当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning.

Classification models for Invasive Ductal Carcinoma Progression, based on gene expression data-trained supervised machine learning.

Abstract：

:Early detection of breast cancer and its correct stage determination are important for prognosis and rendering appropriate personalized clinical treatment to breast cancer patients. However, despite considerable efforts and progress, there is a need to identify the specific genomic factors responsible for, or accompanying Invasive Ductal Carcinoma (IDC) progression stages, which can aid the determination of the correct cancer stages. We have developed two-class machine-learning classification models to differentiate the early and late stages of IDC. The prediction models are trained with RNA-seq gene expression profiles representing different IDC stages of 610 patients, obtained from The Cancer Genome Atlas (TCGA). Different supervised learning algorithms were trained and evaluated with an enriched model learning, facilitated by different feature selection methods. We also developed a machine-learning classifier trained on the same datasets with training sets reduced data corresponding to IDC driver genes. Based on these two classifiers, we have developed a web-server Duct-BRCA-CSP to predict early stage from late stages of IDC based on input RNA-seq gene expression profiles. The analysis conducted by us also enables deeper insights into the stage-dependent molecular events accompanying IDC progression. The server is publicly available at http://bioinfo.icgeb.res.in/duct-BRCA-CSP.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Roy S,Kumar R,Mittal V,Gupta D

doi

10.1038/s41598-020-60740-w

subject

Has Abstract

pub_date

2020-03-05 00:00:00

pages

4113

issue

1

issn

2045-2322

pii

10.1038/s41598-020-60740-w

journal_volume

10

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • Transcriptome response of cassava leaves under natural shade.

    abstract：:Cassava is an important staple crop in tropical and sub-tropical areas. As a common farming practice, cassava is usually cultivated intercropping with other crops and subjected to various degrees of shading, which causes reduced productivity. Herein, a comparative transcriptomic analysis was performed on a series of d...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep31673

    authors： Ding Z,Zhang Y,Xiao Y,Liu F,Wang M,Zhu X,Liu P,Sun Q,Wang W,Peng M,Brutnell T,Li P

    更新日期：2016-08-19 00:00:00

  • A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer.

    abstract：:Long non-coding RNAs (lncRNAs) have been implicated in human pathology, however, their role in colorectal carcinogenesis have not been fully elucidated. In the current study, whole-transcriptome analysis was performed in 3 pairs of colorectal cancer (CRC) and matched normal mucosa (NM) by RNA sequencing (RNA-seq). Fol...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-18407-6

    authors： Yamada A,Yu P,Lin W,Okugawa Y,Boland CR,Goel A

    更新日期：2018-01-12 00:00:00

  • Loss of Gαi proteins impairs thymocyte development, disrupts T-cell trafficking, and leads to an expanded population of splenic CD4+PD-1+CXCR5+/- T-cells.

    abstract：:Thymocyte and T cell trafficking relies on signals initiated by G-protein coupled receptors. To address the importance of the G-proteins Gαi2 and Gαi3 in thymocyte and T cell function, we developed several mouse models. Gαi2 deficiency in hematopoietic progenitors led to a small thymus, a double negative (DN)1/DN2 thy...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-04537-4

    authors： Hwang IY,Harrison K,Park C,Kehrl JH

    更新日期：2017-06-23 00:00:00

  • System dynamics modelling of urbanization under energy constraints in China.

    abstract：:The rapid urbanization in China has been associated with a growing hunger for energy consumption and steadily-increasing CO2 emissions. In this paper, an integrated system dynamics model composed of four sub-models is developed to simulate the urbanization and energy consumption in China from 1998 to 2050. Three scena...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-66125-3

    authors： Gu C,Ye X,Cao Q,Guan W,Peng C,Wu Y,Zhai W

    更新日期：2020-06-19 00:00:00

  • Functional conservation of EXA1 among diverse plant species for the infection by a family of plant viruses.

    abstract：:Since the propagation of plant viruses depends on various host susceptibility factors, deficiency in them can prevent viral infection in cultivated and model plants. Recently, we identified the susceptibility factor Essential for poteXvirus Accumulation 1 (EXA1) in Arabidopsis thaliana, and revealed that EXA1-mediated...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-42400-w

    authors： Yusa A,Neriya Y,Hashimoto M,Yoshida T,Fujimoto Y,Hosoe N,Keima T,Tokumaru K,Maejima K,Netsu O,Yamaji Y,Namba S

    更新日期：2019-04-11 00:00:00

  • Histological grading evaluation of non-alcoholic fatty liver disease after bariatric surgery: a retrospective and longitudinal observational cohort study.

