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ingenuity pathway analysis (ipa, qiagen inc.) on the canonical pathway module and upstream regulator module  (Qiagen)


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    Qiagen ingenuity pathway analysis (ipa, qiagen inc.) on the canonical pathway module and upstream regulator module
    Ingenuity Pathway Analysis (Ipa, Qiagen Inc.) On The Canonical Pathway Module And Upstream Regulator Module, supplied by Qiagen, 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/product/ingenuity+canonical+pathway+analysis/ingenuity+pathway+analysis/pm40139876-148-22-14
    Average 90 stars, based on 1 article reviews
    ingenuity pathway analysis (ipa, qiagen inc.) on the canonical pathway module and upstream regulator module - by Bioz Stars, 2026-09
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    Related Articles

    other:

    Article Title: Aberrant chromatin landscape following loss of the H3.3 chaperone Daxx in haematopoietic precursors leads to Pu.1-mediated neutrophilia and inflammation
    Article Snippet: For the Ingenuity canonical pathway analysis (Qiagen) enhancer specific ERV-overlapping closed and opened peak sets were first annotated with annotatePeaks.pl to identify the closest promoter RefSeq ID.

    Activation Assay:

    Article Title: DiPRO1 distinctly reprograms muscle and mesenchymal cancer cells.
    Article Snippet: .. Ingenuity canonical pathway (Qiagen) analysis showed differential activation of several pathways involved in myogenesis, striated muscle contraction and cardiac conduction in shDiPRO1 myoblast cells, consistent with the observed cellular phenotype (Fig. F). ..



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    (A) Volcano plot of bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. (B) Number of up and downregulated bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. (C) Number of up and downregulated DEGs separated by cell type. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. RG: radial glia; IN: inhibitory-like neuron; EN: excitatory-like neuron; ChP: choroid plexus; IP: intermediate progenitor. (D) Top 50 <t>canonical</t> <t>pathways</t> identified through QIAGEN <t>Ingenuity</t> <t>Pathway</t> <t>Analysis</t> (IPA) grouped by category. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC) ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Table S1 for all pathways.
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    (A) Volcano plot of bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. (B) Number of up and downregulated bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. (C) Number of up and downregulated DEGs separated by cell type. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. RG: radial glia; IN: inhibitory-like neuron; EN: excitatory-like neuron; ChP: choroid plexus; IP: intermediate progenitor. (D) Top 50 canonical pathways identified through QIAGEN Ingenuity Pathway Analysis (IPA) grouped by category. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC) ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Table S1 for all pathways.

    Journal: bioRxiv

    Article Title: Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids

    doi: 10.1101/2024.02.09.579672

    Figure Lengend Snippet: (A) Volcano plot of bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. (B) Number of up and downregulated bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. (C) Number of up and downregulated DEGs separated by cell type. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. RG: radial glia; IN: inhibitory-like neuron; EN: excitatory-like neuron; ChP: choroid plexus; IP: intermediate progenitor. (D) Top 50 canonical pathways identified through QIAGEN Ingenuity Pathway Analysis (IPA) grouped by category. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC) ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Table S1 for all pathways.

    Article Snippet: Qiagen Ingenuity Pathway Analysis canonical pathways for 6 week organoids.

    Techniques:

    (A) Volcano plot of bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. (B) Number of up and downregulated bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. (C) Number of up and downregulated DEGs separated by cell type. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. RG: radial glia; IN: inhibitory-like neuron; EN: excitatory-like neuron; ChP: choroid plexus; IP: intermediate progenitor; Mes: mesenchymal; HSP: heat shock protein. (D) Top 50 canonical pathways identified through QIAGEN Ingenuity Pathway Analysis (IPA) grouped by category. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Table S2 for all pathways.

    Journal: bioRxiv

    Article Title: Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids

    doi: 10.1101/2024.02.09.579672

    Figure Lengend Snippet: (A) Volcano plot of bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. (B) Number of up and downregulated bulk DEGs between H9 UBE3A m-/p- and H9 WT organoids. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. (C) Number of up and downregulated DEGs separated by cell type. DEG defined as log 2 FC>|1|, and false discovery rate q<0.05. RG: radial glia; IN: inhibitory-like neuron; EN: excitatory-like neuron; ChP: choroid plexus; IP: intermediate progenitor; Mes: mesenchymal; HSP: heat shock protein. (D) Top 50 canonical pathways identified through QIAGEN Ingenuity Pathway Analysis (IPA) grouped by category. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Table S2 for all pathways.

    Article Snippet: Qiagen Ingenuity Pathway Analysis canonical pathways for 6 week organoids.

    Techniques:

    (A) Brightfield images showing fluid-filled cyst and sinuous tissue morphologies in organoids. Scale bars = 200 μm. (B) Quantification of ChP-like morphologies. n = 3 independent organoid batches each with ≥ 5 organoids per genotype. CHP: choroid plexus. Error bars are 95% confidence intervals. (C) TTR immunostaining in fluid-filled cysts and invaginations. Scale bars = 500 μm. (D) Canonical pathways deregulated by the absence of UBE3A in 6 week and 11 week organoid scRNAseq data. Top 25 canonical pathways are shown. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Tables S1 and S2 for all pathways. (E) Spatiotemporal localization of UBE3A in ChP-like tissue. Distinct nuclear UBE3A observed in early H9 WT organoids weakens over time in TTR+ ChP cells. Scale bars = 25 μm.

    Journal: bioRxiv

    Article Title: Loss of UBE3A impacts both neuronal and non-neuronal cells in human cerebral organoids

    doi: 10.1101/2024.02.09.579672

    Figure Lengend Snippet: (A) Brightfield images showing fluid-filled cyst and sinuous tissue morphologies in organoids. Scale bars = 200 μm. (B) Quantification of ChP-like morphologies. n = 3 independent organoid batches each with ≥ 5 organoids per genotype. CHP: choroid plexus. Error bars are 95% confidence intervals. (C) TTR immunostaining in fluid-filled cysts and invaginations. Scale bars = 500 μm. (D) Canonical pathways deregulated by the absence of UBE3A in 6 week and 11 week organoid scRNAseq data. Top 25 canonical pathways are shown. Differentially expressed genes with false discovery rate q < 0.05, log 2 FC ≥|1| were used in this analysis. Pathways related to cancer or inherently from outside the nervous system were omitted. Please refer to Tables S1 and S2 for all pathways. (E) Spatiotemporal localization of UBE3A in ChP-like tissue. Distinct nuclear UBE3A observed in early H9 WT organoids weakens over time in TTR+ ChP cells. Scale bars = 25 μm.

    Article Snippet: Qiagen Ingenuity Pathway Analysis canonical pathways for 6 week organoids.

    Techniques: Immunostaining