Xiaorong Yang, Can Pi, Rong Yu, Xiaojun Fan, Xudong Peng, Xuchao Zhang, Zhihong Chen, Xue Wu, Yang Shao, Yi‐Long Wu, Qing Zhou
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13020-020-00344-8

Transcriptome analyses revealed the ultraviolet B irradiation and phytohormone gibberellins coordinately promoted the accumulation of artemisinin in Artemisia annua L.
Cited by: 10
Author(s): Tingyu Ma, Han Gao, Dong Zhang, Yuhua Shi, Tianyuan Zhang, Xiaofeng Shen, Lan Wu, Xiang Li, Shilin Chen
Software Mentions: 1
Published: about 6 years ago

10.3390/cells9010246

Novel Approaches for Identifying the Molecular Background of Schizophrenia
Cited by: 10
Author(s): Arkadiy K. Golov, Nikolay Kondratyev, G. P. Kostyuk, And Vera E Golimbet
Software Mentions: 1
Published: over 6 years ago

10.1016/j.celrep.2019.12.087

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
Cited by: 19
Author(s): Enrique Martín‐Gayo, Ce Gao, Hsiao Rong Chen, Zhengyu Ouyang, Dhohyung Kim, Kellie E. Kolb, Alex K. Shalek, Bruce D. Walker, Mathias Lichterfeld, Xu G. Yu
Software Mentions: 1
Published: over 6 years ago

10.7150/ijms.61771

PD-L1 correlated gene expression profiles and tumor infiltrating lymphocytes in pancreatic cancer
Cited by: 2
Author(s): Jiajin Li, Lu Yin, Yumei Chen, Shuxian An, Yi Xiong, Gang Huang, Jianjun Li
Software Mentions: 1
Published: over 5 years ago

10.1111/cpr.12386

Spontaneous generation of a novel foetal human retinal pigment epithelium ( <scp>RPE</scp> ) cell line available for investigation on phagocytosis and morphogenesis
Cited by: 7
Author(s): Zhihua Shao, Haiyun Wang, Xinping Zhou, Baosen Guo, Xuehu Gao, Zengrong Xiao, Liesu Meng, Sha Jihong, Chunlian Jiang, Yuan Luo, Zhixue Liu, Siguang Li
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41421-019-0129-3

Twin-peak temporal regulation during human neocortical development
Cited by: 5
Author(s): Wei Wang, Guang-Zhong Wang
Software Mentions: 1
Published: over 6 years ago

10.3390/metabo9080157

Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma
Cited by: 27
Author(s): Eitan Halper-Stromberg, Lucas A. Gillenwater, Charmion Cruickshank‐Quinn, Wanda K. O’Neal, Nichole Reisdorph, Irina Petrache, Yonghua Zhuang, Wassim W. Labaki, Jeffrey L. Curtis, James M. Wells, Stephen I. Rennard, Katherine Pratte, Prescott G. Woodruff, Kathleen A. Stringer, Katerina Kechris, Russell P. Bowler
Software Mentions: 1
Published: about 7 years ago

10.3390/nu11061265

Network Analysis of the Potential Role of DNA Methylation in the Relationship between Plasma Carotenoids and Lipid Profile
Cited by: 18
Author(s): Bénédicte L. Tremblay, Frédéric Guénard, Benoı̂t Lamarche, Louis Pérusse, Marie‐Claude Vohl
Software Mentions: 1
Published: over 7 years ago

10.22038/IJBMS.2018.29498.7123

Gene co-expression network analysis identifies BRCC3 as a key regulator in osteogenic differentiation of osteoblasts through a β-catenin signaling dependent pathway.
Cited by: 0
Author(s): Lixiong Cai, Zhiqian Huo, Huiling Yang, HE Feng-chun, Zheng-lin Cao, Feng Wu, Lianjun Liu, Bing‐Yin Sun
Software Mentions: 1
Published: over 7 years ago

10.1038/cddiscovery.2017.73

Interplay of neuronal and non-neuronal genes regulates intestinal DAF-16-mediated immune response during Fusarium infection of Caenorhabditis elegans
Cited by: 8
Author(s): Papri Nag, Pooja Aggarwal, Sudip Ghosh, Kanika Narula, Rajul Tayal, Nidhi Maheshwari, Niranjan Chakraborty, Subhra Chakraborty
Software Mentions: 1
Published: almost 9 years ago