    abstract：:Non-alcoholic fatty liver disease (NAFLD) is a chronic disease with several degrees of histological features which may progress to cirrhosis. Obesity is an important risk factor and although NAFLD has no specific pharmacological treatment, bariatric surgery has been associated with NAFLD regression in severely obese p...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-65556-2

    authors： Chaim FDM,Pascoal LB,Chaim FHM,Palma BB,Damázio TA,da Costa LBE,Carvalho R,Cazzo E,Gestic MA,Utrini MP,Milanski M,Chaim EA,Leal RF

    更新日期：2020-05-22 00:00:00

  • Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus.

    abstract：:Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protei...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep31586

    authors： Wu W,Yang YL,He WM,Rouard M,Li WM,Xu M,Roux N,Ge XJ

    更新日期：2016-08-17 00:00:00

  • In-column ATR-FTIR spectroscopy to monitor affinity chromatography purification of monoclonal antibodies.

    abstract：:In recent years many monoclonal antibodies (mAb) have entered the biotherapeutics market, offering new treatments for chronic and life-threatening diseases. Protein A resin captures monoclonal antibody (mAb) effectively, but the binding capacity decays over repeated purification cycles. On an industrial scale, replaci...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep30526

    authors： Boulet-Audet M,Kazarian SG,Byrne B

    更新日期：2016-07-29 00:00:00

  • An eigenvalue transformation technique for predicting drug-target interaction.

    abstract：:The prediction of drug-target interactions is a key step in the drug discovery process, which serves to identify new drugs or novel targets for existing drugs. However, experimental methods for predicting drug-target interactions are expensive and time-consuming. Therefore, the in silico prediction of drug-target inte...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep13867

    authors： Kuang Q,Xu X,Li R,Dong Y,Li Y,Huang Z,Li Y,Li M

    更新日期：2015-09-09 00:00:00

  • Decoding the dynamic representation of musical pitch from human brain activity.

    abstract：:In music, the perception of pitch is governed largely by its tonal function given the preceding harmonic structure of the music. While behavioral research has advanced our understanding of the perceptual representation of musical pitch, relatively little is known about its representational structure in the brain. Usin...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-19222-3

    authors： Sankaran N,Thompson WF,Carlile S,Carlson TA

    更新日期：2018-01-16 00:00:00

  • CPT1C promotes human mesenchymal stem cells survival under glucose deprivation through the modulation of autophagy.

    abstract：:Human mesenchymal stem cells (hMSCs) are widely used in regenerative medicine. In some applications, they must survive under low nutrient conditions engendered by avascularity. Strategies to improve hMSCs survival may be of high relevance in tissue engineering. Carnitine palmitoyltransferase 1 C (CPT1C) is a pseudoenz...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-25485-7

    authors： Roa-Mansergas X,Fadó R,Atari M,Mir JF,Muley H,Serra D,Casals N

    更新日期：2018-05-03 00:00:00

  • Legionella SBT applied directly to respiratory samples as a rapid molecular epidemiological tool.

    abstract：:Legionnaires' disease (LD) is an atypical pneumonia caused by the inhalation of Legionella. The methods used for the diagnosis of LD are direct culture of respiratory samples and urinary antigen detection. However, the sensitivity of culture is low, and the urinary antigen test is specific only for L. pneumophila sg1....

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-36924-w

    authors： Quero S,Párraga-Niño N,Sabria M,Barrabeig I,Sala MR,Jané M,Mateu L,Sopena N,Pedro-Botet ML,Garcia-Nuñez M

    更新日期：2019-01-24 00:00:00

  • NAMPT and NAPRT1: novel polymorphisms and distribution of variants between normal tissues and tumor samples.

    abstract：:Nicotinamide phosphoribosyltransferase (NAMPT) and nicotinate phosphoribosyltransferase domain containing 1 (NAPRT1) are the main human NAD salvage enzymes. NAD regulates energy metabolism and cell signaling, and the enzymes that control NAD availability are linked to pathologies such as cancer and neurodegeneration. ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep06311

    authors： Duarte-Pereira S,Silva SS,Azevedo L,Castro L,Amorim A,Silva RM

    更新日期：2014-09-09 00:00:00

  • Solvent-free bulk polymerization of lignin-polycaprolactone (PCL) copolymer and its thermoplastic characteristics.

    abstract：:The pristine lignin molecules contain multiple reactive hydroxyl [OH] groups, some of which undergo limited polymerization depending on their configuration (aromatic or aliphatic) or conformation. The key issue in lignin-polymerization is to quantify the number of hydroxyl groups in the pristine molecules for subseque...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-43296-2

    authors： Park IK,Sun H,Kim SH,Kim Y,Kim GE,Lee Y,Kim T,Choi HR,Suhr J,Nam JD

    更新日期：2019-05-07 00:00:00

  • An absorbance method for analysis of enzymatic degradation kinetics of poly(ethylene terephthalate) films.

