A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes.

Abstract:

:Colorectal cancer (CRC) is a cancer of growing incidence that associates with a high mortality rate worldwide. There is a poor understanding of the heterogeneity of CRC with regard to causative genetic mutations and gene regulatory mechanisms. Previous studies have identified several susceptibility genes in small-scale experiments. However, the information has not been comprehensively and systematically compiled and interpreted. In this study, we constructed the gbCRC, the first literature-based gene resource for investigating CRC-related human genes. The features of our database include: (i) manual curation of experimentally-verified genes reported in the literature; (ii) comprehensive integration of five reliable data sources; and (iii) pre-computed regulatory patterns involving transcription factors, microRNAs and long non-coding RNAs. In total, 2067 genes associating with 2819 PubMed abstracts were compiled. Comprehensive functional annotations associated with all the genes, including gene expression profiles, homologous genes in other model species, protein-protein interactions, somatic mutations, and potential methylation sites. These comprehensive annotations and this pre-computed regulatory information highlighted the importance of the gbCRC with regard to the unexplored regulatory network of CRC. This information is available in a plain text format that is free to download.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Zhao M,Liu Y,Huang F,Qu H

doi

10.1038/srep30624

subject

Has Abstract

pub_date

2016-08-01 00:00:00

pages

30624

issn

2045-2322

pii

srep30624

journal_volume

6

pub_type

杂志文章
  • Relative abundance of chemical forms of Cu(II) and Cd(II) on soybean roots as influenced by pH, cations and organic acids.

    abstract::Little information is available on chemical forms of heavy metals on integrate plant roots. KNO3 (1 M), 0.05M EDTA at pH6 and 0.01 M HCl were used sequentially to extract the exchangeable, complexed and precipitated forms of Cu(II) and Cd(II) from soybean roots and then to investigate chemical form distribution of Cu(...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36373

    authors: Zhou Q,Liu ZD,Liu Y,Jiang J,Xu RK

    更新日期:2016-11-02 00:00:00

  • Novel approach on reduction in GHG emissions from sludge lime stabilization as an emergent and regional treatment in China.

    abstract::As a typical organic solid waste, sludge plays an important role in contributing to greenhouse gas (GHG) emissions resulted by its treatment and disposal. As a temporary and emergent treatment measurement, sludge lime stabilization is regionally adopted in most sludge generated units in China. In present case, sludge ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-35052-9

    authors: Liu H

    更新日期:2018-11-08 00:00:00

  • Verification of radiodynamic therapy by medical linear accelerator using a mouse melanoma tumor model.

    abstract::Combined treatment with 5-aminolevulinic acid (5-ALA) and X-rays improves tumor suppression in vivo. This is because the accumulated protoporphyrin IX from 5-ALA enhances the generation of ROS by the X-ray irradiation. In the present study, a high-energy medical linear accelerator was used instead of a non-medical low...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-21152-z

    authors: Takahashi J,Murakami M,Mori T,Iwahashi H

    更新日期:2018-02-09 00:00:00

  • In silico re-assessment of a diagnostic RT-qPCR assay for universal detection of Influenza A viruses.

    abstract::The ongoing evolution of microbial pathogens represents a significant issue in diagnostic PCR/qPCR. Many assays are burdened with false negativity due to mispriming and/or probe-binding failures. Therefore, PCR/qPCR assays used in the laboratory should be periodically re-assessed in silico on public sequences to evalu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37869-w

    authors: Nagy A,Jiřinec T,Jiřincová H,Černíková L,Havlíčková M

    更新日期:2019-02-07 00:00:00

  • Accelerated age-related olfactory decline among type 1 Usher patients.

    abstract::Usher Syndrome (USH) is a rare disease with hearing loss, retinitis pigmentosa and, sometimes, vestibular dysfunction. A phenotype heterogeneity is reported. Recent evidence indicates that USH is likely to belong to an emerging class of sensory ciliopathies. Olfaction has recently been implicated in ciliopathies, but ...

