메뉴 건너뛰기




Volumn 1757, Issue , 2018, Pages 251-305

Navigating xenbase: An integrated xenopus genomics and gene expression database

Author keywords

Anatomy ontology; BLAST; GBrowse; Gene expression analysis; Genome database; Polyploid genome; Textpresso; Xenopus

Indexed keywords

ANTIBODY; BONE MORPHOGENETIC PROTEIN 4; MICRORNA; MORPHOLINO OLIGONUCLEOTIDE; NUCLEIC ACID; NUCLEOTIDE; PROTEIN; REAGENT; TRANSCRIPTOME;

EID: 85047124746     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-7737-6_10     Document Type: Chapter
Times cited : (25)

References (38)
  • 1
    • 0000869397 scopus 로고
    • The developmental capacity of nuclei taken from differentiating endoderm cells of Xenopus laevis
    • Gurdon JB (1960) The developmental capacity of nuclei taken from differentiating endoderm cells of Xenopus laevis. J Embryol Exp Morphol 8:505–526
    • (1960) J Embryol Exp Morphol , vol.8 , pp. 505-526
    • Gurdon, J.B.1
  • 2
    • 0001981347 scopus 로고
    • Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei
    • Gurdon JB, Elsdale TR, Fischberg M (1958) Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei. Nature 182(4627):64–65
    • (1958) Nature , vol.182 , Issue.4627 , pp. 64-65
    • Gurdon, J.B.1    Elsdale, T.R.2    Fischberg, M.3
  • 3
    • 85010843659 scopus 로고    scopus 로고
    • Using Xenopus to understand human disease and developmental disorders
    • Sater AK, Moody SA (2017) Using Xenopus to understand human disease and developmental disorders. Genesis 55(1-2). https://doi. org/10.1002/dvg.22997
    • (2017) Genesis , vol.55 , Issue.1-2
    • Sater, A.K.1    Moody, S.A.2
  • 5
    • 84986880062 scopus 로고    scopus 로고
    • The Virtual Xenbase: Transitioning an online bioinformatics resource to a private cloud
    • Karimi K, Vize PD (2014) The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. Database (Oxford) 2014:bau108. https://doi.org/10.1093/database/bau108
    • (2014) Database (Oxford) 2014:Bau108
    • Karimi, K.1    Vize, P.D.2
  • 8
    • 84941937321 scopus 로고    scopus 로고
    • Database and informatic challenges in representing both diploid and tetraploid Xenopus species in Xenbase
    • Vize PD, Liu Y, Karimi K (2015) Database and informatic challenges in representing both diploid and tetraploid Xenopus species in Xenbase. Cytogenet Genome Res 145(3-4):278–282. https://doi.org/10.1159/000430427
    • (2015) Cytogenet Genome Res , vol.145 , Issue.3-4 , pp. 278-282
    • Vize, P.D.1    Liu, Y.2    Karimi, K.3
  • 9
    • 84941941730 scopus 로고    scopus 로고
    • A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis
    • Matsuda Y, Uno Y, Kondo M, Gilchrist MJ, Zorn AM, Rokhsar DS, Schmid M, Taira M (2015) A new nomenclature of Xenopus laevis chromosomes based on the phylogenetic relationship to Silurana/Xenopus tropicalis. Cytogenet Genome Res 145(3-4):187–191. https://doi.org/10.1159/000381292
    • (2015) Cytogenet Genome Res , vol.145 , Issue.3-4 , pp. 187-191
    • Matsuda, Y.1    Uno, Y.2    Kondo, M.3    Gilchrist, M.J.4    Zorn, A.M.5    Rokhsar, D.S.6    Schmid, M.7    Taira, M.8
  • 10
    • 53249127138 scopus 로고    scopus 로고
    • An ontology for Xenopus anatomy and development
    • Segerdell E, Bowes JB, Pollet N, Vize PD (2008) An ontology for Xenopus anatomy and development. BMC Dev Biol 8:92. https://doi.org/10.1186/1471-213X-8-92
    • (2008) BMC Dev Biol , vol.8 , pp. 92
    • Segerdell, E.1    Bowes, J.B.2    Pollet, N.3    Vize, P.D.4
  • 11
    • 84892511644 scopus 로고    scopus 로고
    • Large-scale gene function analysis with the PANTHER classification system
    • Mi H, Muruganujan A, Casagrande JT, Thomas PD (2013) Large-scale gene function analysis with the PANTHER classification system. Nat Protoc 8(8):1551–1566. https://doi.org/10.1038/nprot.2013.092
    • (2013) Nat Protoc , vol.8 , Issue.8 , pp. 1551-1566