    abstract：:Increased interest in poly(ethylene terephthalate) (PET)-degrading enzymes (PETases) have generated efforts to find mutants with improved catalytic activity and thermostability. Here, we present a simple and fast method to determine relative enzyme kinetics through bulk absorbance measurements of released products ove...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-79031-5

    authors： Zhong-Johnson EZL,Voigt CA,Sinskey AJ

    更新日期：2021-01-13 00:00:00

  • Autophagy inhibition of hsa-miR-19a-3p/19b-3p by targeting TGF-β R II during TGF-β1-induced fibrogenesis in human cardiac fibroblasts.

    abstract：:Transforming growth factor-β1 (TGF-β1) plays an important role on fibrogenesis in heart disease. MicroRNAs have exhibited as crucial regulators of cardiac homeostasis and remodeling in various heart diseases. MiR-19a-3p/19b-3p expresses with low levels in the plasma of heart failure patients. The purpose of our study ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep24747

    authors： Zou M,Wang F,Gao R,Wu J,Ou Y,Chen X,Wang T,Zhou X,Zhu W,Li P,Qi LW,Jiang T,Wang W,Li C,Chen J,He Q,Chen Y

    更新日期：2016-04-21 00:00:00

  • Dislocation-twin boundary interactions induced nanocrystalline via SPD processing in bulk metals.

    abstract：:This report investigated dislocation-twin boundary (TB) interactions that cause the TB to disappear and turn into a high-angle grain boundary (GB). The evolution of the microstructural characteristics of Hadfield steel was shown as a function of severe plastic deformation processing time. Sessile Frank partial disloca...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep08981

    authors： Zhang F,Feng X,Yang Z,Kang J,Wang T

    更新日期：2015-03-11 00:00:00

  • Hydrogen motion in rutile TiO2.

    abstract：:Uniaxial-stress experiments have been performed for the 3287- and 2445-cm-1 local vibrational modes assigned to the positive charge state of interstitial hydrogen [Formula: see text] and deuterium [Formula: see text], respectively, occurring in mono-crystalline rutile TiO2. The onset of the defect alignment under the ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-16660-3

    authors： Hupfer AJ,Monakhov EV,Svensson BG,Chaplygin I,Lavrov EV

    更新日期：2017-12-06 00:00:00

  • Mean platelet volume predicts survival in pancreatic cancer patients with synchronous liver metastases.

    abstract：:Most pancreatic cancer (PC) patients manifest multiple liver metastases at the time of diagnosis. Activated platelets play a key role in tumor growth and tumor metastases. Mean platelet volume (MPV) is a platelet index and is altered in patients with malignancies. This study aimed to evaluate whether MPV can effective...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-24539-0

    authors： Yin JB,Wang X,Zhang X,Liu L,Wang RT

    更新日期：2018-04-16 00:00:00

  • Enhancing innate antiviral immune responses in rainbow trout by double stranded RNA delivered with cationic phytoglycogen nanoparticles.

    abstract：:Innate immunity is induced when pathogen-associated molecular patterns (PAMPs) bind host pattern recognition receptors (PRRs). Polyinosinic:polycytidylic acid [poly(I:C)] is a synthetic analogue of viral dsRNA that acts as a PAMP, inducing type I interferons (IFNs) in vertebrates. In the present study, the immunostimu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-49931-2

    authors： Alkie TN,de Jong J,Jenik K,Klinger KM,DeWitte-Orr SJ

    更新日期：2019-09-20 00:00:00

  • Quantitative metabolic imaging using endogenous fluorescence to detect stem cell differentiation.

    abstract：:The non-invasive high-resolution spatial mapping of cell metabolism within tissues could provide substantial advancements in assessing the efficacy of stem cell therapy and understanding tissue development. Here, using two-photon excited fluorescence microscopy, we elucidate the relationships among endogenous cell flu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep03432

    authors： Quinn KP,Sridharan GV,Hayden RS,Kaplan DL,Lee K,Georgakoudi I

    更新日期：2013-12-05 00:00:00

  • Quercetin liposomes ameliorate streptozotocin-induced diabetic nephropathy in diabetic rats.

    abstract：:The effects of quercetin liposomes (Q-PEGL) on streptozotocin (STZ)-induced diabetic nephropathy (DN) was investigated in rats. Male Sprague Dawley rats were used to establish a STZ induced DN model. DN rats randomly received one of the following treatments for 8 weeks: blank treatment (DN), free quercetin (Que), pegy...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-59411-7

    authors： Tang L,Li K,Zhang Y,Li H,Li A,Xu Y,Wei B

    更新日期：2020-02-12 00:00:00

  • Combination of OipA, BabA, and SabA as candidate biomarkers for predicting Helicobacter pylori-related gastric cancer.

