Journal: PLoS ONE

Article Title: Fyn-Dependent Gene Networks in Acute Ethanol Sensitivity

doi: 10.1371/journal.pone.0082435

Figure Lengend Snippet: (A) ErmineJ heatmap of NAC gene expression showing a coherent decrease for myelin-related basal gene expression in Fyn knockouts compared to control. (B) Ingenuity Pathway Analysis (IPA) of myelin-related genes and literature associations; numbers shown are mean S-score of three biological replicates. Red indicates increased expression in Fyn knockout vs controls and green fill indicates decreased expression in the Fyn knockout. (C) Table display of ErmineJ corrected p-values (10% FDR) for myelin gene expression in NAC, PFC, and VMB.

Article Snippet: However, literature association analysis using curated resources from Ingenuity Pathway Analysis (IPA) and GeneGo did suggest network-level differences in ethanol-regulated gene expression between knockout and control animals ( and and ) as discussed below.

Techniques: Gene Expression, Control, Expressing, Knock-Out

Journal: Scientific Reports

Article Title: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer

doi: 10.1038/s41598-017-10675-6

Figure Lengend Snippet: Susceptibility genetics. ( a ) Expression and localization in human brain utilizing Allen Brain Atlas of genes with alleles conferring susceptibility to congenital toxoplasmosis in National Collaborative Chicago Based Congenital Toxoplasmosis Study (NCCCTS). Transcript expression is visualized for brain of the youngest donor (H0351.2001, 24 years, male, African-American). Z-score of microarray data ranges between −3 and +3 to quantify the lowest to highest expression (see Supplement B: Table ). ( b ) Ingenuity Pathway Analysis (IPA) of NCCCTS susceptibility genes and upstream regulators. Cut off of p value at 5 × 10 −3 generated a network of 117 predicted upstream regulators (see Supplement B: Table ). Upstream regulators and susceptibility genes are consolidated/bundled and graphically mapped. Susceptibility genes are manually relocated in IPA graphic to show connectivity to upstream regulators. Note NFκB and TGFβ are central nodes that are visual.

Article Snippet: The Reconstruction-Deconvolution analysis was completed at BrainMicro LLC using Ingenuity Pathway Analysis tool (IPA, Inc.) , and STRING v9.1 web-tool .

Techniques: Expressing, Microarray, Generated

Journal: Scientific Reports

Article Title: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer

doi: 10.1038/s41598-017-10675-6

Figure Lengend Snippet: Deconvolution of brain infectome by disease correlation. The 3rd deconvolution approach of the total brain infectome predicts correlation between T. gondii infection and common neurological diseases using IPA disease and function tool (see Supplement B: Table ). ( a ) Grouping of disease annotations included p-value and group size. The 4 disease groups are detected for all Type I, II and III infections. ( b ) Alzheimer group included Alzheimer’s disease, tauopathy and amyloidosis annotations. IPA Canonical analysis indicates this disease gene network is mediated by signaling pathways of adaptor protein 14-3-3 (7 genes), retinoic acid receptor LXR/RXR (7 genes), tumor suppressor protein p53 (7 genes), cytokine IL-17A (5 genes) and glucocorticoid receptor (13 genes). ( c ) Movement disorders. This entails predictions for movement disorders, disorder of basal ganglia, neuromuscular disease, dyskinesia and Huntington’s Disease. IPA canonical analysis of this gene network indicates signaling pathways mediated by G-Protein coupled receptor (13 genes), by cAMP (10 genes), transcriptional regulator 14-3-3 (7 genes), cytokine Endothelin-1 (8 genes), polypeptide hormone relaxin (9 genes) and corticotropin releasing hormone (8 genes). ( d ) Epileptic disorders pathways for seizures, seizure disorder and epileptic seizure. IPA canonical analysis of the 81-gene network indentifies top-ranking signaling pathways that are associated with retinoic acid receptor (6 genes), endothelin-1 (6 genes), Gaq protein (5 genes) and corticotropin releasing hormone (5 genes). ( e ) Cancer group. This illustrated mechanisms of cancer, malignant solid tumor, abdominal neoplasm, abdominal cancer, urogenital cancer and genital tumor that are potentially activated in the infected brain. The top 10 canonical pathways (Supplement B: Tables , ) reveal important mechanisms that may potentiate cancer development in the T. gondii infected brain, such as Wnt/Ca + pathway (14 genes) and role of IL-17A in arthritis (14 genes). Wnt/Ca + pathway annotation contains 6 frizzled class receptors (FZD2, FZD3, FZD4, FZD5, FZD8, FZD9) and receptor tyrosine kinase-like ROR1. Not shown in diagram is the association with the schizophrenia 19-gene network: ABAT, ABCB1, ADRA1D, ANK3, APOL1, CHRNA5, CHRNA7, E2F1, EGR3, EGR4, GAP43, GRIN2A, HOMER1, IL6, PMP22, PTGS2, SCG2, SOD2, TMTC1.

Article Snippet: The Reconstruction-Deconvolution analysis was completed at BrainMicro LLC using Ingenuity Pathway Analysis tool (IPA, Inc.) , and STRING v9.1 web-tool .

Techniques: Infection, Protein-Protein interactions