Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development.


:Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo (Phyllostachys edulis) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits. We integrated the genome sequence of moso bamboo and 78 transcriptome data sets to build genome-wide global and conditional co-expression networks. We overlaid the gene expression results onto the network with multiple dimensions (different development stages). Through combining the co-expression network, module classification and function enrichment tools, we identified 1,896 functional modules related to bamboo development, which covered functions such as photosynthesis, hormone biosynthesis, signal transduction, and secondary cell wall biosynthesis. Furthermore, an online database ( was built for searching the moso bamboo co-expression network and module enrichment analysis. Our database also includes cis-element analysis, gene set enrichment analysis, and other tools. In summary, we integrated public and in-house bamboo transcriptome data sets and carried out co-expression network analysis and functional module identification. Through data mining, we have yielded some novel insights into the regulation of growth and development. Our established online database might be convenient for the bamboo research community to identify functional genes or modules with important traits.


Front Genet


Frontiers in genetics


Ma X,Zhao H,Xu W,You Q,Yan H,Gao Z,Su Z




Has Abstract


2018-11-27 00:00:00








  • New Insights From Imputed Whole-Genome Sequence-Based Genome-Wide Association Analysis and Transcriptome Analysis: The Genetic Mechanisms Underlying Residual Feed Intake in Chickens.

    abstract::Poultry feed constitutes the largest cost in poultry production, estimated to be up to 70% of the total cost. Moreover, there is pressure on the poultry industry to increase production to meet the protein demand of humans and simultaneously reduce emissions to protect the environment. Therefore, improving feed efficie...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Ye S,Chen ZT,Zheng R,Diao S,Teng J,Yuan X,Zhang H,Chen Z,Zhang X,Li J,Zhang Z

    更新日期:2020-04-03 00:00:00

  • Transcriptome Analyses Identify an RNA Binding Protein Related Prognostic Model for Clear Cell Renal Cell Carcinoma.

    abstract::RNA binding proteins (RBPs) play a key role in post-transcriptional gene regulation. They have been shown to be dysfunctional in a variety of cancers and are closely related to the occurrence and progression of cancers. However, the biological function and clinical significance of RBPs in clear cell renal carcinoma (c...

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    pub_type: 杂志文章


    authors: Wu Y,Wei X,Feng H,Hu B,Liu B,Luan Y,Ruan Y,Liu X,Liu Z,Wang S,Liu J,Wang T

    更新日期:2021-01-07 00:00:00

  • The Value of Mouse Models of Rare Diseases: A Spanish Experience.

    abstract::Animal models are invaluable for biomedical research, especially in the context of rare diseases, which have a very low prevalence and are often complex. Concretely mouse models provide key information on rare disease mechanisms and therapeutic strategies that cannot be obtained by using only alternative methods, and ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Murillo-Cuesta S,Artuch R,Asensio F,de la Villa P,Dierssen M,Enríquez JA,Fillat C,Fourcade S,Ibáñez B,Montoliu L,Oliver E,Pujol A,Salido E,Vallejo M,Varela-Nieto I

    更新日期:2020-10-14 00:00:00

  • Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies.

    abstract::In the last few years, the role of non-coding regulatory elements and their involvement in human disease have received great attention. Among the non-coding regulatory sequences, enhancers are particularly important for the proper establishment of cell type-specific gene-expression programs. Furthermore, the disruptio...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Sánchez-Gaya V,Mariner-Faulí M,Rada-Iglesias A

    更新日期:2020-07-20 00:00:00

  • A Novel Approach to Clustering Genome Sequences Using Inter-nucleotide Covariance.

    abstract::Classification of DNA sequences is an important issue in the bioinformatics study, yet most existing methods for phylogenetic analysis including Multiple Sequence Alignment (MSA) are time-consuming and computationally expensive. The alignment-free methods are popular nowadays, whereas the manual intervention in those ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Dong R,He L,He RL,Yau SS

    更新日期:2019-04-09 00:00:00

  • Testing for direct genetic effects using a screening step in family-based association studies.

    abstract::In genome wide association studies (GWAS), family-based studies tend to have less power to detect genetic associations than population-based studies, such as case-control studies. This can be an issue when testing if genes in a family-based GWAS have a direct effect on the phenotype of interest over and above their po...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Lutz SM,Vansteelandt S,Lange C

    更新日期:2013-11-21 00:00:00

  • Molecular Characterization of New FBXL4 Mutations in Patients With mtDNA Depletion Syndrome.

