Genome-Wide Analysis of Small RNA and Novel MicroRNA Discovery in Human Acute Lymphoblastic Leukemia Based on Extensive Sequencing Approach
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{"title"=>"Genome-wide analysis of small RNA and novel microRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach", "type"=>"journal", "authors"=>[{"first_name"=>"Hua", "last_name"=>"Zhang", "scopus_author_id"=>"7409202858"}, {"first_name"=>"Jian Hua", "last_name"=>"Yang", "scopus_author_id"=>"35303990300"}, {"first_name"=>"Yu Sheng", "last_name"=>"Zheng", "scopus_author_id"=>"55713181900"}, {"first_name"=>"Peng", "last_name"=>"Zhang", "scopus_author_id"=>"9245727000"}, {"first_name"=>"Xiao", "last_name"=>"Chen", "scopus_author_id"=>"57192469966"}, {"first_name"=>"Jun", "last_name"=>"Wu", "scopus_author_id"=>"57150354400"}, {"first_name"=>"Ling", "last_name"=>"Xu", "scopus_author_id"=>"57199907077"}, {"first_name"=>"Xue Qun", "last_name"=>"Luo", "scopus_author_id"=>"7402871254"}, {"first_name"=>"Zhi Yong", "last_name"=>"Ke", "scopus_author_id"=>"24390956800"}, {"first_name"=>"Hui", "last_name"=>"Zhou", "scopus_author_id"=>"56233512400"}, {"first_name"=>"Liang Hu", "last_name"=>"Qu", "scopus_author_id"=>"7103292439"}, {"first_name"=>"Yue Qin", "last_name"=>"Chen", "scopus_author_id"=>"8161796000"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-70149095956", "sgr"=>"70149095956", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0006849", "pmid"=>"19724645", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"355242732"}, "id"=>"fb8ffeab-d88c-3fa1-9dab-d0ec00b43a72", "abstract"=>"BACKGROUND: MicroRNAs (miRNAs) have been proved to play an important role in various cellular processes and function as tumor suppressors or oncogenes in cancers including leukemia. The identification of a large number of novel miRNAs and other small regulatory RNAs will provide valuable insights into the roles they play in tumorgenesis. METHODOLOGY/PRINCIPAL FINDINGS: To gain further understanding of the role of miRNAs relevant to acute lymphoblastic leukemia (ALL), we employed the sequencing-by-synthesis (SBS) strategy to sequence small RNA libraries prepared from ALL patients and normal donors. In total we identified 159 novel miRNAs and 116 novel miRNA*s from both libraries. Among the 159 novel miRNAs, 42 were identified with high stringency in our data set. Furthermore, we demonstrated the different expression patterns of 20 newly identified and several known miRNAs between ALL patients and normal donors, suggesting these miRNAs may be associated with ALL and could constitute an ALL-specific miRNA signature. Interestingly, GO \"biological process\" classifications revealed that a set of significantly abnormally expressed miRNAs are associated with disease relapse, which implies that these dysregulated miRNAs might promote the progression of ALL by regulating genes involved in the pathway of the disease development. CONCLUSION/SIGNIFICANCE: The study presents a comprehensive picture of the expression of small RNAs in human acute lymphoblastic leukemia and highlights novel and known miRNAs differentially expressed between ALL patients and normal donors. To our knowledge, this is the first study to look at genome-wide known and novel miRNA expression patterns in in human acute lymphoblastic leukemia. Our data revealed that these deregulated miRNAs may be associated with ALL or the onset of relapse.", "link"=>"http://www.mendeley.com/research/genomewide-analysis-small-rna-novel-microrna-discovery-human-acute-lymphoblastic-leukemia-based-exte-6", "reader_count"=>6, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>3}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}}, "group_count"=>0}

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  • {"files"=>["https://ndownloader.figshare.com/files/885712"], "description"=>"<p>The top 6 up-regulated and 14 down-regulated novel miRNAs differentially expressed in patient group (fold changes>2.0 and <i>P</i>-value of <0.001).</p>", "links"=>[], "tags"=>["up-regulated", "14", "down-regulated", "mirnas", "differentially"], "article_id"=>556155, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_top_6_up_regulated_and_14_down_regulated_novel_miRNAs_differentially_expressed_in_patient_group_fold_changes_2_0_and_P_value_of_/556155", "title"=>"The top 6 up-regulated and 14 down-regulated novel miRNAs differentially expressed in patient group (fold changes>2.0 and <i>P</i>-value of <0.001).