|Table of Contents|

Research Progress on Digital Gene Expression Profiling Based on High-throughput Sequencing(PDF)

《北方园艺》[ISSN:1001-0009/CN:23-1247/S]

Issue:
2015年10
Page:
170-176
Research Field:
Publishing date:

Info

Title:
Research Progress on Digital Gene Expression Profiling Based on High-throughput Sequencing
Author(s):
ZHANG YuLIU Yu-jieGUO Dan-niLI Hui-minQIN Xin-min
(Laboratory of Ecology of Rare and Endangered Species and Environmental Protection,Ministry of Education,College of Life Science,Guangxi Normal University,Guilin,Guangxi 541004)
Keywords:
digital gene expression profilinghigh-throughput sequencingdifferentially expressed gene
PACS:
Q 343
DOI:
10.11937/bfyy.201510043
Abstract:
Digital gene expression profiling (DGE) is a high-throughput sequencing technologies,which can comprehensively and quickly detect gene expression in a specific tissue under certain conditions of a species.The related information about gene transcription,gene regulation,signal transduction pathway and protein function can be obtained by the search,comparison and analysis on bioinformatics of gene expression profiling.This paper mainly described the principles of digital gene expression profiling and applications in biological,medicine and so on.

References:


[1]Ness R W,Siol M,Barrett S C.De novo sequence assembly and characterization of the floral transcriptome in cross-and self-fertilizing plants [J].BMC Genomics,2011,12:298-310.
[2]滕晓坤,肖华胜.基因芯片与高通量DNA测序技术前景分析[J].中国科学,2008,38(10):891-899.
[3]Alagna F,Torchia L,Servili M,et al.Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development[J].BMC Genomics,2009,10:399-413.[4]Severin A J,Woody J L,Bolon Y T,et al.RNA-Seq Atlas of Glycine max:A guide to the soybean transcriptome [J].BMC Plant Biology,2010,10:160-165.
[5]Morrissy A S,Morin R D,Delaney A,et al.Next-generation tag sequencing for cancer gene expression profiling[J].Genome Research,2009,19:1825-1835.
[6]Zoltán H,Anna Z,Vilmos C ,et al.Deep sequencing of the zebrafish transcriptome response to mycobacterium infection[J].Molecular Immunology,2009,46:2918-2930.
[7]Xiao S Q,Jia J Y,Mo D L,et al.Undetstanding PRRSV infection in porcine lung based on genome-wide transcriptome response identified by deep sequencing[J].PLoS ONE,2010,5:1-16.
[8]Zhong Z,Zhang L L,Ye X,et al.Transcriptome profiling and digital gene expression analysis of Nile tilapia (Oreochromis niloticus) infected by Streptococcus agalactiae[J].Mol Biol Rep,2013,40:5657-5668.
[9]Mu Y N,Ding F,Cui P,et al.Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection[J].BMC Genomics,2010,11:506-513.
[10]de Lorgeril J,Reda Z,Rafael D,et al.Whole transcriptome profiling of successful immune response to vibrio infections in the oyster crassostrea gigas by digital gene expression analysis[J].PLoS ONE,2011,6(8):e23142.
[11]罗庆苗,秦晓玉,苗向阳.利用数字基因表达谱对小尾寒羊高繁性状相关基因的筛选研究[J].中国农学通报,2012,28(23):18-25.
[12]秦宁.猪骨骼肌数字基因表达谱分析与差异表达基因验证[D].长春:吉林农业大学,2012.
[13]Xiao S Q,Mo D L,Wang Q W,et al.Aberrant host immune response induced by highly virulent PRRSV identified by digital gene expression tag profiling[J].BMC Genomics 2010,11:544-561.
[14]Cheung F,Haas B J,Goldberg S M,et al.Sequencing Medicago truncatula expressed sequenced tag using 454 life sciences technology[J].BMC Genomics,2006,7:272-282.[15]Emrich S J,Barbazuk W B,Li L,et al.Gene discovery and annotation using LCM-454 transciptome sequencing[J].Genome Res,2007,17:69-73.
[16]Wang L,Li P,Brutnell T P.Exploring plant transcriptomes using ultra high-throughput sequencing[J].Brief Funct Genomics,2010,9:118-128.
[17]Wu T,Qin Z,Zhou X,et al.Transcriptome profile analysis of floral sex determination in cucumber[J].J Plant Physiol,2010,167:905-913.
[18]Nisha L,Gopal J,Bhardwaj A R,et al.Identification and characterization of miRNAome in root,stem,leaf and tuber developmental stages of potato (Solanum tuberosum L.) by high-throughput sequencing[J].BMC Plant Biology,2014,14:1-31.
[19]Nishiyama R,Le D T,Watanabe Y,et al.Transcriptome analyses of a salt-tolerant cytokiiiin-deficient mutant reveal differential regulation of salt stress response by cytokinin deficiency[J].PLoS One,2012,7(2):e32124.
