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  1. 4541
    “…Gene Set Enrichment Analysis and Ingenuity Pathway Analysis were carried out for bioinformatic characterizations of pathways and networks. …”
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    Proteomic and transcriptomic profiling of Pten gene‐knockout mouse model of prostate cancer
  2. 4542
    “…Epitopes identified by this approach were compared with human peptides for local sequence similarity using BLAST optimized for short peptide sequences in order to identify host proteins that could mimic TOXO antigens. Ingenuity Pathway Analysis was then used to interpret and synthesize possible biological relationships between predicted autoantigens and schizophrenia. …”
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    S184. IN SILICO PREDICTION OF T-CELL-MEDIATED MOLECULAR MIMICRY IN TOXOPLASMOSIS AND SCHIZOPHRENIA
  3. 4543
    “…Slc7a11 overexpression restored redox states of 104 (69%) of these proteins. Ingenuity Pathway Analysis (IPA) showed that age-dependent Slc7a11-responsive proteins were involved in pathways of protein translation initiation, ubiquitin-proteasome-mediated degradation, and integrin-cytoskeleton-associated signaling. …”
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    Redox States of Protein Cysteines in Pathways of Protein Turnover and Cytoskeleton Dynamics Are Changed with Aging and Reversed by Slc7a11 Restoration in Mouse Lung Fibroblasts
  4. 4544
    “…The differentially abundant proteins were investigated by ingenuity pathway analysis (IPA). The network pathway identified related to infectious disease, inflammatory disease, organismal injury and abnormalities, and the connectivity map focused around two central nodes, namely the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and p38 mitogen-activated protein kinase (MAPK) pathways. …”
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    Plasma-Based Proteomics Profiling of Patients with Hyperthyroidism after Antithyroid Treatment
  5. 4545
    “…We also found that the two e-cig aerosols dysregulated the expression of lung genes. Ingenuity Pathway Analysis revealed that the gene networks that are dysregulated by the VG/PG e-cig aerosol are associated with metabolism of cellular proteins and lipids. …”
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    Electronic-Cigarette Vehicles and Flavoring Affect Lung Function and Immune Responses in a Murine Model
  6. 4546
    “…Differential gene expression was computed after data normalization followed by pathway analysis using Kyoto Encyclopedia Genes and Genomes (KEGG), Panther, Gene Ontology (GO), and Ingenuity Pathway Analysis (IPA) upstream regulator algorithm tools. …”
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    Progesterone Receptor Signaling Selectively Modulates Cytokine-Induced Global Gene Expression in Human Cervical Stromal Cells
  7. 4547
    “…Functional enrichment analyses were performed on metabolites and their candidate genes using the Ingenuity Pathway Analysis software. Eleven metabolites showed low to moderate heritability that ranged from 0.09 ± 0.15 to 0.36 ± 0.15, while heritability estimates for 22 metabolites were zero or negligible. …”
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    Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle
  8. 4548
    “…Using both PANTHER gene classification and Ingenuity Pathway Analysis (IPA) software, we found that the main biological processes in which the 52 deregulated proteins are involved, include “catalytic activity,” “binding,” “metabolic process,” and “cellular process.” …”
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    Effects of the Oncoprotein PAX3-FOXO1 on Modulation of Exosomes Function and Protein Content: Implications on Oxidative Stress Protection and Enhanced Plasticity
  9. 4549
    “…However, fostamatinib was able to inhibit both parental and SR HCC cells in vitro and in xenograft models. Ingenuity pathway analysis of fostamatinib gene expression signature from LINCS predicted JAK/STAT, PI3K/AKT, ERK/MAPK pathways as potential targets of fostamatinib that were validated by Western blot analysis. …”
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    Transcriptomics-Based Drug Repurposing Approach Identifies Novel Drugs against Sorafenib-Resistant Hepatocellular Carcinoma
  10. 4550
    “…Potential regulatory pathways were analyzed using ingenuity pathway analysis (IPA) and differentially expressed genes were partially verified by reverse transcription-quantitative PCR (RT-qPCR) and western blotting. …”
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    Knockdown of AMPKα2 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating ETS1 and RPS6KA1