10.1155/2021/6664791

Coexpressed Genes That Promote the Infiltration of M2 Macrophages in Melanoma Can Evaluate the Prognosis and Immunotherapy Outcome
Cited by: 13
Author(s): Kexin Yan, Yutao Wang, Yuxiu Lu, Zhangyong Yan
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-020-03368-y

Oxidative stress activates NORAD expression by H3K27ac and promotes oxaliplatin resistance in gastric cancer by enhancing autophagy flux via targeting the miR-433-3p
Cited by: 39
Author(s): Jizhao Wang, Yehuan Sun, Xing Zhang, Hui Cai, Cheng Zhang, Hangying Qu, Lin Liu, Mingxin Zhang, Junke Fu, Jia Zhang, Jiansheng Wang, Guangjian Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-019-2043-x

Exploring specific prognostic biomarkers in triple-negative breast cancer
Cited by: 53
Author(s): Chang Bao, Yunkun Lu, Jishun Chen, Danni Chen, Weiyang Lou, Bo Ding, Liang Xu, Weimin Fan
Software Mentions: 1
Published: almost 7 years ago

10.3390/metabo11030161

Metabolomic Profiling Reveals Sex Specific Associations with Chronic Obstructive Pulmonary Disease and Emphysema
Cited by: 14
Author(s): Lucas A. Gillenwater, Katerina Kechris, Katherine Pratte, Nichole Reisdorph, Irina Petrache, Wassim W. Labaki, Wanda K. O’Neal, Jerry A. Krishnan, Victor E. Ortega, Dawn L. DeMeo, Russell P. Bowler
Software Mentions: 1
Published: over 5 years ago

10.1155/2021/5518908

Screening Prognosis-Related lncRNAs Based on WGCNA to Establish a New Risk Score for Predicting Prognosis in Patients with Hepatocellular Carcinoma
Cited by: 4
Author(s): Xueliang Zhou, Mengmeng Dou, Zaoqu Liu, Dechao Jiao, Zhaonan Li, Jianjian Chen, Jing Li, Yuan Yao, Lifeng Li, Yahua Li, Xinwei Han
Software Mentions: 1
Published: about 5 years ago

10.1038/s41419-020-03305-z

Weighted gene coexpression network and experimental analyses identify lncRNA SPRR2C as a regulator of the IL-22-stimulated HaCaT cell phenotype through the miR-330/STAT1/S100A7 axis
Cited by: 14
Author(s): Meijunzi Luo, Pan Huang, Yi Pan, Zhu Zhu, Rong Zhou, Zhibo Yang, Chang Wang
Software Mentions: 1
Published: over 5 years ago

10.1186/s13578-021-00633-1

Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa
Cited by: 16
Author(s): Meng Li, Chenxing Zhang, Lei Hou, Weicong Yang, Songshan Liu, Xiaoming Pang, Yingyue Li
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers13122990

Transcriptomic and Genetic Associations between Alzheimer’s Disease, Parkinson’s Disease, and Cancer
Cited by: 24
Author(s): Jaume Forés-Martos, César Boullosa, David Rodrigo-Domínguez, Jon Sánchez-Valle, Beatriz Suay-García, Joan Climent, Antonio Falcó, Alfonso Valencia, Joan Antón Puig-Butillé, Susana Puig, Rafael Tabarés‐Seisdedos
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers12082230

Interplay of tRNA-Derived Fragments and T Cell Activation in Breast Cancer Patient Survival
Cited by: 17
Author(s): Nayang Shan, Ningshan Li, Qile Dai, Lin Hou, Xiting Yan, Amei Amei, Lei Lü, Zuoheng Wang
Software Mentions: 1
Published: about 6 years ago

10.1038/s41388-020-1379-0

Targeting the MAPK7/MMP9 axis for metastasis in primary bone cancer
Cited by: 21
Author(s): Darrell Green, Heather Eyre, Archana Archana, Jessica Taylor, Jason Chu, Lee Jeys, Vaiyapuri P. Sumathi, Aman S. Coonar, Doris M. Rassl, Muhammad Babur, Duncan Forster, Saba Alzabin, Frida Ponthan, Adam McMahon, Brian Bigger, Tristan A. Reekie, Kaye J. Williams, Tamás Dalmay, William D. Fraser, Katherine G. Finegan
Software Mentions: 1
Published: about 6 years ago

