cran: WGCNA | Projects | Ecosyste.ms: Papers

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

10.3390/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

10.1186/s12864-016-3176-2

Large-scale gene co-expression network as a source of functional annotation for cattle genes
Cited by: 16
Author(s): Hamid Beiki, A. Nejati‐Javaremi, A. Pakdel, Ali Masoudi‐Nejad, Zhi-Liang Hu, James M. Reecy
Software Mentions: 1
Published: almost 10 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

10.1186/1471-2164-12-S3-S3

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information
Cited by: 40
Author(s): Langho Lee, Kai Wang, Gang Li, Zhi Xie, Yuli Wang, Jiangchun Xu, Shaoxian Sun, David Pocalyko, Jong Bhak, Chulhong Kim, Kee-Ho Lee, Ye Jin Jang, Young Il Yeom, Hyang Sook Yoo, Seungwoo Hwang
Software Mentions: 1
Published: almost 15 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

10.1371/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

10.1186/s12864-018-5104-0

Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.)
Cited by: 13
Author(s): Guangyan Feng, Lei Xu, Jianping Wang, Gang Nie, B. Shaun Bushman, Wengang Xie, Haidong Yan, Zhongfu Yang, Hao Guan, Linkai Huang, Xinquan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-020-07250-1

Deficiencies in the formation and regulation of anther cuticle and tryphine contribute to male sterility in cotton PGMS line
Cited by: 5
Author(s): Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei, Shuang Yu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-019-5424-8

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening
Cited by: 36
Author(s): Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng, Wanpeng Xi
Software Mentions: 1
Published: over 7 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

10.1007/s13238-016-0247-8

Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation
Cited by: 34
Author(s): Xiaoying Chen, Kunshan Zhang, Libing Zhou, Xinpei Gao, Junbang Wang, Yinan Yao, Fei He, Yuan Luo, Yongchun Yu, Siguang Li, Liming Cheng, Yi Sun
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-019-5773-3

A deficiency in SUMOylation activity disrupts multiple pathways leading to neural tube and heart defects in Xenopus embryos
Cited by: 11
Author(s): Michelle M. Bertke, Kyle M. Dubiak, Laura Cronin, Erliang Zeng, Paul W. Huber
Software Mentions: 1
Published: over 7 years ago

10.1007/s13238-018-0559-y

Unbiased transcriptomic analyses reveal distinct effects of immune deficiency in CNS function with and without injury
Cited by: 9
Author(s): Dandan Luo, Weihong Ge, Xiao Hu, Chen Li, Chia Ming Lee, Libing Zhou, Zhourui Wu, Juehua Yu, Shaochong Lin, Jing Yu, Wei Xu, Lei Chen, Chong Zhang, Kun Jiang, Xuding Zhu, Haotian Li, Xinpei Gao, Yanan Geng, Bo Jing, Zhen Wang, Changhong Zheng, Rongrong Zhu, Yan Qiao, Qing Lin, Keqiang Ye, Yi Sun, Liming Cheng
Software Mentions: 1
Published: about 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

10.3390/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

10.1136/rmdopen-2015-000183

Leucocyte subset-specific type 1 interferon signatures in SLE and other immune-mediated diseases
Cited by: 25
Author(s): Shaun Flint, Vojislav Jovanović, Boon Wee Teo, Anselm Mak, Julian Thumboo, Eoín McKinney, James C. Lee, Paul A. MacAry, David M. Kemeny, David Jayne, Kok Yong Fong, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 1
Published: over 10 years ago

10.1098/rsos.172062

Transcriptional analyses provide new insight into the late-stage immune response of a diseased Caribbean coral
Cited by: 28
Author(s): Lauren E. Fuess, Whitney T. Mann, Lea R. Jinks, Vanessa Brinkhuis, Laura D. Mydlarz
Software Mentions: 1
Published: over 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

