Re-Annotator: Annotation Pipeline for Microarray Probe Sequences
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{"title"=>"Re-Annotator: Annotation pipeline for microarray probe sequences", "type"=>"journal", "authors"=>[{"first_name"=>"Janine", "last_name"=>"Arloth", "scopus_author_id"=>"54885385900"}, {"first_name"=>"Daniel M.", "last_name"=>"Bader", "scopus_author_id"=>"55329607000"}, {"first_name"=>"Simone", "last_name"=>"Röh", "scopus_author_id"=>"55804533800"}, {"first_name"=>"Andre", "last_name"=>"Altmann", "scopus_author_id"=>"24448145000"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84947264827", "pui"=>"606879423", "pmid"=>"26426330", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0139516", "sgr"=>"84947264827"}, "id"=>"23fb5fd1-b3f6-393d-8afe-467bf6cc0f91", "abstract"=>"Microarray technologies are established approaches for high throughput gene expression, methylation and genotyping analysis. An accurate mapping of the array probes is essential to generate reliable biological findings. However, manufacturers of the microarray platforms typically provide incomplete and outdated annotation tables, which often rely on older genome and transcriptome versions that differ substantially from up-to-date sequence databases. Here, we present the Re-Annotator, a re-annotation pipeline for microarray probe sequences. It is primarily designed for gene expression microarrays but can also be adapted to other types of microarrays. The Re-Annotator uses a custom-built mRNA reference database to identify the positions of gene expression array probe sequences. We applied Re-Annotator to the Illumina Human-HT12 v4 microarray platform and found that about one quarter (25%) of the probes differed from the manufacturer's annotation. In further computational experiments on experimental gene expression data, we compared Re-Annotator to another probe re-annotation tool, ReMOAT, and found that Re-Annotator provided an improved re-annotation of microarray probes. A thorough re-annotation of probe information is crucial to any microarray analysis. The Re-Annotator pipeline is freely available at http://sourceforge.net/projects/reannotator along with re-annotated files for Illumina microarrays HumanHT-12 v3/v4 and MouseRef-8 v2.", "link"=>"http://www.mendeley.com/research/reannotator-annotation-pipeline-microarray-probe-sequences", "reader_count"=>29, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4, "Student > Bachelor"=>1, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>1, "Agricultural and Biological Sciences"=>16, "Medicine and Dentistry"=>2, "Psychology"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Ukraine"=>1, "Denmark"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2295418"], "description"=>"<p>Contingency tables between expression status and annotation for Re-Annotator and ReMOAT.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561632, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.t003", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contingency_tables_between_expression_status_and_annotation_for_Re_Annotator_and_ReMOAT_/1561632", "title"=>"Contingency tables between expression status and annotation for Re-Annotator and ReMOAT.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295416"], "description"=>"<p>Detailed numbers for probes tat could be aligned (Aligned), that were considered “good” probes after the post-processing, and were aligned without mismatches to the reference genome, or were unique alignments.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561630, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_probe_sequences_at_different_steps_of_the_re_annotation_for_two_Illumina_chips_/1561630", "title"=>"Number of probe sequences at different steps of the re-annotation for two Illumina chips.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295413"], "description"=>"<p>(A) Venn diagram representing the overlap of transcripts annotated with ReMOAT and Re-Annotator. A total of 5% of the probe sequences were annotated with different genes by Re-Annotator and ReMOAT. (B) Bar graph detailing the exclusion reason for probes included by ReMOAT but excluded by Re-Annotator.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561627, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g004", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_Re_Annotator_and_ReMOAT_on_HumanHT_12_v4_probe_sequences_/1561627", "title"=>"Comparison between Re-Annotator and ReMOAT on HumanHT-12 v4 probe sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295412"], "description"=>"<p>(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the <i>in silico</i> mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference and (C) the number of equally top scoring best hits per probe sequence.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561626, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g003", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_re_annotation_of_Illumina_MouseRef_8_v2_probe_sequences_/1561626", "title"=>"Results of the re-annotation of Illumina MouseRef-8 v2 probe sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295415"], "description"=>"<p>The gene is located on chromosome 9; the targeting Illumina probe is ILMN_1651396. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator and (B) manufacturer and ReMOAT.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561629, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g006", "stats"=>{"downloads"=>5, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_USCS_genome_browser_graphic_for_the_human_ABCA9_gene_/1561629", "title"=>"USCS genome browser graphic for the human ABCA9 gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295414"], "description"=>"<p>The gene is located on chromosome 9; the targeting Illumina probes are ILMN_1715931, ILMN_1672024, ILMN_2219556, ILMN_1675421 and ILMN_2341711. Custom tracks represent the probe sequences annotated by (A) the Re-Annotator, (B) manufacturer and (C) ReMOAT.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561628, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g005", "stats"=>{"downloads"=>3, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_USCS_genome_browser_graphic_for_the_human_ISCA1_gene_/1561628", "title"=>"USCS genome browser graphic for the human ISCA1 gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295411"], "description"=>"<p>(A) Barplot of the alignment basis. The left bar represents the array probe sequences that could be aligned to the <i>in silico</i> mRNA reference database. The middle bar represents sequences that were aligned to the whole genome reference subdivided into genic and intergenic alignments. The right bar represents unaligned sequences. Histograms showing (B) the number of mismatches between probe sequence and reference, (C) the number of equally top scoring best hits per probe sequence and (D) the number of SNPs (in the 1000 genomes data) within an aligned probe sequence. (E) Histogram of the annotation of probes, which have no annotation according to the manufacture and now have been rescued and reliably annotated. (F) Histogram showing the changes in annotation from the manufacture to our re-annotation (Manufacture | Re-Annotator).</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561625, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g002", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_re_annotation_of_Illumina_HumanHT_12_v4_probe_sequences_/1561625", "title"=>"Results of the re-annotation of Illumina HumanHT-12 v4 probe sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295410"], "description"=>"<p>Schematic overview of the computational pipeline flow: (top) creating the <i>in silico</i> mRNA reference database and (bottom) step-wise alignment process. Purple sequences in the left column correspond to alignments to the <i>in silico</i> reference and brown sequences in the right column correspond to alignments to the genome.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561624, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_pipeline_/1561624", "title"=>"Annotation pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-01 03:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/2295417"], "description"=>"<p><sup>a</sup>For the test we drew a subsample of the “Both” group to match the sample size of the corresponding comparison group.</p><p>Rows three and four compare the variance for probes in categories InRA, InRM and InRepeat to the two reference categories Both and None, respectively, using a two-sided Wilcoxon test.</p>", "links"=>[], "tags"=>["Microarray platforms", "throughput gene expression", "gene expression microarrays", "annotation pipeline", "annotation tables", "microarray analysis", "mRNA reference database", "gene expression data", "probe information", "transcriptome versions", "genotyping analysis", "gene expression array probe sequences", "array probes", "microarray probe sequences", "Microarray Probe Sequences Microarray technologies", "microarray probes", "Sequence databases"], "article_id"=>1561631, "categories"=>["Uncategorised"], "users"=>["Janine Arloth", "Daniel M. Bader", "Simone Röh", "André Altmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0139516.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Group_size_and_relative_variability_for_the_five_probe_categories_/1561631", "title"=>"Group size and relative variability for the five probe categories.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-01 03:01:53"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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