10.1038/s41388-021-01859-6

LncRNA MIR17HG promotes colorectal cancer liver metastasis by mediating a glycolysis-associated positive feedback circuit
Cited by: 39
Author(s): Senlin Zhao, Bingjie Guan, Yushuai Mi, Debing Shi, Ping Wei, Yanzi Gu, Sanjun Cai, Ye Xu, Xinxiang Li, Dongwang Yan, Mingzhu Huang, Dawei Li
Software Mentions: 1
Published: about 5 years ago

10.3390/nu13072185

Association of Plasma Phospholipids with Age-Related Cognitive Impairment: Results from a Cross-Sectional Study
Cited by: 2
Author(s): Tingting Liu, Shaojie Pang, Shanshan Jia, Qingqing Man, Yuqian Li, Shuang Song, Jian Zhang
Software Mentions: 1
Published: about 5 years ago

10.3390/cancers11040477

Exosomal miRNAs as Novel Pharmacodynamic Biomarkers for Cancer Chemopreventive Agent Early Stage Treatments in Chemically Induced Mouse Model of Lung Squamous Cell Carcinoma
Cited by: 6
Author(s): Yanzhao Zhou, Ming You, Meijun Du, Donghai Xiong, Yian Wang, Altaf Mohammed, Ronald A. Lubet, Liang Wang, Ming You
Software Mentions: 1
Published: over 7 years ago

10.3390/cancers11111688

Secondary Somatic Mutations in G-Protein-Related Pathways and Mutation Signatures in Uveal Melanoma
Cited by: 17
Author(s): Francesca Piaggio, Veronica Tozzo, Cinzia Bernardi, Michela Croce, Roberto Puzone, Silvia Viaggi, Serena Patrone, Annalisa Barla, Domenico Coviello, Martine J. Jager, Pieter A. van der Velden, Michael Zeschnigk, Davide Cangelosi, Alessandra Eva, Ulrich Pfeffer, Adriana Amaro
Software Mentions: 1
Published: almost 7 years ago

10.3390/cancers12071809

Identification of GSN and LAMC2 as Key Prognostic Genes of Bladder Cancer by Integrated Bioinformatics Analysis
Cited by: 16
Author(s): Jia-Lian Yang, Charles C.N. Wang, Jia-Hua Cai, Che‐Yi Chou, Yu‐Hsien Lin, Chin‐Chuan Hung
Software Mentions: 1
Published: about 6 years ago

10.4317/medoral.24385

Whole exome sequencing and system biology analysis support the "two-hit" mechanism in the onset of Ameloblastoma
Cited by: 4
Author(s): Yueqi Shi, Mengyu Li, Yinglan Yu, Yuqiong Zhou, Shaoyi Wang
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers10090307

A Comprehensive Survey of Immune Cytolytic Activity-Associated Gene Co-Expression Networks across 17 Tumor and Normal Tissue Types
Cited by: 4
Author(s): Tian Tian, Ji Wan, Han Yan, Haoran Liu, Feng Gao, Ying Pan, Qi Song, Zhi Wei
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0100690

Novel Insights into the Regulatory Architecture of CD4+ T Cells in Rheumatoid Arthritis
Cited by: 21
Author(s): Adrià Aterido, Carlos Palacio, Sara Marsal, G. Ávila, Antonio Julià
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0039498

A Gene Co-Expression Network in Whole Blood of Schizophrenia Patients Is Independent of Antipsychotic-Use and Enriched for Brain-Expressed Genes
Cited by: 121
Author(s): Simone de Jong, Marco P. Boks, Tova Fuller, Eric Strengman, Esther Janson, Carolien G.F. de Kovel, Anil P.S. Ori, Nancy Vi, Flip Mulder, Jan Dirk Blom, Birte Glenthøj, Chris D. Schubart, Wiepke Cahn, René S. Kahn, Steve Horvath, Roel A. Ophoff
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0154330

Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type
Cited by: 21
Author(s): Juxun Wu, Lili Fu, Hualin Yi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0127376

C9ORF72 GGGGCC Expanded Repeats Produce Splicing Dysregulation which Correlates with Disease Severity in Amyotrophic Lateral Sclerosis
Cited by: 87
Author(s): Johnathan Cooper‐Knock, Joanna J. Bury, Paul R. Heath, Matthew Wyles, Adrian Higginbottom, Catherine Gelsthorpe, J. Robin Highley, Guillaume M. Hautbergue, Magnus Rattray, Janine Kirby, Pamela J. Shaw
Software Mentions: 1
Published: over 11 years ago