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/srep28309

    authors: Ribeiro JC,Oliveiros B,Pereira P,António N,Hummel T,Paiva A,Silva ED

    更新日期:2016-06-22 00:00:00

  • Vitamin D alleviates lead induced renal and testicular injuries by immunomodulatory and antioxidant mechanisms in rats.

    abstract::This study measured the effects of vitamin D (VD) supplementation on the underlying molecular pathways involved in renal and testicular damage induced by lead (Pb) toxicity. Thirty two adult male Wistar rats were divided equally into four groups that were treated individually or simultaneously, except the negative con...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-23258-w

    authors: BaSalamah MA,Abdelghany AH,El-Boshy M,Ahmad J,Idris S,Refaat B

    更新日期:2018-03-19 00:00:00

  • Multicolor emission from intermediate band semiconductor ZnO1-xSex.

    abstract::Photoluminescence and photomodulated reflectivity measurements of ZnOSe alloys are used to demonstrate a splitting of the valence band due to the band anticrossing interaction between localized Se states and the extended valence band states of the host ZnO matrix. A strong multiband emission associated with optical tr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44214

    authors: Welna M,Baranowski M,Linhart WM,Kudrawiec R,Yu KM,Mayer M,Walukiewicz W

    更新日期:2017-03-13 00:00:00

  • Remediation of diesel-contaminated soil enhanced with firefighting foam application.

    abstract::During rescue operations related to the elimination of the effects of industrial accidents or natural disasters, extinguishing agents are used that affect the migration and transformation of contamination in the environment. Firefighting foam sprayed onto an oil spill slowly drains to an aqueous solution and penetrate...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65660-3

    authors: Rakowska J

    更新日期:2020-06-01 00:00:00

  • Non-linear optical flow cytometry using a scanned, Bessel beam light-sheet.

    abstract::Modern flow cytometry instruments have become vital tools for high-throughput analysis of single cells. However, as issues with the cellular labeling techniques often used in flow cytometry have become more of a concern, the development of label-free modalities for cellular analysis is increasingly desired. Non-linear...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10751

    authors: Collier BB,Awasthi S,Lieu DK,Chan JW

    更新日期:2015-05-29 00:00:00

  • Publisher Correction: Multiobjective differential evolution-based multifactor dimensionality reduction for detecting gene-gene interactions.

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

    journal_title:Scientific reports

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41598-017-16210-x

    authors: Yang CH,Chuang LY,Lin YD

    更新日期:2017-11-23 00:00:00

  • A preliminary examination of bacterial, archaeal, and fungal communities inhabiting different rhizocompartments of tomato plants under real-world environments.

    abstract::Plant microbiota is a key determinant of plant health and productivity. The composition and structure of plant microbiota varies according to plant tissue and compartment, which are specific habitats for microbial colonization. To investigate the structural composition of the microbiome associated with tomato roots un...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-45660-8

    authors: Lee SA,Kim Y,Kim JM,Chu B,Joa JH,Sang MK,Song J,Weon HY

    更新日期:2019-06-26 00:00:00

  • Author Correction: Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water.

    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/s41598-018-35437-w

    authors: Li R,Tun HM,Jahan M,Zhang Z,Kumar A,Dilantha Fernando WG,Farenhorst A,Khafipour E

    更新日期:2018-11-22 00:00:00

  • Responses of crop yield growth to global temperature and socioeconomic changes.

    abstract::Although biophysical yield responses to local warming have been studied, we know little about how crop yield growth-a function of climate and technology-responds to global temperature and socioeconomic changes. Here, we present the yield growth of major crops under warming conditions from preindustrial levels as simul...

    journal_title:Scientific reports

    pub_type: 历史文章,杂志文章

    doi:10.1038/s41598-017-08214-4

    authors: Iizumi T,Furuya J,Shen Z,Kim W,Okada M,Fujimori S,Hasegawa T,Nishimori M

    更新日期:2017-08-10 00:00:00

  • Phylogenetic comparison of egg transparency in ascidians by hyperspectral imaging.

    abstract::The transparency of animals is an important biological feature. Ascidian eggs have various degrees of transparency, but this characteristic has not yet been measured quantitatively and comprehensively. In this study, we established a method for evaluating the transparency of eggs to first characterize the transparency...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77585-y

    authors: Shito TT,Hasegawa N,Oka K,Hotta K

    更新日期:2020-11-30 00:00:00

  • Improved adherence and treatment outcomes with an engaging, personalized digital therapeutic in amblyopia.

    abstract::Given the prevalence of poor adherence to therapy and the biases of self-reporting across healthcare, we hypothesized that an engaging, personalized therapy may improve adherence and treatment outcomes in the home. We tested this hypothesis in the initial indication of amblyopia, a neurodevelopmental disorder for whic...

