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baggerly’s proportion-based beta-binomial test  (CLC Bio)

 
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    Structured Review

    CLC Bio baggerly’s proportion-based beta-binomial test
    ChISGs identified by RNA-seq using <t> Baggerly’s </t> test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)
    Baggerly’s Proportion Based Beta Binomial Test, supplied by CLC Bio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/baggerly’s proportion-based beta-binomial test/product/CLC Bio
    Average 90 stars, based on 1 article reviews
    baggerly’s proportion-based beta-binomial test - by Bioz Stars, 2026-04
    90/100 stars

    Images

    1) Product Images from "Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)"

    Article Title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)

    Journal: Veterinary Research

    doi: 10.1186/s13567-016-0363-8

    ChISGs identified by RNA-seq using Baggerly’s test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)
    Figure Legend Snippet: ChISGs identified by RNA-seq using Baggerly’s test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)

    Techniques Used:

    Gene-level visualisation of RNA-seq reads mapped to the chicken genome. Annotated CLC Bio Genomic Workbench views of chicken chromosome Z ( A ) and 4 ( B ) showing the loci around homologues of CCL19 (ENSGALG00000028256) ( A ) and PYURF (ENSGALG00000026229) ( B ). Each panel shows tracks for genes (labeled with Galgal4—annotated names), untranslated regions (UTR), coding sequences (CDS) and mRNA transcripts. Locations of unannotated NCBI Galgal5 Refseq genes LOC 1008571891 ( A ) and LOC422513 ( B ) are indicated. RNA-seq reads from untreated and IFN-treated CEF (6 h, 1000 units) are shown mapped to the genome in the uppermost and lowest tracks, respectively, in each panel (totals mapped to the chromosome are indicated to the left of these tracks). The levels of basal and peak RNA-read mappings are shown to the right of the tracks under “Scale”. Comparison of these figures in conjunction with the size of the peaks allows visual estimates of the levels of differential expression for individual exons (which can be compared with the formal numerical analyses). For instance, IL11RA ( A ) as well as CCGN2 and HERC3 ( B ) show no significant regulation by IFN. In contrast, CCL19 and unannotated LOC100857191 in ( A ) show significant upregulation (96-fold—but with an FDR of 0.031 it fell outside the cut-off for Kal’s analysis and, because of its very low basal expression, was not returned by Baggerly’s). In ( B ) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5.
    Figure Legend Snippet: Gene-level visualisation of RNA-seq reads mapped to the chicken genome. Annotated CLC Bio Genomic Workbench views of chicken chromosome Z ( A ) and 4 ( B ) showing the loci around homologues of CCL19 (ENSGALG00000028256) ( A ) and PYURF (ENSGALG00000026229) ( B ). Each panel shows tracks for genes (labeled with Galgal4—annotated names), untranslated regions (UTR), coding sequences (CDS) and mRNA transcripts. Locations of unannotated NCBI Galgal5 Refseq genes LOC 1008571891 ( A ) and LOC422513 ( B ) are indicated. RNA-seq reads from untreated and IFN-treated CEF (6 h, 1000 units) are shown mapped to the genome in the uppermost and lowest tracks, respectively, in each panel (totals mapped to the chromosome are indicated to the left of these tracks). The levels of basal and peak RNA-read mappings are shown to the right of the tracks under “Scale”. Comparison of these figures in conjunction with the size of the peaks allows visual estimates of the levels of differential expression for individual exons (which can be compared with the formal numerical analyses). For instance, IL11RA ( A ) as well as CCGN2 and HERC3 ( B ) show no significant regulation by IFN. In contrast, CCL19 and unannotated LOC100857191 in ( A ) show significant upregulation (96-fold—but with an FDR of 0.031 it fell outside the cut-off for Kal’s analysis and, because of its very low basal expression, was not returned by Baggerly’s). In ( B ) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5.

