Transcriptional Profiling of Mouse Uterus at Pre-Implantation Stage under VEGF Repression
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{"title"=>"Transcriptional Profiling of Mouse Uterus at Pre-Implantation Stage under VEGF Repression", "type"=>"journal", "authors"=>[{"first_name"=>"Yan", "last_name"=>"Ji", "scopus_author_id"=>"36698831200"}, {"first_name"=>"Xiaodan", "last_name"=>"Lu", "scopus_author_id"=>"55547993000"}, {"first_name"=>"Qingping", "last_name"=>"Zhong", "scopus_author_id"=>"55612596400"}, {"first_name"=>"Peng", "last_name"=>"Liu", "scopus_author_id"=>"57199213585"}, {"first_name"=>"Yao", "last_name"=>"An", "scopus_author_id"=>"55259716900"}, {"first_name"=>"Yuntao", "last_name"=>"Zhang", "scopus_author_id"=>"40561873900"}, {"first_name"=>"Shujie", "last_name"=>"Zhang", "scopus_author_id"=>"55612844500"}, {"first_name"=>"Ruirui", "last_name"=>"Jia", "scopus_author_id"=>"55612744200"}, {"first_name"=>"Isaias G.", "last_name"=>"Tesfamariam", "scopus_author_id"=>"55612592200"}, {"first_name"=>"Abraha G.", "last_name"=>"Kahsay", "scopus_author_id"=>"57196149789"}, {"first_name"=>"Luqing", "last_name"=>"Zhang", "scopus_author_id"=>"37086717100"}, {"first_name"=>"Wensheng", "last_name"=>"Zhu", "scopus_author_id"=>"12647165500"}, {"first_name"=>"Yaowu", "last_name"=>"Zheng", "scopus_author_id"=>"55498102000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84874532635", "pmid"=>"23468957", "sgr"=>"84874532635", "doi"=>"10.1371/journal.pone.0057287", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "pui"=>"368446768"}, "id"=>"e5d636bd-a7e0-3352-9bd0-d947ffadde1c", "abstract"=>"Uterus development during pre-implantation stage affects implantation process and embryo growth. Aberrant uterus development is associated with many human reproductive diseases. Among the factors regulating uterus development, vascular remodeling promoters are critical for uterus function and fertility. Vascular endothelial growth factor (VEGF), as one of the major members, has been found to be important in endothelial cell growth and blood vessel development, as well as in non-endothelial cells. VEGF mediation in reproduction has been broadly studied, but VEGF-induced transcriptional machinery during implantation window has not been systematically studied. In this study, a genetically repressed VEGF mouse model was used to analyze uterus transcriptome at gestation 2.5 (G2.5) by Solexa/Illumina's digital gene expression (DGE) system. A number of 831 uterus-specific and 2398 VEGF-regulated genes were identified. Gene ontology (GO) analysis indicated that genes actively involved in uterus development were members of collagen biosynthesis, cell proliferation and cell apoptosis. Uterus-specific genes were enriched in activities of phosphatidyl inositol phosphate kinase, histone H3-K36 demethylation and protein acetylation. Among VEGF-regulated genes, up-regulated were associated with RNA polymerase III activity while down-regulated were strongly related with muscle development. Comparable numbers of antisense transcripts were identified. Expression levels of the antisense transcripts were found tightly correlated with their sense expression levels, an indication of possibly non-specific transcripts generated around the active promoters and enhancers. The antisense transcripts with exceptionally high or low expression levels and the antisense transcripts under VEGF regulation were also identified. These transcripts may be important candidates in regulation of uterus development. This study provides a global survey on genes and antisense transcripts regulated by VEGF in the pre-implantation stage. Results will contribute to further study the candidate genes and pathways in regulating implantation process and related diseases.", "link"=>"http://www.mendeley.com/research/transcriptional-profiling-mouse-uterus-preimplantation-stage-under-vegf-repression", "reader_count"=>9, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Student > Doctoral Student"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/973999"], "description"=>"<p>Genes with expression level higher than 100 copies were used. <b>BP</b> represents biological processes, <b>CC</b> represents cellular components and <b>MF</b> represents molecular functions.</p>", "links"=>[], "tags"=>["uterus-expressed"], "article_id"=>642176, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g002", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_analysis_of_uterus_expressed_genes_/642176", "title"=>"GO analysis of uterus-expressed genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:49:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/974020", "https://ndownloader.figshare.com/files/974026", "https://ndownloader.figshare.com/files/974032", "https://ndownloader.figshare.com/files/974034", "https://ndownloader.figshare.com/files/974038", "https://ndownloader.figshare.com/files/974040", "https://ndownloader.figshare.com/files/974042", "https://ndownloader.figshare.com/files/974044", "https://ndownloader.figshare.com/files/974045", "https://ndownloader.figshare.com/files/974048", "https://ndownloader.figshare.com/files/974049", "https://ndownloader.figshare.com/files/974050", "https://ndownloader.figshare.com/files/974053", "https://ndownloader.figshare.com/files/974054", "https://ndownloader.figshare.com/files/974055"], "description"=>"<div><p>Uterus