10.3390/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

10.1016/j.redox.2021.101933

Network analysis of nitrate-sensitive oral microbiome reveals interactions with cognitive function and cardiovascular health across dietary interventions
Cited by: 20
Author(s): Anni Vanhatalo, Joanna E. L’Heureux, James Kelly, Jamie R. Blackwell, Lee J. Wylie, Jonathan Fulford, Paul G. Winyard, David Wynne Williams, Mark van der Giezen, Andrew M. Jones
Software Mentions: 1
Published: over 5 years ago

10.1186/s12958-021-00785-2

Abnormally increased DNA methylation in chorionic tissue might play an important role in development of ectopic pregnancy
Cited by: 1
Author(s): Chen Wen, Yang Liu, Ruiqing Zhang, Yang Yao, Shuangdi Li, Jiarong Zhang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-016-3201-5

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass
Cited by: 14
Author(s): Taylor P. Frazier, Nathan A. Palmer, Fuliang Xie, Christian M. Tobias, Teresa Donze-Reiner, Aureliano Bombarely, Kevin L. Childs, Shengqiang Shu, Jerry Jenkins, Jeremy Schmutz, Baohong Zhang, Gautam Sarath, Bingyu Zhao
Software Mentions: 1
Published: almost 10 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

10.1186/s12931-017-0558-1

Network-based analysis reveals novel gene signatures in peripheral blood of patients with chronic obstructive pulmonary disease
Cited by: 31
Author(s): Ma’en Obeidat, Yunlong Nie, Virginia Chen, Casey P. Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rötzschke, Peter J. Castaldi, Craig P. Hersh, Nick Fishbane, Raymond T. Ng, Bruce M. McManus, Bruce E. Miller, Stephen I. Rennard, Peter D. Paré, Don D. Sin
Software Mentions: 1
Published: over 9 years ago

10.1186/s12931-018-0965-y

Do sputum or circulating blood samples reflect the pulmonary transcriptomic differences of COPD patients? A multi-tissue transcriptomic network META-analysis
Cited by: 8
Author(s): Rosa Faner, Jarrett Morrow, Sandra Casas-Recasens, Suzanne M. Cloonan, Guillaume Noell, Alejandra López-Giraldo, Ruth Tal‐Singer, Bruce E. Miller, Edwin K. Silverman, Àlvar Agustí, Craig P. Hersh
Software Mentions: 1
Published: over 7 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

10.1186/s12931-019-1105-z

Multi-level immune response network in mild-moderate Chronic Obstructive Pulmonary Disease (COPD)
Cited by: 33
Author(s): Tamara Cruz, Alejandra López-Giraldo, Guillaume Noell, Sandra Casas-Recasens, Tamara García, Laureano Molins, Manel Juan, Marco A. Fernández, Àlvar Agustí, Rosa Faner
Software Mentions: 1
Published: about 7 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

10.1186/1471-2164-11-589

Is human blood a good surrogate for brain tissue in transcriptional studies?
Cited by: 101
Author(s): Chaochao Cai, Peter Langfelder, Tova Fuller, Michael C. Oldham, Rui Luo, Leonard H van den Berg, Roel A. Ophoff, Steve Horvath
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12284-020-00437-w

Long Non-coding RNAs Responsive to Blast Fungus Infection in Rice
Cited by: 16
Author(s): Lanlan Wang, Jingjing Jin, Lihua Li, Shaohong Qu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12284-020-00439-8

Weighted Gene Co-Expression Network Coupled with a Critical-Time-Point Analysis during Pathogenesis for Predicting the Molecular Mechanism Underlying Blast Resistance in Rice
Cited by: 2
Author(s): Dagang Tian, Zaijie Chen, Yan Lin, Ziqiang Chen, Zonghua Wang, Wang Feng
Software Mentions: 1
Published: almost 6 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

10.1186/1471-2164-10-327

Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
Cited by: 189
Author(s): Mike J. Mason, Guoping Fan, Kathrin Plath, Qing Zhou, Steve Horvath
Software Mentions: 1
Published: about 17 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