    Techniques Used: RNA Sequencing Assay, Labeling, Expressing, Sequencing



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    baggerly’s proportion-based beta-binomial test  (CLC Bio)
    90
    CLC Bio baggerly’s proportion-based beta-binomial test
    ChISGs identified by RNA-seq using <t> Baggerly’s </t> test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)
    Baggerly’s Proportion Based Beta Binomial Test, supplied by CLC Bio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/baggerly’s proportion-based beta-binomial test/product/CLC Bio
    Average 90 stars, based on 1 article reviews
    baggerly’s proportion-based beta-binomial test - by Bioz Stars, 2026-04
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    ChISGs identified by RNA-seq using Baggerly’s test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)

    Journal: Veterinary Research

    Article Title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)

    doi: 10.1186/s13567-016-0363-8

    Figure Lengend Snippet: ChISGs identified by RNA-seq using Baggerly’s test but not Kal’s test using standard criteria (FC > 3 or FDR < 0.01)

    Article Snippet: Triplicate-based analysis using Baggerly’s proportion-based Beta-binomial test [ ; as implemented in the CLC Bio package] at the same settings (FC > 3, FDR < 0.01) returned an additional 37 up-regulated genes.

    Techniques:

    Gene-level visualisation of RNA-seq reads mapped to the chicken genome. Annotated CLC Bio Genomic Workbench views of chicken chromosome Z ( A ) and 4 ( B ) showing the loci around homologues of CCL19 (ENSGALG00000028256) ( A ) and PYURF (ENSGALG00000026229) ( B ). Each panel shows tracks for genes (labeled with Galgal4—annotated names), untranslated regions (UTR), coding sequences (CDS) and mRNA transcripts. Locations of unannotated NCBI Galgal5 Refseq genes LOC 1008571891 ( A ) and LOC422513 ( B ) are indicated. RNA-seq reads from untreated and IFN-treated CEF (6 h, 1000 units) are shown mapped to the genome in the uppermost and lowest tracks, respectively, in each panel (totals mapped to the chromosome are indicated to the left of these tracks). The levels of basal and peak RNA-read mappings are shown to the right of the tracks under “Scale”. Comparison of these figures in conjunction with the size of the peaks allows visual estimates of the levels of differential expression for individual exons (which can be compared with the formal numerical analyses). For instance, IL11RA ( A ) as well as CCGN2 and HERC3 ( B ) show no significant regulation by IFN. In contrast, CCL19 and unannotated LOC100857191 in ( A ) show significant upregulation (96-fold—but with an FDR of 0.031 it fell outside the cut-off for Kal’s analysis and, because of its very low basal expression, was not returned by Baggerly’s). In ( B ) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5.

    Journal: Veterinary Research

    Article Title: Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)

    doi: 10.1186/s13567-016-0363-8

    Figure Lengend Snippet: Gene-level visualisation of RNA-seq reads mapped to the chicken genome. Annotated CLC Bio Genomic Workbench views of chicken chromosome Z ( A ) and 4 ( B ) showing the loci around homologues of CCL19 (ENSGALG00000028256) ( A ) and PYURF (ENSGALG00000026229) ( B ). Each panel shows tracks for genes (labeled with Galgal4—annotated names), untranslated regions (UTR), coding sequences (CDS) and mRNA transcripts. Locations of unannotated NCBI Galgal5 Refseq genes LOC 1008571891 ( A ) and LOC422513 ( B ) are indicated. RNA-seq reads from untreated and IFN-treated CEF (6 h, 1000 units) are shown mapped to the genome in the uppermost and lowest tracks, respectively, in each panel (totals mapped to the chromosome are indicated to the left of these tracks). The levels of basal and peak RNA-read mappings are shown to the right of the tracks under “Scale”. Comparison of these figures in conjunction with the size of the peaks allows visual estimates of the levels of differential expression for individual exons (which can be compared with the formal numerical analyses). For instance, IL11RA ( A ) as well as CCGN2 and HERC3 ( B ) show no significant regulation by IFN. In contrast, CCL19 and unannotated LOC100857191 in ( A ) show significant upregulation (96-fold—but with an FDR of 0.031 it fell outside the cut-off for Kal’s analysis and, because of its very low basal expression, was not returned by Baggerly’s). In ( B ) PYURF shows 24-fold suppression by IFN but the sequence surrounding PYURF shows 87-fold induction from the right-hand end of the unannotated, antisense LOC422513 and considerably higher upregulation from the left-hand end (due to its lower uninduced levels), consistent with these representing homologues of IFN-inducible human genes HERC6 and HERC5.

    Article Snippet: Triplicate-based analysis using Baggerly’s proportion-based Beta-binomial test [ ; as implemented in the CLC Bio package] at the same settings (FC > 3, FDR < 0.01) returned an additional 37 up-regulated genes.

    Techniques: RNA Sequencing Assay, Labeling, Expressing, Sequencing