development during pre-implantation stage affects implantation process and embryo growth. Aberrant uterus development is associated with many human reproductive diseases. Among the factors regulating uterus development, vascular remodeling promoters are critical for uterus function and fertility. Vascular endothelial growth factor (VEGF), as one of the major members, has been found to be important in endothelial cell growth and blood vessel development, as well as in non-endothelial cells. VEGF mediation in reproduction has been broadly studied, but VEGF-induced transcriptional machinery during implantation window has not been systematically studied. In this study, a genetically repressed VEGF mouse model was used to analyze uterus transcriptome at gestation 2.5 (G2.5) by Solexa/Illumina’s digital gene expression (DGE) system. A number of 831 uterus-specific and 2398 VEGF-regulated genes were identified. Gene ontology (GO) analysis indicated that genes actively involved in uterus development were members of collagen biosynthesis, cell proliferation and cell apoptosis. Uterus-specific genes were enriched in activities of phosphatidyl inositol phosphate kinase, histone H3-K36 demethylation and protein acetylation. Among VEGF-regulated genes, up-regulated were associated with RNA polymerase III activity while down-regulated were strongly related with muscle development. Comparable numbers of antisense transcripts were identified. Expression levels of the antisense transcripts were found tightly correlated with their sense expression levels, an indication of possibly non-specific transcripts generated around the active promoters and enhancers. The antisense transcripts with exceptionally high or low expression levels and the antisense transcripts under VEGF regulation were also identified. These transcripts may be important candidates in regulation of uterus development. This study provides a global survey on genes and antisense transcripts regulated by VEGF in the pre-implantation stage. Results will contribute to further study the candidate genes and pathways in regulating implantation process and related diseases.</p> </div>", "links"=>[], "tags"=>["transcriptional", "profiling", "uterus", "pre-implantation", "vegf", "repression"], "article_id"=>642189, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057287.s001", "https://dx.doi.org/10.1371/journal.pone.0057287.s002", "https://dx.doi.org/10.1371/journal.pone.0057287.s003", "https://dx.doi.org/10.1371/journal.pone.0057287.s004", "https://dx.doi.org/10.1371/journal.pone.0057287.s005", "https://dx.doi.org/10.1371/journal.pone.0057287.s006", "https://dx.doi.org/10.1371/journal.pone.0057287.s007", "https://dx.doi.org/10.1371/journal.pone.0057287.s008", "https://dx.doi.org/10.1371/journal.pone.0057287.s009", "https://dx.doi.org/10.1371/journal.pone.0057287.s010", "https://dx.doi.org/10.1371/journal.pone.0057287.s011", "https://dx.doi.org/10.1371/journal.pone.0057287.s012", "https://dx.doi.org/10.1371/journal.pone.0057287.s013", "https://dx.doi.org/10.1371/journal.pone.0057287.s014", "https://dx.doi.org/10.1371/journal.pone.0057287.s015"], "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptional_Profiling_of_Mouse_Uterus_at_Pre_Implantation_Stage_under_VEGF_Repression__/642189", "title"=>"Transcriptional Profiling of Mouse Uterus at Pre-Implantation Stage under VEGF Repression", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-03-01 12:53:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/973997"], "description"=>"<p>(<b>A</b>) Reversible repression system of VEGF gene expression. (<b>B</b>) Relative VEGF mRNA levels by qPCR (n = 5). (<b>C</b>, <b>D</b>) Protein expression by Western blot analysis and the quantification (n = 3). (<b>E</b>) Embryo collection at E3.5 (n = 45). (<b>F</b>) Embryo dissection at E9.5 (n = 11). (<b>G</b>) Embryo transfer experiment (n = 22). Dox+ represented mouse chow with 200 mg/kg doxycycline. Dox<b>−</b> represented regular mouse chow. Data are presented as mean ± SEM. *P<0.05, **P<0.005, ***P<0.001.</p>", "links"=>[], "tags"=>["repression", "implantation"], "article_id"=>642174, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g001", "stats"=>{"downloads"=>1, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_VEGF_repression_effect_on_ovulation_pregnancy_and_implantation_rate_/642174", "title"=>"VEGF repression effect on ovulation, pregnancy and implantation rate.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:49:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/974013"], "description"=>"<p>(<b>A</b>) Low and high expression sense and antisense transcript of Dox+ sample. (<b>B</b>) Low and high expression sense and antisense transcripts of Dox<b>−</b> sample. (<b>C</b>) Expression correlation analysis of sense and antisense transcripts in Dox+ sample (<i>r</i> = 0.9972). (<b>D</b>) Expression correlation analysis of sense and antisense transcripts in Dox<b>−</b> sample (<i>r</i> = 0.9968).