Genome-Wide Analysis of Long Noncoding RNA (lncRNA) Expression in Hepatoblastoma Tissues
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{"title"=>"Genome-wide analysis of long noncoding RNA (lncRNA) expression in hepatoblastoma tissues", "type"=>"journal", "authors"=>[{"first_name"=>"Rui", "last_name"=>"Dong", "scopus_author_id"=>"35217617200"}, {"first_name"=>"Deshui", "last_name"=>"Jia", "scopus_author_id"=>"36243821500"}, {"first_name"=>"Ping", "last_name"=>"Xue", "scopus_author_id"=>"8660744500"}, {"first_name"=>"Ximao", "last_name"=>"Cui", "scopus_author_id"=>"56112885200"}, {"first_name"=>"Kai", "last_name"=>"Li", "scopus_author_id"=>"57001336400"}, {"first_name"=>"Shan", "last_name"=>"Zheng", "scopus_author_id"=>"56305636200"}, {"first_name"=>"Xianghuo", "last_name"=>"He", "scopus_author_id"=>"24465211300"}, {"first_name"=>"Kuiran", "last_name"=>"Dong", "scopus_author_id"=>"26428077600"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"24465615", "doi"=>"10.1371/journal.pone.0085599", "sgr"=>"84898452646", "isbn"=>"1932-6203", "scopus"=>"2-s2.0-84898452646", "issn"=>"19326203", "pui"=>"372817910"}, "id"=>"6d54b55c-1d14-3c00-8db4-82cc162e53c3", "abstract"=>"Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma. Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients. The genome-wide analysis of lncRNA expression in these tissues was performed using a 4×180 K lncRNA microarray and Sureprint G3 Human lncRNA Chips. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of lncRNAs and mRNAs were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using the standard enrichment computation method. Associations between lncRNAs and adjacent protein-coding genes were determined through complex transcriptional loci analysis. We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues. Among these, 1757 lncRNAs were upregulated more than two-fold relative to normal tissues and 979 lncRNAs were downregulated. Moreover, in hepatoblastoma there were 420 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs, and 167 differentially expressed mRNAs. The co-expression network analysis predicted 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs were positive, and 51 pairs were negative. Lastly, qRT-PCR data verified six upregulated and downregulated lncRNAs in hepatoblastoma, plus endothelial cell-specific molecule 1 (ESM1) mRNA. Our results demonstrated that expression of these aberrant lncRNAs could respond to hepatoblastoma development. Further study of these lncRNAs could provide useful insight into hepatoblastoma biology.", "link"=>"http://www.mendeley.com/research/genomewide-analysis-long-noncoding-rna-lncrna-expression-hepatoblastoma-tissues", "reader_count"=>58, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>16, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Other"=>3, "Student > Master"=>7, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Librarian"=>1, "Researcher"=>16, "Student > Ph. D. Student"=>20, "Student > Postgraduate"=>4, "Other"=>3, "Student > Master"=>7, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>28, "Medicine and Dentistry"=>6, "Neuroscience"=>2, "Physics and Astronomy"=>1, "Psychology"=>1, "Computer Science"=>6, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "China"=>1, "Italy"=>1, "Germany"=>1, "India"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1349905"], "description"=>"<p>The box plot is a convenient way to quickly visualize the distributions of a dataset of lncRNA (A) and mRNA (B) profiles. After normalization, the distributions of log<sub>2</sub> ratios among nine samples were nearly the same. The scatter plot is a visualization method used to assess the lncRNA (C) and mRNA (D) expression variations between hepatoblastoma and the paired distant noncancerous tissues. The values of the X- and Y-axes in the scatter plot are the averaged normalized signal values of the group (log<sub>2</sub> scaled). The green lines represent fold change lines (the default fold change given is 2.0).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "lncrnas", "mrnas", "hepatoblastoma", "paired", "noncancerous"], "article_id"=>902930, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_lncRNAs_and_mRNAs_in_4_hepatoblastoma_vs_paired_distant_noncancerous_tissues_/902930", "title"=>"Differentially expressed lncRNAs and mRNAs in 4 hepatoblastoma vs. paired distant noncancerous tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349908"], "description"=>"<p>(A) GO analysis of lncRNA-target genes according to biological process. (B) GO analysis of lncRNA-target genes according to cell component. (C) GO analysis of lncRNA-target genes according to molecular function.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "ontology", "enrichment"], "article_id"=>902933, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_ontology_GO_enrichment_analysis_of_lncRNA_targets_/902933", "title"=>"Gene ontology (GO) enrichment analysis of lncRNA-targets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349910"], "description"=>"<p>The co-expression network was composed of 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs presented as positive, and 51 pairs presented as negative. This co-expression network indicated that one lncRNA could target 11 coding genes at most and that one coding gene could correlate with 128 lncRNAs at most.