10.1186/s12863-015-0311-z

Gene expression in large pedigrees: analytic approaches
Cited by: 5
Author(s): Rita M. Cantor, Heather J. Cordell
Software Mentions: 1
Published: over 10 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: about 13 years ago

10.1038/s41597-021-00828-8

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera
Cited by: 22
Author(s): Hui Li, Xingyu Yang, Yue Zhang, Zhiyan Gao, Yuting Liang, Jin‐Ming Chen, Tao Shi
Software Mentions: 1
Published: over 5 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

10.1186/s12863-018-0648-1

Epigenetics, heritability and longitudinal analysis
Cited by: 5
Author(s): Haakon E. Nustad, Marcio Almeida, Angelo J. Canty, Marissa LeBlanc, Christian M. Page, Phillip E. Melton
Software Mentions: 1
Published: about 8 years ago

10.1038/srep12298

Network analysis of immunotherapy-induced regressing tumours identifies novel synergistic drug combinations
Cited by: 55
Author(s): W. Joost Lesterhuis, Catherine Rinaldi, Anya C. Jones, Esdy N. Rozali, Ian M. Dick, Andrea Khong, Louis Boon, Bruce Robinson, Anna K. Nowak, Anthony Bosco, Richard Lake
Software Mentions: 1
Published: about 11 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: almost 6 years ago

10.1038/srep13248

Derivation of a fifteen gene prognostic panel for six cancers
Cited by: 22
Author(s): Mamata F. Khirade, Girdhari Lal, Sharmila A. Bapat
Software Mentions: 1
Published: about 11 years ago

10.1186/s12876-017-0637-2

miR-363-5p as potential prognostic marker for hepatocellular carcinoma indicated by weighted co-expression network analysis of miRNAs and mRNA
Cited by: 18
Author(s): Jun Zhang, Jia Fan, Chongming Zhou, Yanyu Qi
Software Mentions: 1
Published: about 9 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

10.1038/srep17494

Honey bee microRNAs respond to infection by the microsporidian parasite Nosema ceranae
Cited by: 15
Author(s): Qiang Huang, Yanping Chen, Rui Wu Wang, Ryan S. Schwarz, Jay D. Evans
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep18045

Proteome Analysis of Renoprotection Mediated by a Novel Cyclic Helix B Peptide in Acute Kidney Injury
Cited by: 18
Author(s): Cheng Yang, Junjun Liu, Li Long, Man Hu, Ya‐Qiu Long, Xiaohui Liu, Tongyu Zhu, Xiao Huang, Shouliang Zhao, Shangfeng Liu, Ruiming Rong
Software Mentions: 1
Published: almost 11 years ago

10.1038/srep19430

DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders
Cited by: 66
Author(s): Fan Wang, Hao Xu, Hongyu Zhao, Joel Gelernter, Huiping Zhang
Software Mentions: 1
Published: over 10 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: about 16 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

10.18632/aging.202761

A five-m6A regulatory gene signature is a prognostic biomarker in lung adenocarcinoma patients
Cited by: 12
Author(s): Ximei Wu, Hongxu Sheng, Luming Wang, Pinghui Xia, Yiqing Wang, Li Yu, Wang Lv, Jian Hu
Software Mentions: 1
Published: over 5 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

10.1038/srep25261

Elucidation of molecular and functional heterogeneity through differential expression network analyses of discrete tumor subsets
Cited by: 6
Author(s): Rutika R. Naik, Nilesh Gardi, Sharmila A. Bapat
Software Mentions: 1
Published: over 10 years ago

10.1038/srep26396

The simple neuroendocrine-immune regulatory network in oyster Crassostrea gigas mediates complex functions
Cited by: 38
Author(s): Zhaoqun Liu, Lingling Wang, Zhi Zhou, Ying Sun, Mengqiang Wang, Hao Wang, Zujun Hou, Dahai Gao, Qiang Gao, Linsheng Song
Software Mentions: 1
Published: over 10 years ago

