Ipa software package

Manufactured by Qiagen

Sourced in United States

The IPA software package is a comprehensive bioinformatics tool designed to analyze and interpret complex biological and chemical data. The core function of IPA is to provide researchers with a powerful platform for the integration, analysis, and interpretation of omics data, enabling them to gain deeper insights into biological processes, pathways, and networks.

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IPA software (351 citations) Ingenuity Pathway Analysis software package (IPA 9.0) (3 citations) IPA package (2 citations)

5 protocols using ipa software package

Functional Enrichment Analysis of Datasets

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Gene Ontology Enrichment Analysis (GO), and Kyoto Ency-clopedia of Genes and Genomes (KEGG) analysis was conducted using the functional annotation tool DAVID (https://david.ncifcrf.gov/). Ingenuity pathway analysis (IPA) was performed using the IPA software package (Qiagen). Enriched ontological terms and pathways with P-values less than 0.05 were selected.

Scoles D.R., Dansithong W., Pflieger L.T., Paul S., Gandelman M., Figueroa K.P., Rigo F., Bennett C.F, & Pulst S.M. (2020). ALS-associated genes in SCA2 mouse spinal cord transcriptomes. Human Molecular Genetics, 29(10), 1658-1672.

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Differentially Expressed Protein Profiling

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Differentially expressed protein profiles (P <0.05) were selected and the ones with differential expression ratio of over ±1.2 were retained. The capability of the resulting differentially expressed proteins in differentiating two groups of samples was then evaluated by hierarchical cluster analysis. For this purpose, the Cluster 3.0 (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm) and the Java Tree view software (http://jtreeview.sourceforge.net) were used. Disease analysis, pathway and network generation were performed using IPA software package (QIAGEN). IPA is a knowledge database relying on published literature related to protein function, localization, relevant interactions and biological mechanisms. Calculated the z-score can infer the activation states (‘activated’ or ‘inhibited’) of implicated biological processes.

Ullah K., Rahman T.U., Pan H.T., Guo M.X., Dong X.Y., Liu J., Jin L.Y., Cheng Y., Ke Z.H., Ren J., Lin X.H., Qiu X.X., Wang T.T., Huang H.F, & Sheng J.Z. (2017). Serum estradiol levels in controlled ovarian stimulation directly affect the endometrium. Journal of Molecular Endocrinology, 59(2), 105-119.

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Proteomic Pathway and Function Analysis

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Proteomic data were uploaded into the IPA software package (Qiagen). Associations between protein groups in the data set and canonical pathways were measured similarly to the over-representation analysis described for the microarray data above. IPA software was also used to compare protein expression patterns against the IPA biological function database. IPA software calculates a Benjamini & Hochberg-adjusted p-value for the association of protein abundance changes with each biological function, and a weighted z-score, which estimates whether the protein abundance changes found associated with a specific biological function are likely to enhance (positive z values) or inhibit (negative) the function.

Hladik F., Burgener A., Ballweber L., Gottardo R., Vojtech L., Fourati S., Dai J.Y., Cameron M.J., Strobl J., Hughes S.M., Hoesley C., Andrew P., Johnson S., Piper J., Friend D.R., Ball T.B., Cranston R.D., Mayer K.H., McElrath M.J, & McGowan I. (2015). Mucosal effects of tenofovir 1% gel. eLife, 4, e04525.

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Differential Expression Profiling Analysis

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All DEPs (p-value < 0.05) were selected and the ones with the differential expression ratio of over ± 1.2 were retained. The capability of the resulting DEPs in differentiating two groups of samples was then evaluated by hierarchical cluster analysis. For this purpose, the Cluster 3.0 (http://bonsai.hgc.jp/∼mdehoon/software/cluster/software.htm) and the Java Tree view software (http://jtreeview.sourceforge.net) were used. Disease analysis, pathway and network generation were performed using IPA software package (QIAGEN, Redwood 185 City, CA, USA). IPA is a knowledge database relying on published literature related to protein function, localization, relevant interactions and biological mechanisms. Calculated the Z-score can infer the activation states (“activated” or “inhibited”) of implicated biological processes. Fisher’s exact test was used to calculate a p-value to determine the probability that the association between proteins in the dataset, and, the biological process could be explained by chance alone.

Rahman T.U., Ullah K., Guo M.X., Pan H.T., Liu J., Ren J., Jin L.Y., Zhou Y.Z., Cheng Y., Sheng J.Z, & Huang H.F. (2018). Androgen-induced alterations in endometrial proteins crucial in recurrent miscarriages. Oncotarget, 9(37), 24627-24641.

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Integrated Analysis of SCA2 miRNA-Transcriptome

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Ingenuity Pathway Analysis (IPA) was performed using the IPA software package from Qiagen, accessible at the IPA Ingenuity website.²⁷ In this study, we used miRNA target filter and core analysis tools in IPA software package to identify target genes of DEmiRs within in the SCA2 mouse transcriptomes and then performed pathway analyses.

Paul S., Dansithong W., Gandelman M., Figueroa K.P., Scoles D.R, & Pulst S.M. (2024). Cerebellar Micro-RNA Profile in a Mouse Model of Spinocerebellar Ataxia Type 2. Neurology: Genetics, 10(2), e200144.

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