</p>", "links"=>[], "tags"=>["transcripts"], "article_id"=>642185, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g007", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Antisense_transcripts_analysis_/642185", "title"=>"Antisense transcripts analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:52:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/974011"], "description"=>"<p>Genes with expression level higher than 200 copies (Dox+ plus Dox<b>−</b> ≥200) were used. Pathway analysis was based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The Y-axis represents the pathway category and the X-axis represents the log10 (p-value) of the significant pathways.</p>", "links"=>[], "tags"=>["vegf-regulated"], "article_id"=>642183, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g006", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_KEGG_analysis_of_VEGF_regulated_genes_/642183", "title"=>"KEGG analysis of VEGF-regulated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:51:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/974005"], "description"=>"<p>Genes with combined expression level equal or higher than 200 copies (Dox+ plus Dox<b>−</b> ≥200) were used.</p>", "links"=>[], "tags"=>["up-regulated", "genes", "vegf"], "article_id"=>642179, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_analysis_of_up_regulated_genes_by_VEGF_repression_/642179", "title"=>"GO analysis of up-regulated genes by VEGF repression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:51:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/974002"], "description"=>"<p>Genes with expression level higher than 100 copies were used. Genes expressed in uterus were compared with genes in the liver, muscle and brain.</p>", "links"=>[], "tags"=>["uterus-specific"], "article_id"=>642178, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_analysis_of_uterus_specific_genes_/642178", "title"=>"GO analysis of uterus-specific genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:50:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/974015"], "description"=>"<p>Representative genes were selected to validate the DGE results, (<b>A</b>) up-regulated genes and (<b>B</b>) down-regulated genes by VEGF repression. The Y-axis indicates the fold change of gene expression. Error bars represent standard error.</p>", "links"=>[], "tags"=>["differentially", "genes"], "article_id"=>642186, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g008", "stats"=>{"downloads"=>2, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_differentially_expressed_genes_by_qPCR_/642186", "title"=>"Validation of differentially expressed genes by qPCR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:52:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005808"], "description"=>"<p>Top 20 VEGF<i>-</i>regulated genes.</p>", "links"=>[], "tags"=>["20"], "article_id"=>666423, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.t002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_20_VEGF_regulated_genes_/666423", "title"=>"Top 20 VEGF<i>-</i>regulated genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-28 01:47:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005833"], "description"=>"<p>Gene expression levels classified by copy number.</p>", "links"=>[], "tags"=>["classified"], "article_id"=>666451, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.t001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_levels_classified_by_copy_number_/666451", "title"=>"Gene expression levels classified by copy number.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-28 01:47:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/974006"], "description"=>"<p>GO analysis of down-regulated genes by VEGF repression.</p>", "links"=>[], "tags"=>["down-regulated", "genes", "vegf"], "article_id"=>642180, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.g005", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GO_analysis_of_down_regulated_genes_by_VEGF_repression_/642180", "title"=>"GO analysis of down-regulated genes by VEGF repression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-01 12:51:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/1005782"], "description"=>"<p>VEGF-regulated genes associated to estrogen stimulus.</p>", "links"=>[], "tags"=>["genes", "estrogen"], "article_id"=>666399, "categories"=>["Physiology", "Biological Sciences", "Cancer", "Mathematics", "Genetics"], "users"=>["Yan Ji", "Xiaodan Lu", "Qingping Zhong", "Peng Liu", "Yao An", "Yuntao Zhang", "Shujie Zhang", "Ruirui Jia", "Isaias G. Tesfamariam", "Abraha G. Kahsay", "Luqing Zhang", "Wensheng Zhu", "Yaowu Zheng"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057287.t003", "stats"=>{"downloads"=>4, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_VEGF_regulated_genes_associated_to_estrogen_stimulus_/666399", "title"=>"VEGF-regulated genes associated to estrogen stimulus.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-28 01:46:39"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Developmental biology", "average_usage"=>[275, 472, 605, 720, 822, 921, 1013, 1106, 1200, 1289, 1378, 1459, 1531]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}]}
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