10.1097/MD.0000000000009738

Identification of gene expression models for laryngeal squamous cell carcinoma using co-expression network analysis
Cited by: 9
Author(s): Chao Yang, Shufang Wang, Xiangli Yang, Lin Wang, Lin Niu, Jixiang Liu
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0255718

A propagation-based seed-centric local community detection for multilayer environment: The case study of colon adenocarcinoma
Cited by: 0
Author(s): Ehsan Pournoor, Zaynab Mousavian, Abbas Nowzari-Dalini, Ali Masoudi‐Nejad
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0203919

Vertical stratification of bacteria and the chemical compounds in crude oil-contaminated soil layers of the semi-deserted Dzungharian Basin
Cited by: 3
Author(s): Ji Hyun Yang, Jianfang Liang, Lu-Mei Xiao, Yang Yang, Qun-Fang Chao
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0167519

Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals
Cited by: 22
Author(s): Lisette J. A. Kogelman, Jingyuan Fu, Lude Franke, J.W.M. Greve, Marten H. Hofker, Sander S. Rensen, Haja N. Kadarmideen
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0198935

The influence of adolescent nicotine exposure on ethanol intake and brain gene expression
Cited by: 4
Author(s): Constanza P. Silva, W. J. Horton, Michael J. Caruso, Aswathy Sebastian, Laura Cousino Klein, István Albert, Helen M. Kamens
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0180972

Integrative functional analyses using rainbow trout selected for tolerance to plant diets reveal nutrigenomic signatures for soy utilization without the concurrence of enteritis
Cited by: 22
Author(s): Jason Abernathy, Andreas Brezas, Kevin Snekvik, Ronald W. Hardy, Ken Overturf
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0026683

Weighted Correlation Network Analysis (WGCNA) Applied to the Tomato Fruit Metabolome
Cited by: 137
Author(s): Matthew V. DiLeo, Gary D. Strahan, Meghan den Bakker, Owen A. Hoekenga
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0227547

Age-related transcriptional modules and TF-miRNA-mRNA interactions in neonatal and infant human thymus
Cited by: 6
Author(s): Fernanda Bernardi Bertonha, Sílvia Yumi Bando, Leandro Ferreira, Paulo Chaccur, Christiana de Freitas Vinhas, Maria Cláudia Nogueira Zerbini, Magda Carneiro‐Sampaio, Carlos Alberto Moreira-Filho
Software Mentions: 1
Published: over 6 years ago

10.1007/s00335-016-9656-5

Uncovering the liver’s role in immunity through RNA co-expression networks
Cited by: 11
Author(s): Kylie K. Harrall, Katerina Kechris, Boris Tabakoff, Paula L. Hoffman, Lisa M. Hines, Hidekazu Tsukamoto, Michal Pravenec, Morton P. Printz, Laura Saba
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0237526

Transcriptome analysis of table grapes (Vitis vinifera L.) identified a gene network module associated with berry firmness
Cited by: 9
Author(s): Lan Ma, Sun LingJun, Yongfeng Guo, Hong Lin, Zhendong Liu, Kun Li, Xuewu Guo
Software Mentions: 1
Published: about 6 years ago

10.26508/lsa.202101091

Serum proteomics reveals disorder of lipoprotein metabolism in sepsis
Cited by: 2
Author(s): Xi Liang, Tianzhou Wu, Qi Chen, Jing Jiang, Yongpo Jiang, Yiwen Ruan, Huaping Zhang, Sheng Zhang, Zhang Chao, Peng Chen, Yuhang Lv, Jiaojiao Xin, Dongyan Shi, Xin Chen, Li Jun, Yinghe Xu
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0182463

Cutaneous transcriptome analysis in NIH hairless mice
Cited by: 5
Author(s): Zhong-Hao Ji, Jian Chen, Wei Gao, Jinyu Zhang, Fu‐Shi Quan, Jian Hu, Bao Yuan, Wenzhi Ren
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0058951

Differential Network Analysis Reveals Genetic Effects on Catalepsy Modules
Cited by: 20
Author(s): Ovidiu D. Iancu, Denesa Oberbeck, Priscila Darakjian, Sunita Kawane, Jason Erk, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0147418

Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield
Cited by: 11
Author(s): Eunsoo Choe, Jenny Drnevich, Martin Williams
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0224497