  11. 4551
    “…Statistical analyses were performed using Pearson's chi-square test, Kaplan–Meier estimates of DSS and MFS, and the Cox proportional hazards model. We used Ingenuity Pathway Analysis (IPA) to clarify the functional significance of dysregulated FBLN2 in UC. …”
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    Prognostic Utility of FBLN2 Expression in Patients With Urothelial Carcinoma
  12. 4552
    “…Both, Rpx and LSBPs reduced cell proliferation in vitro, but their anti-proliferative effects were decreased by 15–20% in the presence of galactose. The program “Ingenuity Pathway Analysis” identified 2,415 genes showing significantly modulated mRNA expression following exposure of Suit2-007 cells to Rpx in vitro. …”
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    Riproximin Exhibits Diversity in Sugar Binding, and Modulates some Metastasis-Related Proteins with Lectin like Properties in Pancreatic Ductal Adenocarcinoma
  13. 4553
    “…Bioinformatics was conducted using Ingenuity Pathway Analysis (IPA) software (Qiagen, CA) with P < 0.05 and 1.3-fold differential expression cutoff values. …”
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    Long-Term Soy Protein Isolate Consumption Reduces Liver Steatosis Through Changes in Global Transcriptomics in Obese Zucker Rats
  14. 4554
    “…Network pathway analysis was performed by Ingenuity Pathway Analysis (IPA). A total of 2815 probe set IDs were significantly different between intestinal- and diffuse-type GC data in cBioPortal Cancer Genomics. …”
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    Molecular Network Profiling in Intestinal- and Diffuse-Type Gastric Cancer
  15. 4555
    “…Bioinformatics analyses were performed using the DAVID functional annotation tool and Ingenuity Pathway Analysis (IPA). The gene expression microarray data and LC-MS/MS data were validated using qRT-PCR and ELISA, respectively. …”
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    Long-term transcriptomic and proteomic effects in Sprague Dawley rat thyroid and plasma after internal low dose (131)I exposure
  16. 4556
    “…Secondly, we investigated the signaling pathways and co-regulatory protein–protein interaction networks underlying these three cancers by leveraging the Ingenuity Pathway Analysis software. In detail, we discovered 1,643 expression similarity signatures (638 downregulated and 1,005 upregulated genes, with respect to normal phenotype), denoted as tumor-associated genes. …”
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    An Integrative Computational Approach Based on Expression Similarity Signatures to Identify Protein–Protein Interaction Networks in Female-Specific Cancers
  17. 4557
    “…A ceRNA network was constructed that included 82 mRNAs, 4 miRNAs, and 2 lnRNAs. An ingenuity pathway analysis (IPA)-based interaction network for mRNAs differentially expressed in the ceRNA identified several biological processes, including “cellular development, connective tissue development and function, tissue development.” …”
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    Identification of Slc6a19os and SOX11 as Two Novel Essential Genes in Neuropathic Pain Using Integrated Bioinformatic Analysis and Experimental Verification
  18. 4558
    “…Gene ontology analysis of the common DEPs using DAVID (https://david.ncifcrf.gov/) showed significant enrichment for terms related to cellular morphology, learning, memory and positive regulation of NF-kappaB signaling. Ingenuity Pathway Analysis showed significant induction of inflammation in FGR pups, whereas significant induction of cell migration and cell spreading were observed in non-FGR pups. …”
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    The Effect of Prenatal Food Restriction on Brain Proteome in Appropriately Grown and Growth Restricted Male Wistar Rats
  19. 4559
    “…Functions annotation of these identified genes, using the ingenuity pathway analysis (IPA), predicted cumulative actions of decreased cell viability/proliferation, tumor growth and reactive oxygen species (ROS), and increased apoptosis in response to SIRT3 knockdown. …”
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    Genetic Manipulation of Sirtuin 3 Causes Alterations of Key Metabolic Regulators in Melanoma
  20. 4560
    “…Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), “lipid metabolism” was found as the top function associated with the differentially expressed proteins. …”
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    SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina
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