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-02 01:42:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/885574"], "description"=>"<p>All genes with statistically over-represented GO annotations were included (P<0.001).</p>", "links"=>[], "tags"=>["over-represented", "ontology", "classes", "targets", "differential", "micrornas", "p-value"], "article_id"=>556012, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_over_represented_Gene_Ontology_GO_classes_in_predicted_targets_of_differential_microRNAs_fold_changes_gt_2_0_and_P_value_of_lt_0_001_/556012", "title"=>"Clustering of over-represented Gene Ontology (GO) classes in predicted targets of differential microRNAs (fold changes>2.0 and P-value of <0.001).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-02 01:40:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/885405"], "description"=>"<p>The expressions of four miRNA were validated in the patient group compared with the control group using qRT-PCR.</p>", "links"=>[], "tags"=>["expressions", "mirna", "validated", "compared"], "article_id"=>555847, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_expressions_of_four_miRNA_were_validated_in_the_patient_group_compared_with_the_control_group_using_qRT_PCR_/555847", "title"=>"The expressions of four miRNA were validated in the patient group compared with the control group using qRT-PCR.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-02 01:37:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/438741", "https://ndownloader.figshare.com/files/438800", "https://ndownloader.figshare.com/files/438867", "https://ndownloader.figshare.com/files/438986", "https://ndownloader.figshare.com/files/439050", "https://ndownloader.figshare.com/files/439145", "https://ndownloader.figshare.com/files/439286"], "description"=>"<div><h3>Background</h3><p>MicroRNAs (miRNAs) have been proved to play an important role in various cellular processes and function as tumor suppressors or oncogenes in cancers including leukemia. The identification of a large number of novel miRNAs and other small regulatory RNAs will provide valuable insights into the roles they play in tumorgenesis.</p><h3>Methodology/Principal Findings</h3><p>To gain further understanding of the role of miRNAs relevant to acute lymphoblastic leukemia (ALL), we employed the sequencing-by-synthesis (SBS) strategy to sequence small RNA libraries prepared from ALL patients and normal donors. In total we identified 159 novel miRNAs and 116 novel miRNA*s from both libraries. Among the 159 novel miRNAs, 42 were identified with high stringency in our data set. Furthermore, we demonstrated the different expression patterns of 20 newly identified and several known miRNAs between ALL patients and normal donors, suggesting these miRNAs may be associated with ALL and could constitute an ALL-specific miRNA signature. Interestingly, GO “biological process” classifications revealed that a set of significantly abnormally expressed miRNAs are associated with disease relapse, which implies that these dysregulated miRNAs might promote the progression of ALL by regulating genes involved in the pathway of the disease development.</p><h3>Conclusion/Significance</h3><p>The study presents a comprehensive picture of the expression of small RNAs in human acute lymphoblastic leukemia and highlights novel and known miRNAs differentially expressed between ALL patients and normal donors. To our knowledge, this is the first study to look at genome-wide known and novel miRNA expression patterns in in human acute lymphoblastic leukemia. Our data revealed that these deregulated miRNAs may be associated with ALL or the onset of relapse.</p></div>", "links"=>[], "tags"=>["genome-wide", "rna", "microrna", "acute", "lymphoblastic", "leukemia", "based", "sequencing"], "article_id"=>146517, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0006849.s001", "https://dx.doi.org/10.1371/journal.pone.0006849.s002", "https://dx.doi.org/10.1371/journal.pone.0006849.s003", "https://dx.doi.org/10.1371/journal.pone.0006849.s004", "https://dx.doi.org/10.1371/journal.pone.0006849.s005", "https://dx.doi.org/10.1371/journal.pone.0006849.s006", "https://dx.doi.org/10.1371/journal.pone.0006849.s007"], "stats"=>{"downloads"=>22, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Analysis_of_Small_RNA_and_Novel_MicroRNA_Discovery_in_Human_Acute_Lymphoblastic_Leukemia_Based_on_Extensive_Sequencing_Approach/146517", "title"=>"Genome-Wide Analysis of Small RNA and Novel MicroRNA Discovery in Human Acute Lymphoblastic Leukemia Based on Extensive Sequencing Approach", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-09-02 01:48:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/885660"], "description"=>"<p>42 novel candidate miRNAs identified from control and patient group.