Functional classification and pathway analyses of the list of candidate genes were carried out using the Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, http://www.ingenuity.com ). Significance levels for enrichment of each canonical pathway in the list of candidate genes were calculated using Fisher’s exact test and the resulting p-values were corrected for multiple-test using the Benjamini and Hochberg algorithm [42 ]; the cut-off for considering an enrichment as significant was established at a corrected p-value < 0.05.
Ingenuity pathways analysis software ipa
Manufactured by Qiagen
Sourced in United States
Ingenuity Pathways Analysis (IPA) software is a bioinformatics application that enables the analysis and interpretation of biological and chemical systems. The core function of IPA is to provide a comprehensive understanding of complex biological and chemical systems by integrating various data types, including gene expression, metabolomics, and proteomics, into a unified analysis platform.
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Lab products found in correlation
Genechip human genome u133 plus 2, by Thermo Fisher Scientific (1 mentions)
Genespring gx, by Agilent Technologies (1 mentions)
Ac4mannaz, by Thermo Fisher Scientific (1 mentions)
Trizol reagent, by Thermo Fisher Scientific (1 mentions)
Nanodrop spectrophotometer, by Thermo Fisher Scientific (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Human gene 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Rneasy mini kit, by Thermo Fisher Scientific (1 mentions)
Spotfire decisionsite software, by TIBCO Software (1 mentions)
Hiseq 2500 machine, by Illumina (1 mentions)
Rneasy plus micro kit, by Qiagen (1 mentions)
25 protocols using ingenuity pathways analysis software ipa
1
Functional and Pathway Analysis of Candidate Genes
2
Pathway Analysis of VLCAD Deficient Mice
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Pathway associations of differentially expressed proteins in deficient mice in either the fed or fasted state were analyzed with the Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, Redwood City, CA; www.ingenuity.com ) (21). The taxonomy was set to “mouse”. The filters and general settings for the core analysis were set to consider all molecules including endogenous chemicals, as well as both direct and indirect relationships. All data sources except cell lines were considered. Scores of 2 or higher (Fisher's exact test, p<0.05) having at least a 99% confidence were considered as significant. In this analysis, we selected the top 2 networks as the most significant. The Global Functional Analysis (GFA) and Global Canonical Pathways (GCP) analysis were utilized to identify the canonical pathways and associated diseases that were related to the differentially expressed proteins. Toxic analysis of the IPA was designed to characterize specific organ system changes related to exposure to suspected toxins. This function was utilized to identify patterns of altered protein expression in VLCAD deficient mice in both the fed and fasting states to assess the secondary physiologic impact of the primary ACADVL gene defect and fasting.
3
Pathway Analysis of Differentially Expressed Genes
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To define biological networks, interaction and functional analysis among the differentially regulated genes in KC, pathway analyses were performed using Ingenuity Pathways Analysis software (IPA) (Ingenuity Systems, Redwood City, CA). Statistically differentially expressed datasets with probesets ID, Gene symbol and Entrez gene ID as clone identifier, p-value and fold change values were uploaded into IPA. The functional/pathway analysis of IPA identifies the biological functions and/or diseases and pathways that are most significantly altered for the differentially expressed gene set. The significance of the connection between the expression data and the canonical pathways were calculated by ratio and/or Fisher’s exact test.
4
Transcriptome and Metabolome Profiling of 2A-DNT Exposure
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Effects of 2A-DNT exposure on gene network and metabolic pathway inferences were derived using differential expression datasets for transcripts and proteins. Affected gene networks and metabolic pathways were identified using Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, Redwood, CA, USA) and the Database for Annotation, Visualization and Integrated Discovery (DAVID v6.7, http://david.abcc.ncifcrf.gov/ , [18 (link)]), respectively. Gene lists for were converted to Gallus gallus gene homologs for IPA and DAVID analyses. Gene network analysis in IPA calculated p-values for the overlap between the input data and the known molecular interactions curated within IPA knowledgebase. Fisher’s exact tests (p = 0.05) were conducted to determine the probability that each molecular network was enriched by chance. For significantly enriched molecular networks, the top 5 were used to interpret biological outcomes resulting from 2A-DNT exposure. Enrichment of metabolic pathways curated by the Kyoto Encyclopedia of Genes and Genomes Database (KEGG, http://www.genome.jp/kegg/pathway.html ) were investigated using DAVID where enrichment was calculated using the Gallus gallus reference genome as the background gene set and the cutoff for significant enrichment was p < 0.10.
