Research Article

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2017 Apr 05
Arthritis, Rheumatoid; Gene expression profiling; Humans; Models, Genetic; Monte Carlo method; Signal transduction; Transcriptome

We attempted to identify significant pathway cross-talk in rheumatoid arthritis (RA) by the Monte Carlo cross-validation (MCCV) method. We therefore obtained and preprocessed the gene expression profile of RA. MCCV involves identifying differentially expressed genes (DEGs), identifying differential pathways (DPs), calculating the discriminating score (DS) of the pathway cross-talk, and random ... more

W. Song; Y.M. Zhang; T. Ma; J. Wang; K.Z. Wang
2017 May 10
Alleles; Animals; Expressed sequence tags; Genetic markers; Heterozygote; Microsatellite Repeats; Perciformes; Polymorphism, Genetic; Transcriptome

Expressed sequence tags (ETSs) are the sources of microsatellite development. In this study, we isolated and characterized microsatellite markers for Odontobutis potamophila by using Illumina RNA-sequencing. We sequenced a large number of ESTs and screened 200 potential microsatellites. Consequently, a total of 56 novel polymorphic microsatellite repeat markers were identified in thirty-two ... more

P.P. Wang; M. Ren; S.Q. Chen; S.W. Yin; C. Zhao; H.Y. Zhang; X.R. Li; Q.Q. Cao; G.Q. Zhou
2017 May 25
Droughts; Gene Expression Regulation, Plant; Osmotic pressure; Plant Leaves; Saccharum; Transcriptome

Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and ... more

A.A. Belesini; F.M.S. Carvalho; B.R. Telles; G.M. de Castro; P.F. Giachetto; J.S. Vantini; S.D. Carlin; J.O. Cazetta; D.G. Pinheiro; M.I.T. Ferro
2017 Sep 21
Animals; Chromosomes; Female; Genotype; Hybridization, Genetic; Karyotype; Liver; male; Microsatellite Repeats; Polymorphism, Genetic; Quantitative Trait, Heritable; Transcriptome; Turtles

Chinese soft-shelled turtle Pelodiscus sinensis has been an important aquaculture species in Southeast Asian countries. To breed a new variety of soft-shelled turtle with excellent properties and to evaluate the effect of hybridization of two turtle strains with a highly different trait phenotype, inheritance, microsatellite loci, and transcriptome analysis were studied in the hybrid turtles ... more

H.Q. Zhang; X.J. Xu; Z.Y. He; J.Z. Shao; X.H. Zhang; Q.H. Meng; F.Y. Huang
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The butterflies are one of the insect groups which undergo typical complete metamorphosis in their life history. However, up to now, little is known about the genomic mechanism that regulates the butterfly metamorphosis. In this study, using a swallowtail butterfly P. polytes as a model organism, a high-throughput sequencing platform was employed to perform the ... more

S. Yao; Yliang Wang; Rsong Tao; Cyong Su; Jsheng Hao
Allium species; Chinese chive; SSR marker; Transcriptome; Transferability

Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species’ transcriptome, with 626, 643, and 536 of the makers located in ... more

Q. Tang; L. Yi; X. Yuan; F. Li
Magnaporthe oryzae; Oryza sativa; Transcriptome; Weighted gene co-expression network; WGCNA

Rice blast disease is a major threat to rice production worldwide; the causative pathogenic fungus Magnaporthe oryzae induces rice (Oryza sativa) plants to undergo molecular changes that help them to circumvent this fungal attack. Transcriptome studies have demonstrated that many genes are involved in the defense response of rice to M. oryzae ... more

R. Bevitori; S. Sircar; R.N. de Mello; R.C. Togawa; M.V.C.B. Côrtes; T.S. Oliveira; M.F. Grossi-de-Sá; N. Parekh