pathway analysis software ipa 84978992  (Ingenuity Systems)

Journal: Nutrients

Article Title: Aquilaria crassna Extract Exerts Neuroprotective Effect against Benzo[a]pyrene-Induced Toxicity in Human SH-SY5Y Cells: An RNA-Seq-Based Transcriptome Analysis

doi: 10.3390/nu16162727

Figure Lengend Snippet: Gene ontology analysis of DEGs among the different treatment conditions in differentiated SH-SY5Y cells. The top 5 canonical pathways, diseases/disorders, and biological functions that are significantly associated with DEGs were predicted using IPA software. Fisher’s exact test was used to calculate the p value, which is considered significant at p < 0.05. A range of p values is provided for the subcategories of diseases/disorders and biological functions under a general category of the database.

Article Snippet: Ingenuity Pathway Analysis (IPA) software version number 84978992 (Qiagen Inc., Santa Clarita, CA, USA) was also employed to investigate the potential pathways, biological functions, diseases, and regulatory networks associated with the identified DEGs.

Techniques: Software

Journal: Nutrients

Article Title: Aquilaria crassna Extract Exerts Neuroprotective Effect against Benzo[a]pyrene-Induced Toxicity in Human SH-SY5Y Cells: An RNA-Seq-Based Transcriptome Analysis

doi: 10.3390/nu16162727

Figure Lengend Snippet: DEG-associated neurological diseases and nervous system development/functions among the different treatment conditions in differentiated SH-SY5Y cells. The top neurological diseases and nervous system development/functions that are significantly associated with DEGs were predicted using IPA software. p values were calculated by Fisher’s exact test, which is considered significant at p < 0.05.

Article Snippet: Ingenuity Pathway Analysis (IPA) software version number 84978992 (Qiagen Inc., Santa Clarita, CA, USA) was also employed to investigate the potential pathways, biological functions, diseases, and regulatory networks associated with the identified DEGs.

Techniques: Software

Journal: Nutrients

Article Title: Aquilaria crassna Extract Exerts Neuroprotective Effect against Benzo[a]pyrene-Induced Toxicity in Human SH-SY5Y Cells: An RNA-Seq-Based Transcriptome Analysis

doi: 10.3390/nu16162727

Figure Lengend Snippet: Analyses of the enriched canonical pathways associated with the identified DEGs among the treatment conditions in the RA-differentiated SH-SY5Y cells. The canonical pathways associated with DEGs were identified from ( A ) the cells treated with B[a]P and ( B ) the cells co-treated with B[a]P and ACEE relative to the control (RA). The DEG-associated canonical pathways were analyzed by IPA software using the list of DEGs from the RNA-Seq analysis. The bubble plot represents the predicted canonical pathways, with bubble size indicating the number of genes enriched in each pathway and bubble color representing the z-score. The orange bubble denotes a positive z-score and predicted activation state; the blue bubble denotes a negative z-score and predicted inhibition state.

Article Snippet: Ingenuity Pathway Analysis (IPA) software version number 84978992 (Qiagen Inc., Santa Clarita, CA, USA) was also employed to investigate the potential pathways, biological functions, diseases, and regulatory networks associated with the identified DEGs.

Techniques: Control, Software, RNA Sequencing, Activation Assay, Inhibition