Characterization of the placental transcriptome through mid to late gestation in the mare
Cited by: 13
Author(s): Shavahn C. Loux, Pouya Dini, Hesham A. Ali, Theodore S. Kalbfleisch, Barry A. Ball
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0193334

Chemokine expression in the early response to injury in human airway epithelial cells
Cited by: 7
Author(s): Bingqing Xie, Bharathi Laxman, Somaye Hashemifar, Randi Stern, T. Conrad Gilliam, Natalia Maltsev, Steven R. White
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0073413

A Network-Based Method to Assess the Statistical Significance of Mild Co-Regulation Effects
Cited by: 18
Author(s): Emőke-Ágnes Horvát, Jitaovid Da Zhang, Stefan Uhlmann, Özgür Şahin, Katharina Anna Zweig
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pntd.0005123

Blood Transcriptional Profiling Reveals Immunological Signatures of Distinct States of Infection of Humans with Leishmania infantum
Cited by: 46
Author(s): Luiz Gustavo Gardinassi, Gustavo García, Carlos Henrique Nery Costa, Vladimir Costa Silva, Isabel Kinney Ferreira de Miranda Santos
Software Mentions: 1
Published: almost 10 years ago

10.1155/2021/6651009

Candidate Genes Identified in Systemic Sclerosis-Related Pulmonary Arterial Hypertension Were Associated with Immunity, Inflammation, and Cytokines
Cited by: 5
Author(s): Zhixiao Xu, Jiaxing Ruan, Lingyun Pan, Chengshui Chen
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pmed.1003451

Associations among circulating sphingolipids, β-cell function, and risk of developing type 2 diabetes: A population-based cohort study in China
Cited by: 47
Author(s): Huan Yun, Liang Sun, Qingqing Wu, Geng Zong, Qibin Qi, Huaixing Li, Zheng He, Rong Zeng, Liming Liang, Xu Lin
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1002367

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans
Cited by: 122
Author(s): Maxime Rotival, Tanja Zeller, Philipp S. Wild, Seraya Maouche, Silke Szymczak, Arne Schillert, Raphaële Castagné, Arne Deiseroth, Carole Proust, Jessy Brocheton, Tiphaine Godefroy, Claire Perret, Marine Germain, Medea Eleftheriadis, Christoph Sinning, Renate B. Schnabel, Edith Lubos, Karl J. Lackner, Heidi Rossmann, Thomas Münzel, Augusto Rendon, Cardiogenics Consortium, Jeanette Erdmann, Panos Deloukas, Christian Hengstenberg, Patrick Diemert, Gilles Montalescot, Willem H. Ouwehand, Nilesh J. Samani, Heribert Schunkert, David‐Alexandre Trégouët, Andreas Ziegler, Alison H. Goodall, François Cambien, Laurence Tiret, Stefan Blankenberg
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pgen.1001113

An Immune Response Network Associated with Blood Lipid Levels
Cited by: 122
Author(s): Michael Inouye, Kaisa Silander, Eija Hämäläinen, Veikko Salomaa, Kennet Harald, Pekka Jousilahti, Satu Männistö, Johan G. Eriksson, Janna Saarela, Samuli Ripatti, Markus Perola, Gert‐Jan B. van Ommen, Marja‐Riitta Taskinen, Aarno Palotie, Emmanouil T. Dermitzakis, Leena Peltonen
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pgen.1004006

Multi-tissue Analysis of Co-expression Networks by Higher-Order Generalized Singular Value Decomposition Identifies Functionally Coherent Transcriptional Modules
Cited by: 53
Author(s): Xiaolin Xiao, Aida Moreno‐Moral, Maxime Rotival, Leonardo Bottolo, Enrico Petretto
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1007879

An interaction-based model for neuropsychiatric features of copy-number variants
Cited by: 38
Author(s): Matthew Jensen, Santhosh Girirajan
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1008155

Enhancing face validity of mouse models of Alzheimer’s disease with natural genetic variation
Cited by: 58
Author(s): Kristen D. Onos, Asli Uyar, Kelly J. Keezer, Harriet M. Jackson, Christoph Preuß, Casey Acklin, Rita O’Rourke, Rebecca A. Buchanan, Travis Cossette, Stacey J. Sukoff Rizzo, Ileana Soto, Gregory W. Carter, Gareth R. Howell
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms18040828

