Integrative Network Analysis of Differentially Methylated and Expressed Genes for Biomarker Identification in Leukemia.

Abstract:

:Genome-wide DNA methylation and gene expression are commonly altered in pediatric acute lymphoblastic leukemia (PALL). Integrated network analysis of cytosine methylation and expression datasets has the potential to provide deeper insights into the complex disease states and their causes than individual disconnected analyses. With the purpose of identifying reliable cancer-associated methylation signal in gene regions from leukemia patients, we present an integrative network analysis of differentially methylated (DMGs) and differentially expressed genes (DEGs). The application of a novel signal detection-machine learning approach to methylation analysis of whole genome bisulfite sequencing (WGBS) data permitted a high level of methylation signal resolution in cancer-associated genes and pathways. This integrative network analysis approach revealed that gene expression and methylation consistently targeted the same gene pathways relevant to cancer: Pathways in cancer, Ras signaling pathway, PI3K-Akt signaling pathway, and Rap1 signaling pathway, among others. Detected gene hubs and hub sub-networks were integrated by signature loci associated with cancer that include, for example, NOTCH1, RAC1, PIK3CD, BCL2, and EGFR. Statistical analysis disclosed a stochastic deterministic relationship between methylation and gene expression within the set of genes simultaneously identified as DEGs and DMGs, where larger values of gene expression changes were probabilistically associated with larger values of methylation changes. Concordance analysis of the overlap between enriched pathways in DEG and DMG datasets revealed statistically significant agreement between gene expression and methylation changes. These results support the potential identification of reliable and stable methylation biomarkers at genes for cancer diagnosis and prognosis.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Sanchez R,Mackenzie SA

doi

10.1038/s41598-020-58123-2

subject

Has Abstract

pub_date

2020-02-07 00:00:00

pages

2123

issue

1

issn

2045-2322

pii

10.1038/s41598-020-58123-2

journal_volume

10

pub_type

杂志文章
  • A Hypersweet Protein: Removal of The Specific Negative Charge at Asp21 Enhances Thaumatin Sweetness.

    abstract::Thaumatin is an intensely sweet-tasting protein that elicits sweet taste at a concentration of 50 nM, a value 100,000 times larger than that of sucrose on a molar basis. Here we attempted to produce a protein with enhanced sweetness by removing negative charges on the interacting side of thaumatin with the taste recep...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20255

    authors: Masuda T,Ohta K,Ojiro N,Murata K,Mikami B,Tani F,Temussi PA,Kitabatake N

    更新日期:2016-02-03 00:00:00

  • The effect of posterior tethers on the biomechanics of proximal junctional kyphosis: The whole human finite element model analysis.

    abstract::Little is known about the effects of posterior tethers on the development of proximal junctional kyphosis (PJK). We evaluated the ability of posterior tethers to the proximal motion segment stiffness in long instrumented spinal instrumentation and fusion using a whole body human FE model. A series of finite element (F...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59179-w

    authors: Yagi M,Nakahira Y,Watanabe K,Nakamura M,Matsumoto M,Iwamoto M

    更新日期:2020-02-26 00:00:00

  • Rassf Proteins as Modulators of Mst1 Kinase Activity.

    abstract::Rassf1A/5 tumor suppressors serve as adaptor proteins possessing a modular architecture with the C-terminal consisting of a coiled-coil SARAH (Salvador-Rassf-Hippo) domain and the central portion being composed of Ras associated (RA) domain. Here, we investigate the effect of Rassf effectors on Mst1 function by mappin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep45020

    authors: Bitra A,Sistla S,Mariam J,Malvi H,Anand R

    更新日期:2017-03-22 00:00:00

  • Evidence for trivial Berry phase and absence of chiral anomaly in semimetal NbP.

    abstract::The discovery of Weyl semimetals (WSM) has brought forth the condensed matter realization of Weyl fermions, which were previously theorized as low energy excitations in high energy particle physics. Recently, transition metal mono-pnictides are under intense investigation for understanding properties of inversion-symm...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46062

    authors: Sudesh,Kumar P,Neha P,Das T,Patnaik S

    更新日期:2017-04-10 00:00:00

  • Alpha7 nicotinic acetylcholine receptor is required for amyloid pathology in brain endothelial cells induced by Glycoprotein 120, methamphetamine and nicotine.

    abstract::One of the most challenging issues in HIV-associated neurocognitive disorders (HAND) caused by HIV-1 virotoxins and drug abuse is the lack of understanding the underlying mechanisms that are commonly associated with disorders of the blood-brain barrier (BBB), which mainly consists of brain microvascular endothelial ce...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep40467

    authors: Liu L,Yu J,Li L,Zhang B,Liu L,Wu CH,Jong A,Mao DA,Huang SH

    更新日期:2017-01-11 00:00:00

  • Differential Contributions of Nonmuscle Myosin II Isoforms and Functional Domains to Stress Fiber Mechanics.