    journal_title:Scientific reports

    pub_type: 临床试验,杂志文章

    doi:10.1038/s41598-020-65234-3

    authors: Xiao S,Gaier ED,Mazow ML,Stout AU,Travers DA,Angjeli E,Wu HC,Binenbaum G,Hunter DG

    更新日期:2020-05-20 00:00:00

  • ZCF32, a fungus specific Zn(II)2 Cys6 transcription factor, is a repressor of the biofilm development in the human pathogen Candida albicans.

    abstract::As a human fungal pathogen, Candida albicans can cause a wide variety of disease conditions ranging from superficial to systemic infections. Many of these infections are caused by an inherent ability of the pathogen to form biofilms on medical devices resulting in high mortality. Biofilms formed by C. albicans are a c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep31124

    authors: Kakade P,Sadhale P,Sanyal K,Nagaraja V

    更新日期:2016-08-08 00:00:00

  • Identification of proteins involved in the anti-inflammatory properties of Propionibacterium freudenreichii by means of a multi-strain study.

    abstract::Propionibacterium freudenreichii, a dairy starter, can reach a population of almost 109 propionibacteria per gram in Swiss-type cheese at the time of consumption. Also consumed as a probiotic, it displays strain-dependent anti-inflammatory properties mediated by surface proteins that induce IL-10 in leukocytes. We sel...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46409

    authors: Deutsch SM,Mariadassou M,Nicolas P,Parayre S,Le Guellec R,Chuat V,Peton V,Le Maréchal C,Burati J,Loux V,Briard-Bion V,Jardin J,Plé C,Foligné B,Jan G,Falentin H

    更新日期:2017-04-13 00:00:00

  • Global temporal patterns of pancreatic cancer and association with socioeconomic development.

    abstract::Pancreatic cancer induces a substantial global burden. We examined its global incidence/mortality rates and their correlation with socioeconomic development (Human Development Index [HDI] and Gross Domestic Product [GDP] in 2000 as proxy measures). Data on age-standardized incidence/mortality rates in 2012 were retrie...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02997-2

    authors: Wong MCS,Jiang JY,Liang M,Fang Y,Yeung MS,Sung JJY

    更新日期:2017-06-09 00:00:00

  • Next-generation sequencing for identification of actionable gene mutations in intestinal-type sinonasal adenocarcinoma.

    abstract::Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumor carrying poor prognosis and needing new treatment options. The aim of this study was to identify actionable gene mutations that can guide new personalized target-specific therapies in ITAC patients. A series of 48 tumor and 27 corresponding germline DNA s...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-80242-z

    authors: Sánchez-Fernández P,Riobello C,Costales M,Vivanco B,Cabal VN,García-Marín R,Suárez-Fernández L,López F,Cabanillas R,Hermsen MA,Llorente JL

    更新日期:2021-01-26 00:00:00

  • Epithelial to mesenchymal transition is mediated by both TGF-β canonical and non-canonical signaling during axolotl limb regeneration.

    abstract::Axolotls have the amazing ability to regenerate. When compared to humans, axolotls display a very fast wound closure, no scarring and are capable to replace lost appendages perfectly. Understanding the signaling mechanism leading to this perfect healing is a key step to help develop regenerative treatments for humans....

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-38171-5

    authors: Sader F,Denis JF,Laref H,Roy S

    更新日期:2019-02-04 00:00:00

  • A novel allele of L-galactono-1,4-lactone dehydrogenase is associated with enhanced drought tolerance through affecting stomatal aperture in common wheat.

    abstract::In higher plants, L-galactono-1,4-lactone dehydrogenase (GLDH) plays important roles in ascorbic acid (AsA) biosynthesis and assembly of respiration complex I. Here we report three homoeologous genes (TaGLDH-A1, -B1 and -D1) encoding common wheat GLDH isozymes and a unique allelic variant (TaGLDH-A1b) associated with ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30177

    authors: Zhang J,Li B,Yang Y,Mu P,Qian W,Dong L,Zhang K,Liu X,Qin H,Ling H,Wang D

    更新日期:2016-07-22 00:00:00

  • Parameterization of clear-sky surface irradiance and its implications for estimation of aerosol direct radiative effect and aerosol optical depth.

    abstract::Aerosols impact clear-sky surface irradiance () through the effects of scattering and absorption. Linear or nonlinear relationships between aerosol optical depth (τa) and have been established to describe the aerosol direct radiative effect on (ADRE). However, considerable uncertainties remain associated with ADRE due...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep14376

    authors: Xia X

    更新日期:2015-09-23 00:00:00

  • Non-commutativity and local indistinguishability of quantum states.