Delineating the Common Biological Pathways Perturbed by ASD’s Genetic Etiology: Lessons from Network-Based Studies
Cited by: 25
Author(s): Oded Oron, Evan Elliott
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms18071560

Co-Expression Network and Pathway Analyses Reveal Important Modules of miRNAs Regulating Milk Yield and Component Traits
Cited by: 34
Author(s): Duy Ngoc, Pier-Luc Dudemaine, Ran Li, Eveline M. Ibeagha‐Awemu
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1002596

The Transcription Factor Ultraspiracle Influences Honey Bee Social Behavior and Behavior-Related Gene Expression
Cited by: 74
Author(s): Seth A. Ament, Ying Wang, Chieh Chun Chen, Charles Blatti, Feng Hong, Zhengzheng S. Liang, Nicolas Nègre, Kevin P. White, Sandra L. Rodriguez-Zas, Craig A. Mizzen, Saurabh Sinha, Sheng Zhong, Gene E. Robinson
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1004402

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder
Cited by: 90
Author(s): Esther R. Berko, Masako Suzuki, Faygel Beren, Christophe Lemetre, Christine M. Alaimo, R. Brent Calder, Karen Ballaban‐Gil, Batya Gounder, Kaylee Kampf, Jill Kirschen, Shahina Maqbool, Zeineen Momin, David M. Reynolds, Natalie Russo, Lisa H. Shulman, Edyta Stasiek, Jessica N. Tozour, Maria Valicenti-McDermott, Shenglong Wang, Brett S. Abrahams, Joseph Hargitai, Dov Inbar, Zhengdong Zhang, Joseph D. Buxbaum, Sophie Molholm, John J. Foxe, Robert W. Marion, Adam Auton, John M. Greally
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pgen.1004550

Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease
Cited by: 75
Author(s): Michał Mielcarek, Linda Inuabasi, Marie K. Bondulich, Thomas Müller, Georgina F Osborne, Sophie A. Franklin, Donna Smith, Andreas Neueder, Jim Rosinski, Ivan Rattray, Andrea Protti, Gillian P. Bates
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1006490

Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation
Cited by: 97
Author(s): Sarah R. Smith, Jeroen Gillard, Adam B. Kustka, John P. McCrow, Jonathan H. Badger, Hong Zheng, Ashley M. New, Chris L. Dupont, Toshihiro Obata, Alisdair R. Fernie, Andrew E. Allen
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1006152

A High Temperature-Dependent Mitochondrial Lipase EXTRA GLUME1 Promotes Floral Phenotypic Robustness against Temperature Fluctuation in Rice (Oryza sativa L.)
Cited by: 27
Author(s): Biyao Zhang, Shifeng Wu, Yue Zhang, Ting Xu, Feifei Guo, Huashan Tang, Xiang Li, Pengfei Wang, Wenfeng Qian, Yongbiao Xue
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1008734

Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies
Cited by: 23
Author(s): Lulu Shang, Jennifer A. Smith, Xiang Zhou
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms19123829

Childhood-Onset Schizophrenia: Insights from Induced Pluripotent Stem Cells
Cited by: 22
Author(s): Anke Hoffmann, Michael J. Ziller, Dietmar Spengler
Software Mentions: 1
Published: almost 8 years ago

10.1155/2020/3946913

Metabolic Modulation and Potential Biomarkers of the Prognosis Identification for Severe Aortic Stenosis after TAVR by a Metabolomics Study
Cited by: 6
Author(s): Yanbiao Liao, Chang Liu, Tingting Xiong, Mingyue Zhao, Wen Zheng, Yuan Feng, Yijian Li, Yuanweixiang Ou, Zhengang Zhang, Yong Peng, Jiafu Wei, Qiao Li, Wei Meng, Xiaojing Liu, Mao Chen
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms20010178

Polybenzyl Glutamate Biocompatible Scaffold Promotes the Efficiency of Retinal Differentiation toward Retinal Ganglion Cell Lineage from Human-Induced Pluripotent Stem Cells
Cited by: 19
Author(s): Ta-Ching Chen, Pin-Yi She, Dong Feng Chen, Rita Jui-Hsien Lu, Chang-Hao Yang, Ding-Siang Huang, Pao‐Yang Chen, Chenyu Lu, Kin‐Sang Cho, Shee–Uan Chen, Wei‐Fang Su
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1002556