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "lncrna-mrna"], "article_id"=>902935, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_of_lncRNA_mRNA_association_network_/902935", "title"=>"Prediction of lncRNA-mRNA association network.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349914"], "description"=>"<p>The data showed that expressions of lncRNAs TCONS-00090092-MEG3, TCONS-l2-00000179, TCONS-l2-00014091, TCONS-l2-00004424, TCONS-l2-00021262, and TCONS-00014978 and ESM1 mRNA were upregulated and that TCONS-l2-00018070, TCONS-l2-00018071, TCONS-l2-00006843, TCONS-l2-00030560, TCONS-l2-00020565, TCONS-00024647, and TCONS-00014512 were downregulated in hepatoblastoma tissues relative to the paired distant noncancerous tissues, consistent with the microarray data.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "validation", "differentially", "lncrnas", "esm1", "mrna", "hepatoblasoma"], "article_id"=>902939, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_qRT_PCR_validation_of_some_differentially_expressed_lncRNAs_and_ESM1_mRNA_in_these_4_hepatoblasoma_tissue_samples_/902939", "title"=>"qRT-PCR validation of some differentially expressed lncRNAs and ESM1 mRNA in these 4 hepatoblasoma tissue samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349915"], "description"=>"<p>*at serum sample day.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "subjects", "serum", "afp"], "article_id"=>902940, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_study_subjects_and_serum_AFP_levels_/902940", "title"=>"Distribution of study subjects and serum AFP levels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349916"], "description"=>"<p>Primers used for qRT-PCR analysis of lncRNA and mRNA levels.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "qrt-pcr", "lncrna", "mrna"], "article_id"=>902941, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primers_used_for_qRT_PCR_analysis_of_lncRNA_and_mRNA_levels_/902941", "title"=>"Primers used for qRT-PCR analysis of lncRNA and mRNA levels.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-17 02:47:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/1349920", "https://ndownloader.figshare.com/files/1349921", "https://ndownloader.figshare.com/files/1349922", "https://ndownloader.figshare.com/files/1349923", "https://ndownloader.figshare.com/files/1349924", "https://ndownloader.figshare.com/files/1349925"], "description"=>"<div><p>Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. We performed a genome-wide analysis of lncRNA expression in hepatoblastoma tissues to identify novel targets for further study of hepatoblastoma. Hepatoblastoma and normal liver tissue samples were obtained from hepatoblastoma patients. The genome-wide analysis of lncRNA expression in these tissues was performed using a 4×180 K lncRNA microarray and Sureprint G3 Human lncRNA Chips. Quantitative RT-PCR (qRT-PCR) was performed to confirm these results. The differential expressions of lncRNAs and mRNAs were identified through fold-change filtering. Gene Ontology (GO) and pathway analyses were performed using the standard enrichment computation method. Associations between lncRNAs and adjacent protein-coding genes were determined through complex transcriptional loci analysis. We found that 2736 lncRNAs were differentially expressed in hepatoblastoma tissues. Among these, 1757 lncRNAs were upregulated more than two-fold relative to normal tissues and 979 lncRNAs were downregulated. Moreover, in hepatoblastoma there were 420 matched lncRNA-mRNA pairs for 120 differentially expressed lncRNAs, and 167 differentially expressed mRNAs. The co-expression network analysis predicted 252 network nodes and 420 connections between 120 lncRNAs and 132 coding genes. Within this co-expression network, 369 pairs were positive, and 51 pairs were negative. Lastly, qRT-PCR data verified six upregulated and downregulated lncRNAs in hepatoblastoma, plus endothelial cell-specific molecule 1 (ESM1) mRNA. Our results demonstrated that expression of these aberrant lncRNAs could respond to hepatoblastoma development. Further study of these lncRNAs could provide useful insight into hepatoblastoma biology.</p></div>", "links"=>[], "tags"=>["Computational biology", "genomics", "Genome analysis tools", "Gene ontologies", "Genome expression analysis", "microarrays", "oncology", "Cancers and neoplasms", "Gastrointestinal tumors", "Hepatocellular carcinoma", "pediatrics", "Pediatric oncology", "surgery", "General surgery", "Pediatric surgery", "Surgical oncology", "noncoding", "rna", "hepatoblastoma"], "article_id"=>902945, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Rui Dong", "Deshui Jia", "Ping Xue", "Ximao Cui", "Kai Li", "Shan Zheng", "Xianghuo He", "Kuiran Dong"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0085599.s001", "https://dx.doi.org/10.1371/journal.pone.0085599.s002", "https://dx.doi.org/10.1371/journal.pone.0085599.s003", "https://dx.doi.org/10.1371/journal.pone.0085599.s004", "https://dx.doi.org/10.1371/journal.pone.0085599.s005", "https://dx.doi.org/10.1371/journal.pone.0085599.s006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_Analysis_of_Long_Noncoding_RNA_lncRNA_Expression_in_Hepatoblastoma_Tissues_/902945", "title"=>"Genome-Wide Analysis of Long Noncoding RNA (lncRNA) Expression in Hepatoblastoma Tissues", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-17 02:47:33"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[292, 461]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[327, 511]}]}
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