    • Mi, H.1    Muruganujan, A.2    Casagrande, J.T.3    Thomas, P.D.4
  • 12
    • 84953214164 scopus 로고    scopus 로고
    • Measuring absolute RNA copy numbers at high temporal resolution reveals transcriptome kinetics in development
    • Owens ND, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, Cho KW, Khokha MK (2016) Measuring absolute RNA copy numbers at high temporal resolution reveals transcriptome kinetics in development. Cell Rep 14(3):632–647. https://doi.org/10.1016/j. celrep.2015.12.050
    • (2016) Cell Rep , vol.14 , Issue.3 , pp. 632-647
    • Owens, N.D.1    Blitz, I.L.2    Lane, M.A.3    Patrushev, I.4    Overton, J.D.5    Gilchrist, M.J.6    Cho, K.W.7    Khokha, M.K.8
  • 13
    • 79954452308 scopus 로고    scopus 로고
    • Mapping gene expression in two Xenopus species: Evolutionary constraints and developmental flexibility
    • PubMed ID: 21497761
    • Yanai I, Peshkin L, Jorgensen P, Kirschner MW (2011) Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility. Dev Cell 20(4): 483–496. PubMed ID: 21497761
    • (2011) Dev Cell , vol.20 , Issue.4 , pp. 483-496
    • Yanai, I.1    Peshkin, L.2    Jorgensen, P.3    Kirschner, M.W.4
  • 15
  • 18
    • 84878286239 scopus 로고    scopus 로고
    • VEGFA-dependent and -independent pathways synergise to drive Scl expression and initiate programming of the blood stem cell lineage in Xenopus
    • Ciau-Uitz A, Pinheiro P, Kirmizitas A, Zuo J, Patient R (2013) VEGFA-dependent and -independent pathways synergise to drive Scl expression and initiate programming of the blood stem cell lineage in Xenopus. Development 140(12):2632–2642. https://doi.org/10.1242/dev.090829
    • (2013) Development , vol.140 , Issue.12 , pp. 2632-2642
    • Ciau-Uitz, A.1    Pinheiro, P.2    Kirmizitas, A.3    Zuo, J.4    Patient, R.5
  • 22
    • 33751359804 scopus 로고    scopus 로고
    • Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides
    • Rana AA, Collart C, Gilchrist MJ, Smith JC (2006) Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides. PLoS Genet 2(11):193. https://doi.org/10.1371/jour-nal.pgen.0020193
    • (2006) Plos Genet , vol.2 , Issue.11 , pp. 193
    • Rana, A.A.1    Collart, C.2    Gilchrist, M.J.3    Smith, J.C.4
  • 23
    • 84868594446 scopus 로고    scopus 로고
    • Databases of gene expression in Xenopus development
    • Gilchrist MJ, Pollet N (2012) Databases of gene expression in Xenopus development. Methods Mol Biol 917:319–345. https://doi. org/10.1007/978-1-61779-992-1_19
    • (2012) Methods Mol Biol , vol.917 , pp. 319-345
    • Gilchrist, M.J.1    Pollet, N.2
  • 25
    • 70349633516 scopus 로고    scopus 로고
    • Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis
    • Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA (2009) Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res 19(10):1766–1775. https://doi.org/10.1101/gr.093054.109
    • (2009) Genome Res , vol.19 , Issue.10 , pp. 1766-1775
    • Armisen, J.1    Gilchrist, M.J.2    Wilczynska, A.3    Standart, N.4    Miska, E.A.5
  • 26
    • 85026786863 scopus 로고    scopus 로고
    • The Zahn drawings: New illustrations of Xenopus embryo and tadpole stages for studies of craniofacial development
    • PubMed ID: 28765211
    • Zahn N, Levin M, Adams DS (2017) The Zahn drawings: new illustrations of Xenopus embryo and tadpole stages for studies of craniofacial development. Development 144(15):2708– 2713. PubMed ID: 28765211
    • (2017) Development , vol.144 , pp. 2708-2713
    • Zahn, N.1    Levin, M.2    Adams, D.S.3
  • 28
    • 0023154191 scopus 로고
    • Fates of the blastomeres of the 16-cell stage Xenopus embryo
    • Moody SA (1987) Fates of the blastomeres of the 16-cell stage Xenopus embryo. Dev Biol 119(2):560–578
    • (1987) Dev Biol , vol.119 , Issue.2 , pp. 560-578
    • Moody, S.A.1
  • 29
    • 0023395841 scopus 로고
