Journal: Molecular Oncology

Article Title: Proteomic characterization of peroxisome proliferator‐activated receptor‐γ (PPARγ) overexpressing or silenced colorectal cancer cells unveils a novel protein network associated with an aggressive phenotype

doi: 10.1016/j.molonc.2016.07.006

Figure Lengend Snippet: Visual representation of the network generated by Ingenuity Pathway Analysis (IPA). The network included the 5 identified/validated proteins and PPARg with direct and indirect interactions (EZR, LMNA, ENOA, PHB, and RUVBL2 orange stained) with PPARg ...

Article Snippet: Protein network analyses The MS‐identified proteins whose expression change was confirmed by western blotting were further analyzed by (Ingenuity Pathway Analysis) IPA software (GeneGo Inc., St. Joseph, MI, USA).

Techniques: Generated, Staining

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of KEGG pathways and canonical pathways analysis in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched KEGG pathways were the Adherens Junction (a), JAK-STAT (d), NOD like receptor (g), Apoptosis (j), WNT (m), and MAPK (p) signaling pathways. The heat maps showing the dynamic expression of the core enrichment genes involved in these signaling pathways (b, e, h, k, n, q). The PPI network shows the interaction of the proteins involved in the above signaling pathways (c, f, i, l, o, r). The enrichment heat-map showing the dynamic activity of canonical pathways at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (s). Each pathway is depicted with a pseudo color (orange for an activated pathway with positive Z-score ≥2, blue for an inhibited pathway with negative Z-score ≤−2, and spot for a non-active pathway with −2 ≤ Z-score ≤2). The canonical pathways were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Protein-Protein interactions, Expressing, Activity Assay

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of GO biological process gene sets in the DRG tissues post-surgery. Ranked by NES score, the selected six of top 20 enriched GO biological process gene sets were nitric oxide mediated transduction (a), central nervous system neuron axongenesis (c), positive regulation of epithelial mesenchymal transition (e), regulation of JNK cascade (j), regulation of cellular response to insulin stimulus (i), and maintenance of blood brain barrier (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO biological process gene sets (b, d, f, h, j, l). The enrichment heat-map showing the dynamic activity of diseases and functions at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each disease and function are depicted with a pseudo color (orange for an activated disease and function with positive Z-score ≥2, blue for an inhibited disease and function with negative Z-score ≤−2, and spot for a non-active disease and function with −2 ≤ Z-score ≤2). The diseases and functions were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Transduction, Expressing, Activity Assay

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: GSEA of GO cellular component, molecular function, and upstream regulators prediction in the DRG tissues post-surgery. Ranked by NES score, the selected three of top 20 enriched GO cellular component gene sets were cytoplasmic stress granule (a), P body (c), actin-based cell projection (e), the selected three of top 20 enriched GO molecular function gene sets were ATPase binding (g), kinase inhibitor activity (i), and Smad binding (k). The heatmaps showing the dynamic expression of the core enrichment genes involved in these GO cellular component (b, d, f) and molecular function (h, j, l) gene sets. The enrichment heatmap showing the predicted upstream regulators at 6 h, 12 h, 1 d, 4 d, 7 d, and 14 d post-surgery (m). Each predicted upstream regulator is depicted with a pseudo color (orange for an activated upstream regulator with positive Z-score ≥2, blue for an inhibited upstream regulator with negative Z-score ≤−2, and spot for a non-active upstream regulator with −2 ≤ Z-score ≤2). The predicted upstream regulators were classified into different types according to the IPA database. IPA, Ingenuity Pathway Analysis. GSEA, gene set enrichment analysis; NES, normalized enrichment score; PPI, protein–protein interaction. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Binding Assay, Activity Assay, Expressing

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: The impact of DRG neuron axonal promotion via SKP-SCs. (a) Schematic illustration of DRG neurons culture in vitro. The cultured DRG neurons for 20 h and 40 h (b) showed increased neurite outgrowth. Scale bar: 50 μm. (c) The β-Tubulin III cell immunofluorescent staining (red) showed neurites are undergoing a process of growth in length from 48 h to 96 h. Scale bar: 50 μm. Schematic illustration showed the direct (d) and in-direct (Transwell®) (e) co-culture of DRG neurons and SKP-SCs. (h) After direct co-culture 48 h, GFP-SKP-SCs promoted DRGs neurite outgrowth significantly compared to control group (i). (k) After in-direct co-culture 72 h, GFP-SKP-SCs promoted DRGs neurite outgrowth (j) significantly compared to control group (g). Scale bar: 50 μm for f, g, i, j. (l) Morphological changes under phase contrast microscopy in DRG neurons and SKP-SCs direct co-culture, DRG neurons in separate culture, and in-direct (Transwell®) co-culture of DRG neurons and SKP-SCs after 24 h, 48 h, and 72 h. Scale bar: 100 μm. (m) Schematic illustration of LC-MS/MS analysis to identify the secreted proteins from SKP-SCs cultured in serum free basic medium for 4 h. After concentration, the cleared conditioned medium was collected for LC-MS/MS analysis, database search, and protein identification. The enrichment analysis showed top 20 diseases and functions (n) and canonical pathways (o) according to the IPA database. The PPI network shows the interaction of the proteins involved in the functions highly correlated with regeneration (p). Among them, functions as formation of lamellipodia, extension of neurites, extension of cellular protrusions, and related proteins were highlighted (q). Functions as migration of endothelial cells, development of endothelial tissue, vasculogenesis, development of epithelial tissue, endothelial cell development, and related proteins were highlighted (r). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: In Vitro, Cell Culture, Staining, Co-Culture Assay, Control, Microscopy, Liquid Chromatography with Mass Spectroscopy, Concentration Assay, Migration, Activation Assay, Inhibition

