Keyan Zhao

University of Iowa, Iowa City, Iowa, United States

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Publications (2)14.8 Total impact

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    Keyan Zhao · Zhi-Xiang Lu · Juw Won Park · Qing Zhou · Yi Xing
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    ABSTRACT: To characterize the genetic variation of alternative splicing, we develop GLiMMPS, a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. GLiMMPS takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. Analyses of simulated and real RNA-seq datasets demonstrate that GLiMMPS outperforms competing statistical models. Quantitative RT-PCR tests of 26 randomly selected GLiMMPS sQTLs yielded a validation rate of 100%. As population-scale RNA-seq studies become increasingly affordable and popular, GLiMMPS provides a useful tool for elucidating the genetic variation of alternative splicing in humans and model organisms.
    Full-text · Article · Jul 2013 · Genome biology
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    Jinsil Kim · Keyan Zhao · Peng Jiang · Zhi-xiang Lu · Jinkai Wang · Jeffrey C Murray · Yi Xing
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    ABSTRACT: Tables S1 and S2 and Figures S1-3 Supplemental Table S1. Mapping statistics of RNA-Seq data from placenta and HBM2.0 tissues. Supplemental Table S2. Distribution of gene expression level (FPKM) of RNA-Seq data from placenta and HBM2.0 tissues. Figure S1. Distribution of gene expression values (FPKM) for all tissues examined in the study. Figure S2. qRT-PCR validation of placenta-enriched SFs ESRP1 and MBNL3. Figure S3. Functional interaction network analysis of genes with enriched expression (EE) and differential splicing (DS) that intersect all three placental tissues: module 2. Circular node: a query gene. Diamond-shaped node: a linker gene. Node color was determined based on whether the query gene shows EE (green), DS (pink), or both (red). The most significantly enriched pathways were highlighted in bigger node size: integrin signaling pathway and ECM-receptor interaction pathway.
    Preview · Dataset · Mar 2012
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    Jinsil Kim · Keyan Zhao · Peng Jiang · Zhi-xiang Lu · Jinkai Wang · Jeffrey C Murray · Yi Xing
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    ABSTRACT: Table S3 Enriched pathways (FDR < 0.05) in the whole network and submodules (module size > 50) from functional interaction network analysis.
    Preview · Dataset · Mar 2012
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    Jinsil Kim · Keyan Zhao · Peng Jiang · Zhi-xiang Lu · Jinkai Wang · Jeffrey C Murray · Yi Xing
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    ABSTRACT: Table S4 FPKM expression levels in all tissues for the novel TARs identified from the placental tissues.
    Preview · Dataset · Mar 2012
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    ABSTRACT: The placenta is a key component in understanding the physiological processes involved in pregnancy. Characterizing genes critical for placental function can serve as a basis for identifying mechanisms underlying both normal and pathologic pregnancies. Detailing the placental tissue transcriptome could provide a valuable resource for genomic studies related to placental disease. We have conducted a deep RNA sequencing (RNA-Seq) study on three tissue components (amnion, chorion, and decidua) of 5 human placentas from normal term pregnancies. We compared the placental RNA-Seq data to that of 16 other human tissues and observed a wide spectrum of transcriptome differences both between placenta and other human tissues and between distinct compartments of the placenta. Exon-level analysis of the RNA-Seq data revealed a large number of exons with differential splicing activities between placenta and other tissues, and 79% (27 out of 34) of the events selected for RT-PCR test were validated. The master splicing regulator ESRP1 is expressed at a proportionately higher level in amnion compared to all other analyzed human tissues, and there is a significant enrichment of ESRP1-regulated exons with tissue-specific splicing activities in amnion. This suggests an important role of alternative splicing in regulating gene function and activity in specific placental compartments. Importantly, genes with differential expression or splicing in the placenta are significantly enriched for genes implicated in placental abnormalities and preterm birth. In addition, we identified 604-1007 novel transcripts and 494-585 novel exons expressed in each of the three placental compartments. Our data demonstrate unique aspects of gene expression and splicing in placental tissues that provide a basis for disease investigation related to disruption of these mechanisms. These data are publicly available providing the community with a rich resource for placental physiology and disease-related studies.
    Full-text · Article · Mar 2012 · BMC Genomics
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    Jinsil Kim · Keyan Zhao · Peng Jiang · Zhi-xiang Lu · Jinkai Wang · Jeffrey C Murray · Yi Xing
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    ABSTRACT: Table S5 Exon inclusion levels and primer sequences for exons selected for RT-PCR validation.
    Preview · Dataset · Mar 2012
  • Source
    Jinsil Kim · Keyan Zhao · Peng Jiang · Zhi-xiang Lu · Jinkai Wang · Jeffrey C Murray · Yi Xing
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    ABSTRACT: Figure S4 RT-PCR analysis of 34 exons that showed significant differential splicing (> 10% difference in exon inclusion level, FDR < 0.1) between placental and HBM2.0 tissues. Figure S5. RT-PCR analysis of 21 ESRP1target exons.
    Preview · Dataset · Mar 2012