    abstract::Encephalomyopathic mitochondrial DNA (mtDNA) depletion syndrome 13 (MTDPS13) is a rare genetic disorder caused by defects in F-box leucine-rich repeat protein 4 (FBXL4). Although FBXL4 is essential for the bioenergetic homeostasis of the cell, the precise role of the protein remains unknown. In this study, we report t...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Emperador S,Garrido-Pérez N,Amezcua-Gil J,Gaudó P,Andrés-Sanz JA,Yubero D,Fernández-Marmiesse A,O'Callaghan MM,Ortigoza-Escobar JD,Iriondo M,Ruiz-Pesini E,García-Cazorla A,Gil-Campos M,Artuch R,Montoya J,Bayona-Bafaluy MP

    更新日期:2020-01-08 00:00:00

  • Highlighting the DNA damage response with ultrashort laser pulses in the near infrared and kinetic modeling.

    abstract::Our understanding of the mechanisms governing the response to DNA damage in higher eucaryotes crucially depends on our ability to dissect the temporal and spatial organization of the cellular machinery responsible for maintaining genomic integrity. To achieve this goal, we need experimental tools to inflict DNA lesion...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Ferrando-May E,Tomas M,Blumhardt P,Stöckl M,Fuchs M,Leitenstorfer A

    更新日期:2013-07-16 00:00:00

  • The Spectrum of Neurological and White Matter Changes and Premutation Status Categories of Older Male Carriers of the FMR1 Alleles Are Linked to Genetic (CGG and FMR1 mRNA) and Cellular Stress (AMPK) Markers.

    abstract::The fragile X premutation (PM) allele contains a CGG expansion of 55-200 repeats in the FMR1 gene's promoter. Male PM carriers have an elevated risk of developing neurological and psychiatric changes, including an approximately 50% risk of the fragile X-associated tremor/ataxia syndrome (FXTAS). The aim of this study ...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Loesch DZ,Trost N,Bui MQ,Hammersley E,Lay ST,Annesley SJ,Sanislav O,Allan CY,Tassone F,Chen ZP,Ngoei KRW,Kemp BE,Francis D,Fisher PR,Storey E

    更新日期:2018-11-12 00:00:00

  • Comparative Genomic Analysis Reveals Extensive Genetic Variations of WRKYs in Solanaceae and Functional Variations of CaWRKYs in Pepper.

    abstract::As a conserved protein family, WRKY has been shown to be involved in multiple biological processes in plants. However, the mechanism of functional diversity for WRKYs in pepper has not been well elucidated. Here, a total of 223 WRKY members from solanaceae crops including pepper, tomato and potato, were analyzed using...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Cheng Y,Ahammed GJ,Yao Z,Ye Q,Ruan M,Wang R,Li Z,Zhou G,Wan H

    更新日期:2019-05-28 00:00:00

  • A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus).

    abstract::Goats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion, and utilisation of marginal grazing. There are excellent genetic an...

    journal_title:Frontiers in genetics

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    authors: Muriuki C,Bush SJ,Salavati M,McCulloch MEB,Lisowski ZM,Agaba M,Djikeng A,Hume DA,Clark EL

    更新日期:2019-11-04 00:00:00

  • Ideal Cereals With Lower Arsenic and Cadmium by Accurately Enhancing Vacuolar Sequestration Capacity.

    abstract::Cereals are a staple food for many people around the world; however, they are also a major dietary source of toxic metal(loid)s. Many agricultural regions throughout the world are contaminated with toxic metal(loid)s, which can accumulate to high levels in the grains of cereals cultivated in these regions, posing seri...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Deng F,Yu M,Martinoia E,Song WY

    更新日期:2019-04-09 00:00:00

  • Dual Convolutional Neural Networks With Attention Mechanisms Based Method for Predicting Disease-Related lncRNA Genes.

    abstract::A lot of studies indicated that aberrant expression of long non-coding RNA genes (lncRNAs) is closely related to human diseases. Identifying disease-related lncRNAs (disease lncRNAs) is critical for understanding the pathogenesis and etiology of diseases. Most of the previous methods focus on prioritizing the potentia...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Xuan P,Cao Y,Zhang T,Kong R,Zhang Z

    更新日期:2019-05-03 00:00:00

  • DNA methylation changes in the postmortem dorsolateral prefrontal cortex of patients with schizophrenia.

    abstract:BACKGROUND:Schizophrenia is a complex psychiatric disorder with a lifetime morbidity rate of 0.5-1.0%. The pathophysiology of schizophrenia still remains obscure. Accumulating evidence indicates that DNA methylation, which is the addition of a methyl group to the cytosine in a CpG dinucleotide, might play an important ...