    abstract::While is widely acknowledged that nonmuscle myosin II (NMMII) enables stress fibers (SFs) to generate traction forces against the extracellular matrix, little is known about how specific NMMII isoforms and functional domains contribute to SF mechanics. Here we combine biophotonic and genetic approaches to address thes...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep13736

    authors: Chang CW,Kumar S

    更新日期:2015-09-04 00:00:00

  • Chains of carbon nanotetrahedra/nanoribbons.

    abstract::Flattening of a carbon nanotube results in the formation of a carbon nanoribbon with well-defined edges. In addition, a switching of the flattening direction by about a right angle yields a carbon nanotetrahedron at the switching point in a nanoribbon. Here, we report that chains of carbon nanotetrahedra/nanoribbons a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08430

    authors: Kohno H,Hasegawa T

    更新日期:2015-02-12 00:00:00

  • Evaluating novel synthetic compounds active against Bacillus subtilis and Bacillus cereus spores using Live imaging with SporeTrackerX.

    abstract::An empirical approach was taken to screen a novel synthetic compound library designed to be active against Gram-positive bacteria. We obtained five compounds that were active against spores from the model organism Bacillus subtilis and the food-borne pathogen Bacillus cereus during our population based experiments. Us...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-27529-4

    authors: Omardien S,Ter Beek A,Vischer N,Montijn R,Schuren F,Brul S

    更新日期:2018-06-14 00:00:00

  • Exploring the dog-human relationship by combining fMRI, eye-tracking and behavioural measures.

    abstract::Behavioural studies revealed that the dog-human relationship resembles the human mother-child bond, but the underlying mechanisms remain unclear. Here, we report the results of a multi-method approach combining fMRI (N = 17), eye-tracking (N = 15), and behavioural preference tests (N = 24) to explore the engagement of...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-79247-5

    authors: Karl S,Boch M,Zamansky A,van der Linden D,Wagner IC,Völter CJ,Lamm C,Huber L

    更新日期:2020-12-17 00:00:00

  • Publisher Correction: Mass & secondary structure propensity of amino acids explain their mutability and evolutionary replacements.

    abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-21981-y

    authors: Bohórquez HJ,Suárez CF,Patarroyo ME

    更新日期:2018-03-06 00:00:00

  • Propagation of Subseasonal Equatorially-Forced Coastal Trapped Waves down to the Benguela Upwelling System.

    abstract::The oceanic connection between the coastal variability along the southwestern African coasts and the linear equatorial dynamics at subseasonal time-scales (<120 days) is examined using a variety of model outputs, ranging from linear to general circulation models. We focus on the equatorially-forced fast and weakly dis...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-41847-1

    authors: Illig S,Bachèlery ML

    更新日期:2019-03-28 00:00:00

  • A Low Permeability Microfluidic Blood-Brain Barrier Platform with Direct Contact between Perfusable Vascular Network and Astrocytes.

    abstract::A novel three dimensional blood brain barrier (BBB) platform was developed by independently supplying different types of media to separate cell types within a single device. One channel (vascular channel, VC) is connected to the inner lumen of the vascular network while the other supplies media to the neural cells (ne...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07416-0

    authors: Bang S,Lee SR,Ko J,Son K,Tahk D,Ahn J,Im C,Jeon NL

    更新日期:2017-08-14 00:00:00

  • Anatomical study of the female reproductive system and bacteriome of Diaphorina citri Kuwayama, (Insecta: Hemiptera, Liviidae) using micro-computed tomography.

    abstract::Huanglongbing (HLB) (citrus greening disease) is one of the most serious bacterial diseases of citrus. It is caused by (1) Candidatus Liberibacter africanus, transmitted by Trioza erytreae and (2) C.L. asiaticus and C.L. americanus, transmitted by Diaphorina citri. As part of a multidisciplinary project on D. citri (w...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-64132-y

    authors: Alba-Alejandre I,Alba-Tercedor J,Hunter WB

    更新日期:2020-04-28 00:00:00

  • Precision and safety of Multilevel Cervical Transpedicular Screw Fixation with 3D Patient-Specific Guides; A Cadaveric Study.