10.1186/s12862-017-1036-6

Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication
Cited by: 12
Author(s): Yun-Mei Wang, Haibo Xu, Mingshan Wang, Newton O. Otecko, Lingqun Ye, Dongdong Wu, Yaping Zhang
Software Mentions: 1
Published: about 9 years ago

10.1038/srep28422

Construction and application of a co-expression network in Mycobacterium tuberculosis
Cited by: 31
Author(s): Jun Jiang, Xian Sun, Wei Wu, Li Li, Hai Wu, Lu Zhang, Guohua Yu, Yao Li
Software Mentions: 1
Published: about 10 years ago

10.18632/aging.101550

A seven-long noncoding RNA signature predicts overall survival for patients with early stage non-small cell lung cancer
Cited by: 39
Author(s): Ting Lin, Yunong Fu, Xing Zhang, Jingxian Gu, Xiaojie Ma, Runchen Miao, Xiaohong Xiang, Wenquan Niu, Kai Qu, Chang Liu, Qifei Wu
Software Mentions: 1
Published: about 8 years ago

10.1038/srep29052

Integrative Network-based Analysis of Magnetic Resonance Spectroscopy and Genome Wide Expression in Glioblastoma multiforme
Cited by: 19
Author(s): Dieter Henrik Heiland, Irina Mader, Pascal Schlosser, Dietmar Pfeifer, Maria Stella Carro, Thomas Lange, Ralf Schwarzwald, Ioannis Vasilikos, Horst Urbach, Astrid Weyerbrock
Software Mentions: 1
Published: about 10 years ago

10.1038/srep28663

Indexing Effects of Copy Number Variation on Genes Involved in Developmental Delay
Cited by: 35
Author(s): Mohammed Uddin, Giovanna Pellecchia, Bhooma Thiruvahindrapuram, Lia D’Abate, Daniele Merico, Ada J.S. Chan, Mehdi Zarrei, Kristiina Tammimies, Susan Walker, Matthew J. Gazzellone, Thomas Nalpathamkalam, Ryan K. C. Yuen, Koenraad Devriendt, Géraldine Mathonnet, Emmanuelle Lemyre, Sonia Nizard, Mary Shago, Ann M. Joseph-George, Abdul Noor, Melissa T. Carter, Grace Yoon, Peter Kannu, Frédérique Tihy, Erik C. Thorland, Christian R. Marshall, Janet A. Buchanan, Marsha Speevak, Dimitri J. Stavropoulos, Stephen W. Scherer
Software Mentions: 1
Published: about 10 years ago

10.1186/s12872-016-0217-3

Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease
Cited by: 66
Author(s): Jing Liu, Ling Jing, Xilin Tu
Software Mentions: 1
Published: over 10 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

10.1186/s12872-021-01973-z

Comparative transcriptome analysis of transcripts of uncertain coding potential in septic myocardial depression
Cited by: 1
Author(s): Tie-Ning Zhang, Ri Wen, Ni Yang, Chunfeng Liu
Software Mentions: 1
Published: over 5 years ago

10.1038/srep31851

Single-cell RNA-seq reveals distinct injury responses in different types of DRG sensory neurons
Cited by: 109
Author(s): Ganlu Hu, Kevin Huang, Youjin Hu, Guizhen Du, Zhigang Xue, Xianmin Zhu, Guoping Fan
Software Mentions: 1
Published: about 10 years ago

10.1038/srep32005

Integrative effect of drought and low temperature on litchi (Litchi chinensis Sonn.) floral initiation revealed by dynamic genome-wide transcriptome analysis
Cited by: 24
Author(s): Jiyuan Shen, Qiusheng Xiao, Haiji Qiu, Chengjie Chen, Houbin Chen
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33227

Network Analysis of Fine Particulate Matter (PM2.5) Emissions in China
Cited by: 12
Author(s): Shaomin Yan, Guang Wu
Software Mentions: 1
Published: about 10 years ago