Journal: Journal of Advanced Research

Article Title: Dynamic molecular landscape in dorsal root ganglion for peripheral nerve regeneration promoted by tissue engineered nerve graft

doi: 10.1016/j.jare.2025.07.059

Figure Lengend Snippet: The transcriptional alteration of DRG neurons co-cultured with SKP-SCs. (a) Representative images of phase contrast microscopy of SKP-SCs in the upper chamber and lower ventricular DRG neurons after 48 h co-culture. Scale bar: 100 μm. (b) Schematic illustration of transcriptional analysis of lower ventricular DRG neurons for 48 h co-culture, and bioinformatics. The enrichment analysis showed top 20 diseases and functions (c) and canonical pathways (d) according to the IPA database. The PPI network shows the interaction of the key proteins involved in the functions highly correlated with regeneration (e). Up-regulated EGR2 (red) was selected to show multi-functions highly correlated with neuroregeneration (f). The interaction network of downstream regulators of EGR2, its downstream up-regulated (red) genes and down-regulated (green) proteins and their functions (g). Orange nodes stand for a predicted activation state. Blue nodes stand for a predicted inhibition state. Color intensity of the nodes in networks were proportional to differentially expression level. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: The Ingenuity Pathway Analysis (IPA) software suite (Ingenuity Systems, Redwood City, CA) was employed to identify canonical pathways that are significantly overrepresented.

Techniques: Cell Culture, Microscopy, Co-Culture Assay, Activation Assay, Inhibition, Expressing

Journal: BMC Medical Genomics

Article Title: Long non-coding RNA profiling of pediatric Medulloblastoma

doi: 10.1186/s12920-020-00744-7

Figure Lengend Snippet: Top 10 disease and function identified by IPA from DE lncRNAs in WNT subgroup

Article Snippet: Functional analysis of differentially expressed lncRNAs was done by Ingenuity pathway analysis (IPA) software from BioRad, Inc. We used default parameters and checked all the node types, all species (except uncharted), and all tissue types for core analysis in IPA.

Techniques: Activation Assay, Migration

Journal: BMC Medical Genomics

Article Title: Long non-coding RNA profiling of pediatric Medulloblastoma

doi: 10.1186/s12920-020-00744-7

Figure Lengend Snippet: Top 10 disease and function identified by IPA from DE lncRNAs in SHH subgroup

Article Snippet: Functional analysis of differentially expressed lncRNAs was done by Ingenuity pathway analysis (IPA) software from BioRad, Inc. We used default parameters and checked all the node types, all species (except uncharted), and all tissue types for core analysis in IPA.

Techniques: Activation Assay, Migration

Journal: BMC Medical Genomics

Article Title: Long non-coding RNA profiling of pediatric Medulloblastoma

doi: 10.1186/s12920-020-00744-7

Figure Lengend Snippet: Top 10 disease and function identified by IPA from DE lncRNAs in Group 3 MB

Article Snippet: Functional analysis of differentially expressed lncRNAs was done by Ingenuity pathway analysis (IPA) software from BioRad, Inc. We used default parameters and checked all the node types, all species (except uncharted), and all tissue types for core analysis in IPA.

Techniques: Activation Assay, Gene Expression, Migration

Journal: BMC Medical Genomics

Article Title: Long non-coding RNA profiling of pediatric Medulloblastoma

doi: 10.1186/s12920-020-00744-7

Figure Lengend Snippet: Top 10 disease and function identified by IPA from DE lncRNAs in Group 4 MB

Article Snippet: Functional analysis of differentially expressed lncRNAs was done by Ingenuity pathway analysis (IPA) software from BioRad, Inc. We used default parameters and checked all the node types, all species (except uncharted), and all tissue types for core analysis in IPA.

Techniques: Activation Assay, Gene Expression, Migration, Methylation

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