    abstract::The aim is to design a patient-specific instrument (PSI) for multilevel cervical pedicle screw placement from C2 to C7, as well as verifying reliability and reproducibility. Computed tomography (CT) scans were obtained from 7 cadaveric cervical spines. Using Mimics software, semiautomatic segmentation was performed fo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-51936-w

    authors: Sallent A,Ramírez M,Catalá J,Rodríguez-Baeza A,Bagó J,de Albert M,Vélez R

    更新日期:2019-10-30 00:00:00

  • Nutrient allocation strategies of woody plants: an approach from the scaling of nitrogen and phosphorus between twig stems and leaves.

    abstract::Allocation of limited nutrients, such as nitrogen (N) and phosphorus (P), among plant organs reflects the influences of evolutionary and ecological processes on functional traits of plants, and thus is related to functional groups and environmental conditions. In this study, we tested this hypothesis by exploring the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20099

    authors: Yan Z,Li P,Chen Y,Han W,Fang J

    更新日期:2016-02-05 00:00:00

  • FMNL2 and -3 regulate Golgi architecture and anterograde transport downstream of Cdc42.

    abstract::The Rho-family small GTPase Cdc42 localizes at plasma membrane and Golgi complex and aside from protrusion and migration operates in vesicle trafficking, endo- and exocytosis as well as establishment and/or maintenance of cell polarity. The formin family members FMNL2 and -3 are actin assembly factors established to r...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-09952-1

    authors: Kage F,Steffen A,Ellinger A,Ranftler C,Gehre C,Brakebusch C,Pavelka M,Stradal T,Rottner K

    更新日期:2017-08-29 00:00:00

  • Alterations in voltage-sensing of the mitochondrial permeability transition pore in ANT1-deficient cells.

    abstract::The probability of mitochondrial permeability transition (mPT) pore opening is inversely related to the magnitude of the proton electrochemical gradient. The module conferring sensitivity of the pore to this gradient has not been identified. We investigated mPT's voltage-sensing properties elicited by calcimycin or H2...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep26700

    authors: Doczi J,Torocsik B,Echaniz-Laguna A,Mousson de Camaret B,Starkov A,Starkova N,Gál A,Molnár MJ,Kawamata H,Manfredi G,Adam-Vizi V,Chinopoulos C

    更新日期:2016-05-25 00:00:00

  • Anti-Nogo-A antibodies prevent vascular leakage and act as pro-angiogenic factors following stroke.

    abstract::Angiogenesis is a key restorative process following stroke but has also been linked to increased vascular permeability and blood brain barrier (BBB) disruption. Previous pre-clinical approaches primarily focused on the administration of vascular endothelial growth factor (VEGF) to promote vascular repair after stroke....

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-56634-1

    authors: Rust R,Weber RZ,Grönnert L,Mulders G,Maurer MA,Hofer AS,Sartori AM,Schwab ME

    更新日期:2019-12-27 00:00:00

  • The effect of thermal treatment on ac/dc conductivity and current fluctuations of PVDF/NMP/[EMIM][TFSI] solid polymer electrolyte.

    abstract::The experimental study deals with the investigation of the effect of diverse crystallinity of imidazolium ionic-liquid-based SPE on conductivity and current fluctuations. The experimental study was carried out on samples consisting of [EMIM][TFSI] as ionic liquid, PVDF as a polymer matrix and NMP as a solvent. After t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-78363-6

    authors: Sedlak P,Gajdos A,Macku R,Majzner J,Holcman V,Sedlakova V,Kubersky P

    更新日期:2020-12-03 00:00:00

  • Intrabasin Variability of East Pacific Tropical Cyclones During ENSO Regulated by Central American Gap Winds.

    abstract::Hurricane Patricia in 2015 was the strongest Pacific hurricane to make landfall in Mexico. Although Patricia fortuitously spared major cities, it reminded us of the threat tropical cyclones (TCs) pose in the eastern North Pacific (ENP) and the importance of improving our understanding and prediction of ENP TCs. Patric...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-01962-3

    authors: Fu D,Chang P,Patricola CM

    更新日期:2017-05-10 00:00:00

  • Profiling the neutralizing antibody response in chronically HIV-1 CRF07_BC-infected intravenous drug users naïve to antiretroviral therapy.

    abstract::Characterizing neutralizing antibody (NAb) responses in individuals infected with diverse HIV-1 strains is necessary to reveal the novel targets for regional preventive and therapeutic strategies development. We evaluated the prevalence, breadth, and potency of NAb responses in 98 CRF07_BC-infected individuals using a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46308

    authors: Hu X,Hu Y,Zhao C,Gao H,Greene KM,Ren L,Ma L,Ruan Y,Sarzotti-Kelsoe M,Montefiori DC,Hong K,Shao Y