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    pub_type: 杂志文章


    authors: Numata S,Ye T,Herman M,Lipska BK

    更新日期:2014-08-26 00:00:00

  • Intra-Familial Phenotypic Heterogeneity and Telomere Abnormality in von Hippel- Lindau Disease: Implications for Personalized Surveillance Plan and Pathogenesis of VHL-Associated Tumors.

    abstract::von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome with poor survival. The current recommendations have proposed uniform surveillance strategies for all patients, neglecting the obvious phenotypic varieties. In this study, we aim to confirm the phenotypic heterogeneity in VHL disease and the underlying me...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Wang J,Peng X,Chen C,Ning X,Peng S,Li T,Liu S,Hong B,Zhou J,Ma K,Cai L,Gong K

    更新日期:2019-04-24 00:00:00

  • MiR-486-5p Serves as a Good Biomarker in Nonsmall Cell Lung Cancer and Suppresses Cell Growth With the Involvement of a Target PIK3R1.

    abstract::MicroRNAs are a class of noncoding RNAs that can be involved in the regulation of gene expression in cancers, including lung cancer. Our previous research has shown that miR-486-5p is one of the most downregulated microRNAs in tissue and serum samples of lung cancer as a good diagnostic biomarker. The objective of thi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Tian F,Wang J,Ouyang T,Lu N,Lu J,Shen Y,Bai Y,Xie X,Ge Q

    更新日期:2019-07-26 00:00:00

  • Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool.

    abstract::Transcriptome analyses have increased our understanding of the molecular mechanisms underlying human diseases. Most approaches aim to identify significant genes by comparing their expression values between healthy subjects and a group of patients with a certain disease. Given that studies normally contain few samples,...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Gonçalves ANA,Lever M,Russo PST,Gomes-Correia B,Urbanski AH,Pollara G,Noursadeghi M,Maracaja-Coutinho V,Nakaya HI

    更新日期:2019-10-24 00:00:00

  • Epigenetic regulation of cardiac myocyte differentiation.

    abstract::Cardiac myocytes (CMs) proliferate robustly during fetal life but withdraw permanently from the cell cycle soon after birth and undergo terminal differentiation. This cell cycle exit is associated with the upregulation of a host of adult cardiac-specific genes. The vast majority of adult CMs (ACMs) do not reenter cell...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Oyama K,El-Nachef D,Zhang Y,Sdek P,MacLellan WR

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  • The anti-miR21 antagomir, a therapeutic tool for colorectal cancer, has a potential synergistic effect by perturbing an angiogenesis-associated miR30.

    abstract::Colon cancer has the third highest incidence and mortality among cancers in the United States. MicroRNA-21 (miR21) has been described as an oncomir that is highly overexpressed in tumor tissue from colorectal cancer. Recent studies showed that silencing of miR21 through use of a miR21 inhibitor (anti-miR21) affected v...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Song MS,Rossi JJ

    更新日期:2014-01-02 00:00:00

  • A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.

    abstract::Pathway analysis is a powerful method for data analysis in genomics, most often applied to gene expression analysis. It is also promising for single-nucleotide polymorphism (SNP) data analysis, such as genome-wide association study data, because it allows the interpretation of variants with respect to the biological p...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: Cirillo E,Parnell LD,Evelo CT

    更新日期:2017-11-07 00:00:00

  • SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin.

    abstract::Cell viability and gene expression profiles are altered in cellular models of neurodegenerative disorders such as Huntington's Disease (HD). Using the yeast model system, we show that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity associated with a mutant, ag...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Ohkuni K,Pasupala N,Peek J,Holloway GL,Sclar GD,Levy-Myers R,Baker RE,Basrai MA,Kerscher O

    更新日期:2018-09-18 00:00:00

  • Genome-Wide Screening of mRNA Expression in Leprosy Patients.

    abstract::Leprosy, an infectious disease caused by Mycobacterium leprae, affects millions of people worldwide. However, little is known regarding its molecular pathophysiological mechanisms. In this study, a comprehensive assessment of human mRNA was performed on leprosy skin lesions by using DNA chip microarrays, which include...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Belone Ade F,Rosa PS,Trombone AP,Fachin LR,Guidella CC,Ura S,Barreto JA,Pinilla MG,de Carvalho AF,Carraro DM,Soares FA,Soares CT

    更新日期:2015-11-20 00:00:00

  • Differential DNA Methylation Encodes Proliferation and Senescence Programs in Human Adipose-Derived Mesenchymal Stem Cells.