10.1038/srep33655

Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression
Cited by: 24
Author(s): Liang‐Jiao Xue, Christopher J. Frost, Chung‐Jui Tsai, Chung‐Jui Tsai
Software Mentions: 1
Published: almost 10 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

10.1371/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

10.3390/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

10.1038/srep38575

Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development
Cited by: 4
Author(s): Zhiping Wen, Geng Chen, Sibo Zhu, Jiaquan Zhu, Bin Li, Yunjie Song, Suqing Li, Leming Shi, Yuanting Zheng, Menglong Li
Software Mentions: 1
Published: almost 10 years ago

10.1038/srep38956

Pan- and core- network analysis of co-expression genes in a model plant
Cited by: 20
Author(s): Fei He, Sergei Maslov
Software Mentions: 1
Published: over 9 years ago

10.1186/s12872-021-02211-2

Identification of key miRNAs and mRNAs related to coronary artery disease by meta-analysis
Cited by: 3
Author(s): Long Liu, Jingze Zhang, Mei Yi Wu, Haiming Xu
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12885-021-08030-0

An energy metabolism-based eight-gene signature correlates with the clinical outcome of esophagus carcinoma
Cited by: 8
Author(s): Wei Zheng, Chaoying Chen, Jianghao Yu, Chengfeng Jin, Tie-Mei Han
Software Mentions: 1
Published: over 5 years ago

10.1038/srep39614

Genetically regulated hepatic transcripts and pathways orchestrate haematological, biochemical and body composition traits
Cited by: 7
Author(s): Siriluck Ponsuksili, Nares Trakooljul, Frieder Hadlich, Fiete Haack, Eduard Muráni, Klaus Wimmers
Software Mentions: 1
Published: over 9 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

10.3390/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

10.1371/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

10.1038/srep43523

Integrative Diffusion-Weighted Imaging and Radiogenomic Network Analysis of Glioblastoma multiforme
Cited by: 18
Author(s): Dieter Henrik Heiland, Carl Philipp Simon-Gabriel, Theo Demerath, Gerrit Haaker, Dietmar Pfeifer, Elias Kellner, Valerij G. Kiselev, Ori Staszewski, Horst Urbach, Astrid Weyerbrock, Irina Mader
Software Mentions: 1
Published: over 9 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

10.1155/2019/9567641

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

10.1371/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

10.1038/s41598-017-00952-9

Global gene expression profiling of healthy human brain and its application in studying neurological disorders
Cited by: 49
Author(s): Simarjeet Negi, Chittibabu Guda
Software Mentions: 1
Published: over 9 years ago

10.18632/aging.202996

Circular RNA circitga7 accelerates glioma progression via miR-34a-5p/VEGFA axis
Cited by: 10
Author(s): Ling Qi, Weiyao Wang, Guifang Zhao, Hong Jiang, Yu Zhang, Donghai Zhao, Hong Jin, Haojun Yu, Haidong Xu
Software Mentions: 1
Published: over 5 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

10.1038/s41598-017-00808-2

Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler
Cited by: 13
Author(s): Jon Y. Suzuki, T.D. Amore, Bernarda Calla, Nathan A. Palmer, Erin D. Scully, Scott E. Sattler, Gautam Sarath, J.S. Lichty, Roxana Y. Myers, Lisa M. Keith, Tracie K. Matsumoto, Scott M. Geib
Software Mentions: 1
Published: over 9 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

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/ijms20194781

The Need for Multi-Omics Biomarker Signatures in Precision Medicine
Cited by: 242
Author(s): Michael Olivier, Reto Asmis, Gregory A. Hawkins, Timothy D. Howard, Laura A. Cox
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pcbi.1006436

Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
Cited by: 17
Author(s): Yafei Lyu, Lingzhou Xue, Feipeng Zhang, Hillary Koch, Laura Saba, Katerina Kechris, Qunhua Li
Software Mentions: 1
Published: almost 8 years ago

Projects: cran: WGCNA

Science Score: 85/100

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Papers Mentioning WGCNA 3,479