    更新日期:2017-04-07 00:00:00

  • Chemical evidence of rare porphyrins in purple shells of Crassostrea gigas oyster.

    abstract::The colour of oyster shells is a very diverse characteristic morphotype, forming intriguing vivid patterns both on the inside and outside of the shell. In the present study, we have identified for the first time, the presence of several porphyrins as constituents of the shell pigmentation of the Crassostrea gigas oyst...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-69133-5

    authors: Bonnard M,Cantel S,Boury B,Parrot I

    更新日期:2020-07-22 00:00:00

  • Physiological demands of a swimming-based video game: Influence of gender, swimming background, and exergame experience.

    abstract::Active video games (exergames) may provide short-term increase in energy expenditure. We explored the effects of gender and prior experience on aerobic and anaerobic energy systems contributions, and the activity profiles of 40 participants playing with a swimming exergame. We recorded oxygen consumption and assessed ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05583-8

    authors: Soltani P,Figueiredo P,Ribeiro J,Fernandes RJ,Vilas-Boas JP

    更新日期:2017-07-12 00:00:00

  • Entropic effect of macromolecular crowding enhances binding between nucleosome clutches in heterochromatin, but not in euchromatin.

    abstract::Sharp increase in macromolecular crowding induces abnormal chromatin compaction in the cell nucleus, suggesting its non-negligible impact on chromatin structure and function. However, the details of the crowding-induced chromatin compaction remain poorly understood. In this work, we present a computer simulation study...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-23753-0

    authors: Oh I,Choi S,Jung Y,Kim JS

    更新日期:2018-04-03 00:00:00

  • Membrane capacitance recordings resolve dynamics and complexity of receptor-mediated endocytosis in Wnt signalling.

    abstract::Receptor-mediated endocytosis is an essential process in signalling pathways for activation of intracellular signalling cascades. One example is the Wnt signalling pathway that seems to depend on endocytosis of the ligand-receptor complex for initiation of Wnt signal transduction. To date, the roles of different endoc...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-49082-4

    authors: Bandmann V,Mirsanaye AS,Schäfer J,Thiel G,Holstein T,Mikosch-Wersching M

    更新日期:2019-09-10 00:00:00

  • Mechanism of splenic cell death and host mortality in a Plasmodium yoelii malaria model.

    abstract::Malaria is a fatal disease that displays a spectrum of symptoms and severity, which are determined by complex host-parasite interactions. It has been difficult to study the effects of parasite strains on disease severity in human infections, but the mechanisms leading to specific disease phenotypes can be investigated...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10776-2

    authors: Lacerda-Queiroz N,Riteau N,Eastman RT,Bock KW,Orandle MS,Moore IN,Sher A,Long CA,Jankovic D,Su XZ

    更新日期:2017-09-05 00:00:00

  • Low Complexity Compression and Speed Enhancement for Optical Scanning Holography.

    abstract::In this paper we report a low complexity compression method that is suitable for compact optical scanning holography (OSH) systems with different optical settings. Our proposed method can be divided into 2 major parts. First, an automatic decision maker is applied to select the rows of holographic pixels to be scanned...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep34724

    authors: Tsang PW,Poon TC,Liu JP,Kim T,Kim YS

    更新日期:2016-10-06 00:00:00

  • Bacterial and archaeal communities in the deep-sea sediments of inactive hydrothermal vents in the Southwest India Ridge.

    abstract::Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected f...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25982

    authors: Zhang L,Kang M,Xu J,Xu J,Shuai Y,Zhou X,Yang Z,Ma K

    更新日期:2016-05-12 00:00:00

  • High chance that current atmospheric greenhouse concentrations commit to warmings greater than 1.5 °C over land.

    abstract::The recent Paris UNFCCC climate meeting discussed the possibility of limiting global warming to 2 °C since pre-industrial times, or possibly even 1.5 °C, which would require major future emissions reductions. However, even if climate is stabilised at current atmospheric greenhouse gas (GHG) concentrations, those warmi...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30294

    authors: Huntingford C,Mercado LM

    更新日期:2016-07-27 00:00:00

  • Structural Studies of Epithelial Mesenchymal Transition Breast Tissues.

    abstract::At the supramolecular level, the proliferation of invasive ductal carcinoma through breast tissue is beyond the range of standard histopathology identification. Using synchrotron small angle x-ray scattering (SAXS) techniques, determining nanometer scale structural changes in breast tissue has been demonstrated to all...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-58932-5

    authors: Mohd Sobri SN,Abdul Sani SF,Sabtu SN,Looi LM,Chiew SF,Pathmanathan D,Chio-Srichan S,Bradley DA

    更新日期:2020-02-06 00:00:00