    • Fates of the blastomeres of the 32-cell-stage Xenopus embryo
    • Moody SA (1987) Fates of the blastomeres of the 32-cell-stage Xenopus embryo. Dev Biol 122(2):300–319
    • (1987) Dev Biol , vol.122 , Issue.2 , pp. 300-319
    • Moody, S.A.1
  • 30
    • 0028230863 scopus 로고
    • The cleavage stage origin of Spemann’s Organizer: Analysis of the movements of blastomere clones before and during gastrulation in Xenopus
    • Bauer DV, Huang S, Moody SA (1994) The cleavage stage origin of Spemann’s Organizer: analysis of the movements of blastomere clones before and during gastrulation in Xenopus. Development 120(5):1179–1189
    • (1994) Development , vol.120 , Issue.5 , pp. 1179-1189
    • Bauer, D.V.1    Huang, S.2    Moody, S.A.3
  • 31
    • 84907962027 scopus 로고    scopus 로고
    • Enhanced XAO: The ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase
    • Segerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM (2013) Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on Xenbase. J Biomed Semantics 4(1):31. https://doi. org/10.1186/2041-1480-4-31
    • (2013) J Biomed Semantics , vol.4 , Issue.1 , pp. 31
    • Segerdell, E.1    Ponferrada, V.G.2    James-Zorn, C.3    Burns, K.A.4    Fortriede, J.D.5    Dahdul, W.M.6    Vize, P.D.7    Zorn, A.M.8
  • 32
    • 84890805562 scopus 로고    scopus 로고
    • Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system
    • Blitz IL, Biesinger J, Xie X, Cho KW (2013) Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system. Genesis 51(12):827–834. https://doi. org/10.1002/dvg.22719
    • (2013) Genesis , vol.51 , Issue.12 , pp. 827-834
    • Blitz, I.L.1    Biesinger, J.2    Xie, X.3    Cho, K.W.4
  • 33
    • 84955414846 scopus 로고    scopus 로고
    • CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus
    • Bhattacharya D, Marfo CA, Li D, Lane M, Khokha MK (2015) CRISPR/Cas9: an inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. Dev Biol 408(2):196–204. https://doi.org/10.1016/j. ydbio.2015.11.003
    • (2015) Dev Biol , vol.408 , Issue.2 , pp. 196-204
    • Bhattacharya, D.1    Marfo, C.A.2    Li, D.3    Lane, M.4    Khokha, M.K.5
  • 34
    • 0033780376 scopus 로고    scopus 로고
    • Effective targeted gene ‘knockdown’ in zebrafish
    • Nasevicius A, Ekker SC (2000) Effective targeted gene ‘knockdown’ in zebrafish. Nat Genet 26(2):216–220. https://doi. org/10.1038/79951
    • (2000) Nat Genet , vol.26 , Issue.2 , pp. 216-220
    • Nasevicius, A.1    Ekker, S.C.2
  • 35
    • 0034213262 scopus 로고    scopus 로고
    • Beta-catenin signaling activity dissected in the early Xenopus embryo: A novel antisense approach
    • Heasman J, Kofron M, Wylie C (2000) Beta-catenin signaling activity dissected in the early Xenopus embryo: a novel antisense approach. Dev Biol 222(1):124–134. https://doi. org/10.1006/dbio.2000.9720
    • (2000) Dev Biol , vol.222 , Issue.1 , pp. 124-134
    • Heasman, J.1    Kofron, M.2    Wylie, C.3
  • 36
    • 0034908648 scopus 로고    scopus 로고
    • Comparison of morpholino based translational inhibition during the development of Xenopus laevis and Xenopus tropicalis
    • Nutt SL, Bronchain OJ, Hartley KO, Amaya E (2001) Comparison of morpholino based translational inhibition during the development of Xenopus laevis and Xenopus tropicalis. Genesis 30(3):110–113
    • (2001) Genesis , vol.30 , Issue.3 , pp. 110-113
    • Nutt, S.L.1    Bronchain, O.J.2    Hartley, K.O.3    Amaya, E.4
  • 38
    • 85020299812 scopus 로고    scopus 로고
    • Naming CRISPR alleles: Endonuclease-mediated mutation nomenclature across species
    • Knowlton MN, Smith CL (2017) Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome 28:367. https://doi.org/10.1007/s00335-017-9698-3
    • (2017) Mamm Genome , vol.28 , pp. 367
    • Knowlton, M.N.1    Smith, C.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.