Networks of Neuronal Genes Affected by Common and Rare Variants in Autism Spectrum Disorders
Cited by: 137
Author(s): Eyal Ben-David, Sagiv Shifman
Software Mentions: 1
Published: over 14 years ago

10.1186/s40170-016-0143-y

Integration of omics: more than the sum of its parts
Cited by: 84
Author(s): Joerg M. Buescher, Edward M. Driggers
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1002038

Mouse Genome-Wide Association and Systems Genetics Identify Asxl2 As a Regulator of Bone Mineral Density and Osteoclastogenesis
Cited by: 107
Author(s): Charles R. Farber, Brian J. Bennett, Luz D. Orozco, Wei Zou, Ana Lira, Emrah Kostem, Hyun Min Kang, Nicholas A. Furlotte, Ani Berberyan, Anatole Ghazalpour, Jaijam Suwanwela, Thomas A. Drake, Eleazar Eskin, Q. Tian Wang, Steven L. Teitelbaum, Aldons J. Lusis
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pcbi.1000117

Geometric Interpretation of Gene Coexpression Network Analysis
Cited by: 663
Author(s): Steve Horvath, Jun Dong
Software Mentions: 1
Published: about 18 years ago

10.3390/ijms20092356

Transcriptomic Analysis Reveals a Comprehensive Calcium- and Phytohormone-Dominated Signaling Response in Leymus chinensis Self-Incompatibility
Cited by: 12
Author(s): Shuangyan Chen, Junjie Jia, Long Cheng, Pincang Zhao, Dongmei Qi, Weiguang Yang, Hui Liu, Xiao Dong, Xiaoxia Li, Gongshe Liu
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1000707

Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells
Cited by: 26
Author(s): Jun Cai, Dan Xie, Z. Fan, Hiram Chipperfield, John I. Marden, Wing Hung Wong, Sheng Zhong
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pcbi.1004332

Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
Cited by: 42
Author(s): Xiaoke Ma, Long Gao, Georgios Karamanlidis, Peng Gao, Chi Fung Lee, Lorena Garcia-Menendez, Rong Tian, Kai Tan
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms20163846

Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass
Cited by: 7
Author(s): Most. Humaira Sultana, FangJie Liu, Md. Alamin, Limin Mao, Jia Lu, Hongyu Chen, Dongya Wu, Yingying Wang, Fei Fu, Sanling Wu, Weidi Wang, Chu-Yu Ye, Qian Zhu, Jie Qiu, Longjiang Fan
Software Mentions: 1
Published: about 7 years ago

10.1155/2019/9567641

Weighted Gene Coexpression Network Analysis Identified MicroRNA Coexpression Modules and Related Pathways in Type 2 Diabetes Mellitus
Cited by: 26
Author(s): Tianyu Feng, Kexin Li, Pingping Zheng, Yanjun Wang, Yaogai Lv, Ли Шен, Chen Yang, Zhiqiang Xue, Bo Li, Lina Jin, Yan Yao
Software Mentions: 1
Published: over 6 years ago

10.1002/cam4.3240

Development and validation of an immune‐related prognostic signature in lung adenocarcinoma
Cited by: 69
Author(s): Sijin Sun, Wei Guo, Zhen Wang, Xin Wang, Guochao Zhang, Hao Zhang, Renda Li, Yibo Gao, Bin Qiu, Fengwei Tan, Yushun Gao, Qi Xue, Shugeng Gao, Jie He
Software Mentions: 1
Published: about 6 years ago

10.3390/jcm8101719

Reformulating Pro-Oxidant Microglia in Neurodegeneration
Cited by: 45
Author(s): Juan García-Revilla, Isabel María Alonso-Bellido, Miguel Ángel Burguillos, Antonio J. Herrera, Ana M. Espinosa-Oliva, Rocío Ruiz, Luis Cruz-Hernández, Irene García-Domínguez, María Angustias Roca-Ceballos, Marti Santiago, José A. Rodríguez‐Gómez, Manuel Sarmiento Soto, Rocío M. de Pablos, José L. Venero
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms20184358

Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
Cited by: 5
Author(s): Xiaoxiang Zhang, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Junpeng Wang, Chang Liu, Yin Su, Juan Zhou, Ning Xiao, Cunhong Pan, Yabin Xu, Guichun Dong, Zefeng Yang, Aihong Li, Jianye Huang, Yulong Wang, Youli Yao
Software Mentions: 1
Published: about 7 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479