    abstract::Adult adipose tissue-derived mesenchymal stem cells (ASCs) constitute a vital population of multipotent cells capable of differentiating into numerous end-organ phenotypes. However, scientific and translational endeavors to harness the regenerative potential of ASCs are currently limited by an incomplete understanding...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Pepin ME,Infante T,Benincasa G,Schiano C,Miceli M,Ceccarelli S,Megiorni F,Anastasiadou E,Della Valle G,Fatone G,Faenza M,Docimo L,Nicoletti GF,Marchese C,Wende AR,Napoli C

    更新日期:2020-04-15 00:00:00

  • Redundancy of the genetic code enables translational pausing.

    abstract::The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptiv...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: D'Onofrio DJ,Abel DL

    更新日期:2014-05-20 00:00:00

  • "Exosomics"-A Review of Biophysics, Biology and Biochemistry of Exosomes With a Focus on Human Breast Milk.

    abstract::Exosomes are biomolecular nanostructures released from cells. They carry specific biomolecular information and are mainly researched for their exquisite properties as a biomarker source and delivery system. We introduce exosomes in the context of other extracellular vesicles, describe their biophysical isolation and c...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章,评审


    authors: de la Torre Gomez C,Goreham RV,Bech Serra JJ,Nann T,Kussmann M

    更新日期:2018-03-27 00:00:00

  • The Toolbox for Fiber Flax Breeding: A Pipeline From Gene Expression to Fiber Quality.

    abstract::The goal of any plant breeding program is to improve quality of a target crop. Crop quality is a comprehensive feature largely determined by biological background. To improve the quality parameters of crops grown for the production of fiber, a functional approach was used to search for genes suitable for the effective...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Galinousky D,Mokshina N,Padvitski T,Ageeva M,Bogdan V,Kilchevsky A,Gorshkova T

    更新日期:2020-11-12 00:00:00

  • Comprehensive RNA-Seq Data Analysis Identifies Key mRNAs and lncRNAs in Atrial Fibrillation.

    abstract::Long non-coding RNAs (lncRNAs) are an emerging class of RNA species that may play a critical regulatory role in gene expression. However, the association between lncRNAs and atrial fibrillation (AF) is still not fully understood. In this study, we used RNA sequencing data to identify and quantify the both protein codi...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Wu DM,Zhou ZK,Fan SH,Zheng ZH,Wen X,Han XR,Wang S,Wang YJ,Zhang ZF,Shan Q,Li MQ,Hu B,Lu J,Chen GQ,Hong XW,Zheng YL

    更新日期:2019-10-02 00:00:00

  • Vitamin D Receptor FokI, ApaI, and TaqI Polymorphisms in Lead Exposed Subjects From Saudi Arabia.

    abstract::Vitamin D receptor (VDR) gene polymorphisms were reported to influence blood lead levels (BLL) and the response of subjects to the symptoms of lead toxicity. However, no studies have been conducted in the Saudi Arabian population which has unique ethnicity and socio-demographic features. This study examined the polymo...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Shaik AP,Alsaeed AH,Faiyaz-Ul-Haque M,Alsaeed MA,Alyousef AA,Bammidi VK,Shaik AS

    更新日期:2019-04-26 00:00:00

  • Six-lncRNA Immune Prognostic Signature for Cervical Cancer.

    abstract:Background:This study searched for immune-related long noncoding RNAs (lncRNAs) to predict the prognosis of patients with cervical cancer. Method:We obtained immunologically relevant lncRNA expression profiles and clinical follow-up data from cervical cancer patients from The Cancer Genome Atlas database and the Molec...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Chen Q,Hu L,Huang D,Chen K,Qiu X,Qiu B

    更新日期:2020-10-14 00:00:00

  • Impact of a Gap Junction Protein Alpha 4 Variant on Clinical Disease Phenotype in F508del Homozygous Patients With Cystic Fibrosis.

    abstract:Background:Lung disease phenotype varies widely even in the F508del (homozygous) genotype. Leukocyte-driven inflammation is important for pulmonary disease pathogenesis in cystic fibrosis (CF). Blood cytokines correlate negatively with pulmonary function in F508del homozygous patients, and gap junction proteins (GJA) m...

    journal_title:Frontiers in genetics

    pub_type: 杂志文章


    authors: Horn T,Ludwig M,Eickmeier O,Neerinex AH,Maitland-van der Zee AH,Smaczny C,Wagner TOF,Schubert R,Zielen S,Majoor C,Bos LD,Schmitt-Grohé S

    更新日期:2020-10-28 00:00:00