[20]Min L,Li Y,Hu Q,et al.Sugar and auxin signaling pathways respond to high temperature stress during anther development as revealed by transcript profiling analysis in cotton[J].Plant Physiology,2014,164:1293-1308.
[21]赖晓娟,严小军,杨悦,等.高温胁迫下坛紫菜的数字基因表达谱研究[J].海洋学报,2014,36(6):104-111.
[22]Qi X H,Xu X W,Lin X J,et al.Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile[J].Genomics,2012,99:160-168.
[23]Chen L M,Zhou X A,Li W B,et al.Genome-wide transcriptional analysis of two soybean genotypes under dehydration and rehydration conditions[J].BMC Genomics,2013,14:687-705.
[24]Jiang L X,Jin L G,Guo Y,et al.Glyphosate effects on the gene expression of the apical bud in soybean (Glycine max)[J].Biochemical and Biophysical Research Communications,2013,437:544-549.
[25]Shao H H,Cao Q H,Tao X,et al.Cloning and characterization of ATP synthase CF1α gene from sweet potato[J].African Journal of Biotechnology,2011,10:19035-19042.
[26]Lai X J,Gu Y H,Tao X,et al.Cloning and characterization of uridine diphosphate glucose dehydrogenase gene from Ipomoea batatas[J].Russian Journal of Plant Physiology,2014,61:298-308.[27]Mahadevan S,Park Y.Multifaceted therapeutic benefits of Ginkgo biiloba L:chemistry,efficacy,safety,and uses[J].Journal of Food Science,2008,73:14-19.
[28]Heiss C,Keen C L,Kelm M.Flavanols and cardiovascular disease prevention[J].European Heart Journal,2010,31:2583-2592.
[29]韦康,王丽鸳,成浩,等.基于数字基因表达谱对茶树类黄酮合成、调控相关基因表达的研究[J].茶叶科学,2014,34(2):195-203.
[30]Zhao W,Xia W,Li J,et al.Transcriptome profiling and digital gene expression analysis of Fallopia multiflora to discover putative genes involved in the biosynthesis of 2,3,5,4′-tetrahydroxy stilbene-2-O-β-d-glucoside[J].Gene,2014,547:126-135.
[31]Hao D C,Ge G B,Xiao P G,et al.The first insight into the tissue specific taxus transcriptome via illumina second generation sequencing[J].PLoS One,2011,6:e21220.
[32]Tang Q,Ma X J,Mo C M,et al.An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis[J].BMC Genomics,2011,12:343-355.
[33]Kulkarni A,Pillai R,Ezekiel A M,et al.Comparison of histopathology to gene expression profiling for the diagnosis of metastatic cancer[J].Diagn Pathol,2012,7:110-119.
[34]宣荣荣,陈海敏.脂多糖活化巨噬细胞的数字基因表达谱分析[J].中国药理学与毒理学杂志,2013,27(6):971-977.
[35]Fan J F,Peng Z P,Zhou C Z,et al.Gene-expression profiling in chinese patients with colon cancer by coupling experimental and bioinformatic genomewide gene-expression analyses[J].Cancer,2008,113:266-275.
[36]Wang I M,Sergey Stepaniants S,Boie Y,et al.Gene expression profiling in patients with chronic obstructive pulmonary disease and lung cancer[J].American Journal of Respiratory and Critical Care Medicine,2008,177:402-411.
[37]Nordlund J,Kiialainen A,Karlberg O,et al.Digital gene expression profiling of primary acute lymphoblastic leukemia cells[J].Leukemia,2012,26,1218-1227.
[38]Bowen N J,Walker L D,Matyunina L V,et al.Gene expression profiling supports the hypothesis that human ovarian surface epithelia are multipotent and capable of serving as ovarian cancer initiating cells[J].BMC Medical Genomics,2009,2:71-84.
[39]Veitch N J,Johnson P C D,Trivedi U,et al.Digital gene expression analysis of two life cycle stages of the human-infective parasite,Trypanosoma brucei gambiense reveals differentially expressed clusters of co-regulated genes[J].BMC Genomics,2010,11:124-137.
[40]郑凯.斜卧青霉基因表达谱的差异分析研究[D].济南:山东大学,2009.
[41]贵甫.草菇数字基因表达谱揭示同核体与异核体CAZymes表达差异[D].福州:福建农业大学,2012.
[42]Li H C,Zhang H,Guan R,et al.Identification of differential expression genes associated with host selection and adaptation between two sibling insect species by transcriptional profile analysis[J].BMC Genomics,2013,14:1-12.
[43]吴小波,王子龙,张飞,等.婚飞行为影响中华蜜蜂性成熟处女蜂王的基因表达[J].昆虫学报,2013,56(5):486-493.
[44]秦秋红.东方蜜蜂与西方蜜蜂学习记忆比较及蜜蜂学习记忆相关分子机理分析[D].南昌:江西农业大学,2013.
[45]Wang Z,Dong D,Ru B H,et al.Digital gene expression tag profiling of bat digits provides robust candidates contributing to wing formation[J].BMC Genomics,2010,11:619-630.

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Last Update: 2015-08-09