    abstract::We study the local indistinguishability problem of quantum states. By introducing an easily calculated quantity, non-commutativity, we present an criterion which is both necessary and sufficient for the local indistinguishability of a complete set of pure orthogonal product states. A constructive distinguishing proced...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep06336

    authors: Ma T,Zhao MJ,Wang YK,Fei SM

    更新日期:2014-09-11 00:00:00

  • Solution structure of the transmembrane domain of the mouse erythropoietin receptor in detergent micelles.

    abstract::Erythropoiesis is regulated by the erythropoietin receptor (EpoR) binding to its ligand. The transmembrane domain (TMD) and the juxtamembrane (JM) regions of the EpoR are important for signal transduction across the cell membrane. We report a solution NMR study of the mouse erythropoietin receptor (mEpoR) comprising t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep13586

    authors: Li Q,Wong YL,Yueqi Lee M,Li Y,Kang C

    更新日期:2015-08-28 00:00:00

  • Randomised trial on clinical performances and biocompatibility of four high-flux hemodialyzers in two mode treatments: hemodialysis vs post dilution hemodiafiltration.

    abstract::This prospective multicenter randomized comparative cross-over trial aimed at evaluating the influence of hemodialysis vs post-dilution hemodiafiltration with high-flux dialyzers in solute clearance and biocompatibility profile. 32 patients were sequentially dialyzed with Leoceed-21HX, Polypure-22S+, Rexsys-27H and VI...

    journal_title:Scientific reports

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1038/s41598-019-54404-7

    authors: Morena M,Creput C,Bouzernidj M,Rodriguez A,Chalabi L,Seigneuric B,Lauret C,Bargnoux AS,Dupuy AM,Cristol JP

    更新日期:2019-12-04 00:00:00

  • Multi-pass transmission electron microscopy.

    abstract::Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-01841-x

    authors: Juffmann T,Koppell SA,Klopfer BB,Ophus C,Glaeser RM,Kasevich MA

    更新日期:2017-05-10 00:00:00

  • Denatured lysozyme-coated carbon nanotubes: a versatile biohybrid material.

    abstract::Carbon nanotubes (CNTs) are among the most versatile nanomaterials, but their exploitation is hindered by limited dispersibility, especially in aqueous solvents. Here, we show that AP-LYS, a highly cationic soluble derivative of denatured hen egg lysozyme, is a very effective tool for the unbundling and solubilisation...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-52701-9

    authors: Siepi M,Donadio G,Dardano P,De Stefano L,Monti DM,Notomista E

    更新日期:2019-11-12 00:00:00

  • 1-Aminocyclopropane-1-carboxylic acid deaminase producing beneficial rhizobacteria ameliorate the biomass characters of Panicum maximum Jacq. by mitigating drought and salt stress.

    abstract::1-Aminocyclopropane-1-carboxylic acid (ACC) is a precursor molecule of ethylene whose concentration is elevated in the plant subjected to biotic and abiotic stress. Several soil microorganisms are reported to produce ACC deaminase (ACCd) which degrades ACC thereby reducing stress ethylene in host plants. This study is...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-35565-3

    authors: Tiwari G,Duraivadivel P,Sharma S,P H

    更新日期:2018-11-30 00:00:00

  • Revisiting metallization boundary of warm dense helium in a wide ρ-T regime from ab initio study.

    abstract::The knowledge of the metallization of warm dense helium has important implications for understanding the thermal histories, stellar structure and magnetic field environment of giant planets. However, it is also a pendent scientific topic. For a revisiting into the properties of warm dense helium, we performed extensiv...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41885

    authors: Zhang W,Li Z,Fu Z,Dai J,Chen Q,Cai L

    更新日期:2017-02-03 00:00:00

  • Rapid Regeneration and Reuse of Silica Columns from PCR Purification and Gel Extraction Kits.

    abstract::Silica columns from PCR purification and gel extraction kits are widely used in laboratories worldwide to assist in gene cloning. However, the use of these columns can generate plastic waste that has an environmental impact due to their one-off design and massive consumption. Thus, it is important to develop a novel m...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-30316-w

    authors: Zhou Y,Zhang Y,He W,Wang J,Peng F,Huang L,Zhao S,Deng W

    更新日期:2018-08-27 00:00:00