</p>", "links"=>[], "tags"=>["mirnas"], "article_id"=>556112, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_42_novel_candidate_miRNAs_identified_from_control_and_patient_group_/556112", "title"=>"42 novel candidate miRNAs identified from control and patient group.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-09-02 01:41:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/885314"], "description"=>"<p>Box plots (median and interquartile range) show the distribution of fold change of expression in ALL patients compared with normal donor samples.</p>", "links"=>[], "tags"=>["mirnas"], "article_id"=>555766, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_of_miRNAs_in_ALL_patients_/555766", "title"=>"Differential expression of miRNAs in ALL patients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-02 01:36:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/885174"], "description"=>"<p>Schematic representation of small RNA library sequencing and subsequent bioinformatic analysis.</p>", "links"=>[], "tags"=>["rna", "sequencing", "bioinformatic"], "article_id"=>555617, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_small_RNA_library_sequencing_and_subsequent_bioinformatic_analysis_/555617", "title"=>"Schematic representation of small RNA library sequencing and subsequent bioinformatic analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-02 01:33:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/885265"], "description"=>"<p>(A) Known miRNAs unique in each group and shared by both. (B) MiRNA*s of known miRNAs unique in each group and shared by both.</p>", "links"=>[], "tags"=>["diagram", "mirnas"], "article_id"=>555711, "categories"=>["Molecular Biology", "Medicine"], "users"=>["Hua Zhang", "Jian-Hua Yang", "Yu-Sheng Zheng", "Peng Zhang", "Xiao Chen", "Jun Wu", "Ling Xu", "Xue-Qun Luo", "Zhi-Yong Ke", "Hui Zhou", "Liang-Hu Qu", "Yue-Qin Chen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0006849.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_of_the_known_miRNAs_and_novel_miRNA_star_s_of_the_known_miRNAs_identified_from_the_control_group_and_the_ALL_patient_group_/555711", "title"=>"Venn diagram of the known miRNAs and novel miRNA*(star)s of the known miRNAs identified from the control group and the ALL patient group.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-09-02 01:35:11"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"5", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}

Relative Metric

{"start_date"=>"2009-01-01T00:00:00Z", "end_date"=>"2009-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[349, 614, 744, 851, 955, 1059, 1167, 1262, 1352, 1431, 1516, 1593, 1668, 1746, 1817, 1883, 1950, 2017, 2075, 2141, 2198, 2254, 2313, 2368, 2424, 2474, 2534, 2591, 2651, 2710, 2776, 2837, 2892, 2953, 3014, 3072, 3130, 3186, 3251, 3307, 3366, 3427, 3500, 3561, 3627, 3688, 3759, 3821, 3888, 3950, 4010, 4070, 4131, 4189, 4242, 4307, 4370, 4431, 4491, 4549, 4608]}, {"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[334, 613, 751, 863, 964, 1078, 1181, 1270, 1358, 1443, 1536, 1616, 1690, 1768, 1826, 1902, 1969, 2031, 2095, 2149, 2202, 2258, 2305, 2349, 2417, 2482, 2541, 2598, 2662, 2720, 2768, 2832, 2897, 2947, 2998, 3058, 3121, 3175, 3235, 3292, 3368, 3442, 3507, 3563, 3621, 3676, 3736, 3802, 3852, 3922, 3977, 4025, 4071, 4141, 4199, 4258, 4316, 4376, 4422, 4467, 4518]}, {"subject_area"=>"/Medicine and health sciences/Anatomy", "average_usage"=>[339, 580, 713, 827, 926, 1032, 1153, 1258, 1348, 1429, 1522, 1603, 1687, 1772, 1834, 1905, 1972, 2029, 2098, 2151, 2214, 2275, 2335, 2388, 2446, 2496, 2553, 2604, 2653, 2705, 2780, 2822, 2890, 2947, 3020, 3070, 3114, 3162, 3226, 3285, 3353, 3433, 3500, 3547, 3592, 3639, 3700, 3769, 3858, 3922, 3967, 4028, 4069, 4137, 4191, 4246, 4302, 4372, 4436, 4498, 4579]}, {"subject_area"=>"/Medicine and health sciences/Pathology and laboratory medicine", "average_usage"=>[302, 565, 710, 814, 921, 1026, 1126, 1222, 1311, 1409, 1491, 1580, 1659, 1736, 1809, 1874, 1947, 2004, 2061, 2133, 2186, 2236, 2302, 2362, 2441, 2494, 2550, 2603, 2651, 2711, 2785, 2840, 2904, 2962, 3018, 3066, 3133, 3181, 3253, 3300, 3357, 3409, 3459, 3556, 3621, 3657, 3709, 3784, 3856, 3886, 3958, 4027, 4081, 4124, 4183, 4241, 4297, 4338, 4391, 4437, 4488]}]}
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