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Co-expression analysis of metabolic pathways in plants.
Loraine A. Loraine A. Methods Mol Biol. 2009;553:247-64. doi: 10.1007/978-1-60327-563-7_12. Methods Mol Biol. 2009. PMID: 19588109 Review.
An observation that a group of genes are co-expressed across diverse experimental conditions suggests they may play similar roles in the cell. ...This chapter explains how to use a Web-based tool (CressExpress) to investigate co-expression of genes involved in metab …
An observation that a group of genes are co-expressed across diverse experimental conditions suggests they may play similar roles in …
CressExpress: a tool for large-scale mining of expression data from Arabidopsis.
Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE. Srinivasasainagendra V, et al. Among authors: loraine ae. Plant Physiol. 2008 Jul;147(3):1004-16. doi: 10.1104/pp.107.115535. Epub 2008 May 8. Plant Physiol. 2008. PMID: 18467456 Free PMC article.
CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data that computes patterns of correlated expression between user-entered query genes and the rest of the genes in the genome. ...Users launch e …
CressExpress is a user-friendly, online, coexpression analysis tool for Arabidopsis (Arabidopsis thaliana) microarray expression data …
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.
Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE. Nicol JW, et al. Among authors: loraine ae. Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4. Bioinformatics. 2009. PMID: 19654113 Free PMC article.
IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers o …
IGB is an open source, desktop graphical display tool implemented in Java that supports real-time zooming and panning through a genom …
Genome-wide characterization of differential transcript usage in Arabidopsis thaliana.
Vaneechoutte D, Estrada AR, Lin YC, Loraine AE, Vandepoele K. Vaneechoutte D, et al. Among authors: loraine ae. Plant J. 2017 Dec;92(6):1218-1231. doi: 10.1111/tpj.13746. Epub 2017 Nov 20. Plant J. 2017. PMID: 29031026 Free article.
Cytokinin induces genome-wide binding of the type-B response regulator ARR10 to regulate growth and development in Arabidopsis.
Zubo YO, Blakley IC, Yamburenko MV, Worthen JM, Street IH, Franco-Zorrilla JM, Zhang W, Hill K, Raines T, Solano R, Kieber JJ, Loraine AE, Schaller GE. Zubo YO, et al. Among authors: loraine ae. Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):E5995-E6004. doi: 10.1073/pnas.1620749114. Epub 2017 Jul 3. Proc Natl Acad Sci U S A. 2017. PMID: 28673986 Free PMC article.
The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a signaling molecule mediates such a diverse array of outputs and how these response pathways are integrated with other inputs remain …
The plant hormone cytokinin affects a diverse array of growth and development processes and responses to the environment. How a
Characterization of the cytokinin-responsive transcriptome in rice.
Raines T, Blakley IC, Tsai YC, Worthen JM, Franco-Zorrilla JM, Solano R, Schaller GE, Loraine AE, Kieber JJ. Raines T, et al. Among authors: loraine ae. BMC Plant Biol. 2016 Dec 8;16(1):260. doi: 10.1186/s12870-016-0932-z. BMC Plant Biol. 2016. PMID: 27931185 Free PMC article.
Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arabidopsis. ...Consistent with the over-representation of genes involved in biotic stress, there is a substantial overlap in the genes r …
Consistent with this, we found that the preferred DNA-binding motif of a rice type-B response regulator is similar to those from Arab …
RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways.
Krizek BA, Bequette CJ, Xu K, Blakley IC, Fu ZQ, Stratmann JW, Loraine AE. Krizek BA, et al. Among authors: loraine ae. Plant Physiol. 2016 Jul;171(3):2069-84. doi: 10.1104/pp.15.01625. Epub 2016 May 20. Plant Physiol. 2016. PMID: 27208279 Free PMC article.
The presence of a number of overrepresented Gene Ontology terms related to plant defense in the set of genes differentially expressed in ant ail6 suggest that ANT and AIL6 also regulate plant defense pathways. ...
The presence of a number of overrepresented Gene Ontology terms related to plant defense in the set of genes differentially expressed …
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq.
Lambirth KC, Whaley AM, Blakley IC, Schlueter JA, Bost KL, Loraine AE, Piller KJ. Lambirth KC, et al. Among authors: loraine ae. BMC Biotechnol. 2015 Oct 1;15:89. doi: 10.1186/s12896-015-0207-z. BMC Biotechnol. 2015. PMID: 26427366 Free PMC article.
The three lines included: ST77, expressing human thyroglobulin protein (hTG), ST111, expressing human myelin basic protein (hMBP), and 764, expressing a mutant, nontoxic form of a staphylococcal subunit vaccine protein (mSEB). ...No significant gene ontology terms w …
The three lines included: ST77, expressing human thyroglobulin protein (hTG), ST111, expressing human myelin basic protein (hMBP), and 764, …
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.
Liu R, Loraine AE, Dickerson JA. Liu R, et al. Among authors: loraine ae. BMC Bioinformatics. 2014 Dec 16;15(1):364. doi: 10.1186/s12859-014-0364-4. BMC Bioinformatics. 2014. PMID: 25511303 Free PMC article.
BACKGROUND: Alternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in eukaryotes. ...Using a real data, the study looks at the consistences between the packages and verifies a subset of the detect …
BACKGROUND: Alternative Splicing (AS) as a post-transcription regulation mechanism is an important application of RNA-seq studies in …
A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser.
Gulledge AA, Vora H, Patel K, Loraine AE. Gulledge AA, et al. Among authors: loraine ae. Methods Mol Biol. 2014;1158:123-37. doi: 10.1007/978-1-4939-0700-7_8. Methods Mol Biol. 2014. PMID: 24792048 Free PMC article.
Alternative splicing is a form of posttranscriptional regulation in which primary RNA transcripts from a single gene can be spliced in multiple ways leading to different RNA and protein products. ...In this protocol, we use IGB and a cold-stress RNA-Seq data …
Alternative splicing is a form of posttranscriptional regulation in which primary RNA transcripts from a single gene can be sp …
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