5
Biological Pathway Analysis of DEGs
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To characterize biological pathways associated with DAB, DEGs were analyzed using Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, Redwood City, CA, USA) for biological functions and canonical pathways.
6
Transcriptional Profiling of A549 Cells Treated with Ac4ManNAz
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The A549 cells were cultured with 0, 10 and 50 μM Ac4ManNAz (Invitrogen, Carlsbad, CA, USA) and harvested. Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and the quantity and quality of total RNA was evaluated using a NanoDrop spectrophotometer (NanoDrop Technologies, Montchanin, DE, USA) and a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). An Affymetrix GeneChip Human Genome U133 plus 2.0 was used for the microarray experiments according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA). For the gene expression array, the data were pre-processed, the cell intensity files (CEL) were generated, and the data were analyzed using GeneSpring GX (v11.0; Agilent Technologies). The data were normalized using a global scale normalization, and differentially expressed genes were selected based on a > 7-fold change. The selected genes were annotated based on NetAffx (http://www.affymetrix.com ). Functional enrichment and network analysis was performed using Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, Redwood, CA, USA).
7
Pathway Analysis of Differentially Expressed Genes in Breast Cancer
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To define biological networks, interaction and functional analysis among the differentially regulated genes in BC, pathway analyses were performed using Ingenuity Pathways Analysis software (IPA) (Ingenuity Systems, Redwood City, CA). Statistically differentially expressed dataset containing 1159 genes and their corresponding probesets ID, Gene symbol, Entrez gene ID as clone identifier, p-value and fold change values were uploaded into the IPA. The functional/pathway analysis of IPA identifies the biological functions and/or diseases and pathways that are most significantly altered for the differentially expressed gene set. The significance of the connection between the expression data and the canonical pathway were calculated by ratio and/or Fisher’s exact.
8
Microarray-based Gene Expression Analysis
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Tumor tissue RNA were isolated and processed for microarray and gene expression analysis as previously described [35 (link)], and data was deposited at the NCBI’s Gene Expression Omnibus under accession number GSE77259. For gene expression analysis, based on differentially expressed probe sets, an unsupervised clustering was performed for Jed36_MN, Jed49_MN Jed04_MN, Jed18_MN, Jed34_MN, and Jed40_MN and visualized in a hierarchical clustering graph containing a colored heat map and adjunct dendrograms for displaying expression values and distance metrics between objects (samples or probe sets), respectively. Biological significance of expression data was interpreted by employing the core functional analysis workflow of the Ingenuity Pathways Analysis Software (IPA) (Ingenuity Systems, Redwood City, CA, USA). The Ingenuity Knowledge Base served as reference data set. Significance of relationships between data set molecules and functional frameworks, e.g. canonical pathways, provided by IPA was indicated by Fisher’s exact test p values.
9
Pathway Analysis of Candidate Genes
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Functional classification and pathway analyses of the annotated candidate genes were carried out using the Ingenuity Pathways Analysis software (IPA; Ingenuity Systems, http://www.ingenuity.com ). Significance levels for enrichment of each canonical pathway in the list of candidate genes were calculated using Fisher’s exact test, and the resulting p-values were corrected for multiple-test using the Benjamini and Hochberg algorithm [75 ]. The cut-off for considering an enrichment as significant was established at a corrected p-value < 0.05.
10
Molecular Interactions in Embryo Implantation
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A mechanistic network was created using the Ingenuity Knowledge Base via the Ingenuity Pathways Analysis software (IPA, Ingenuity Systems, http://www.ingenuity.com , accessed on 1 February 2021). Path explorer was used to identify specific known molecular interactions between implantation of embryo, S100P, AGR3, and AGR2.
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