    abstract：:Helicobacter pylori (H. pylori ) infection is a major cause of chronic gastritis and is highly related to duodenal ulcer (DU) and gastric cancer (GC). To identify H. pylori-related GC biomarkers with high seropositivity in GC patients, differences in levels of protein expression between H. pylori from GC and DU patien...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep36442

    authors： Su YL,Huang HL,Huang BS,Chen PC,Chen CS,Wang HL,Lin PH,Chieh MS,Wu JJ,Yang JC,Chow LP

    更新日期：2016-11-07 00:00:00

  • Metal-free supercapacitor with aqueous electrolyte and low-cost carbon materials.

    abstract：:Electric double-layer capacitors (EDLCs) or supercapacitors (SCs) are fast energy storage devices with high pulse efficiency and superior cyclability, which makes them useful in various applications including electronics, vehicles and grids. Aqueous SCs are considered to be more environmentally friendly than those bas...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep39836

    authors： Blomquist N,Wells T,Andres B,Bäckström J,Forsberg S,Olin H

    更新日期：2017-01-05 00:00:00

  • Supramolecular Controlled Cargo Release via Near Infrared Tunable Cucurbit[7]uril-Gold Nanostars.

    abstract：:The near infrared (NIR) absorption and average particle size of gold nanostars (GNSs) can be precisely controlled by varying the molar ratios of cucurbit[7]urils (CB[7]) and GNSs in aqueous solution. GNSs modified with CB[7] achieved high cargo loading with thermally activated release upon the NIR laser irradiation. ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep22239

    authors： Han Y,Yang X,Liu Y,Ai Q,Liu S,Sun C,Liang F

    更新日期：2016-02-26 00:00:00

  • Selective alteration of human value decisions with medial frontal tDCS is predicted by changes in attractor dynamics.

    abstract：:During value-based decision making, ventromedial prefrontal cortex (vmPFC) is thought to support choices by tracking the expected gain from different outcomes via a competition-based process. Using a computational neurostimulation approach we asked how perturbing this region might alter this competition and resulting ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep25160

    authors： Hämmerer D,Bonaiuto J,Klein-Flügge M,Bikson M,Bestmann S

    更新日期：2016-05-05 00:00:00

  • The Saccharomyces cerevisiae poly(A) binding protein Pab1 as a target for eliciting stress tolerant phenotypes.

    abstract：:When exploited as cell factories, Saccharomyces cerevisiae cells are exposed to harsh environmental stresses impairing titer, yield and productivity of the fermentative processes. The development of robust strains therefore represents a pivotal challenge for the implementation of cost-effective bioprocesses. Altering ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep18318

    authors： Martani F,Marano F,Bertacchi S,Porro D,Branduardi P

    更新日期：2015-12-14 00:00:00

  • Recurrence Quantification Analysis at work: Quasi-periodicity based interpretation of gait force profiles for patients with Parkinson disease.

    abstract：:In this letter, making use of real gait force profiles of healthy and patient groups with Parkinson disease which have different disease severity in terms of Hoehn-Yahr stage, we calculate various heuristic complexity measures of the recurrence quantification analysis (RQA). Using this technique, we are able to evince...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-27369-2

    authors： Afsar O,Tirnakli U,Marwan N

    更新日期：2018-06-14 00:00:00

  • Intrahaplotypic Variants Differentiate Complex Linkage Disequilibrium within Human MHC Haplotypes.

    abstract：:Distinct regions of long-range genetic fixation in the human MHC region, known as conserved extended haplotypes (CEHs), possess unique genomic characteristics and are strongly associated with numerous diseases. While CEHs appear to be homogeneous by SNP analysis, the nature of fine variations within their genomic stru...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep16972

    authors： Lam TH,Tay MZ,Wang B,Xiao Z,Ren EC

    更新日期：2015-11-23 00:00:00

  • Health-related quality of life analysis in differentiated thyroid carcinoma patients after thyroidectomy.

    abstract：:Although differentiated thyroid carcinoma (DTC) has a good prognosis and survival rate, long-term medication and recurrence monitoring might be needed. The factors that affect postoperative health-related quality of life (HRQoL) in patients with DTC in different regions remain unclear or conflicting. The purpose of th...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-62731-3

    authors： Li J,Zhang B,Bai Y,Liu Y,Zhang B,Jin J

    更新日期：2020-04-01 00:00:00