Ingenuity pathway analysis software package ipa 9.0

To precisely characterize the cell types and understand the molecular mechanism of wound healing, we performed pathways enrichment and systems biology analysis. The analysis was performed on transcripts that were significantly dysregulated in the specific cells by comparing healed vs non-healed samples. Pathways and systems biology analysis was performed using the Ingenuity Pathway Analysis software package (IPA 9.0) (Qiagen). A detailed description of IPA is available at the Ingenuity Systems’ website (http://www.ingenuity.com). Systems biology analysis was performed by analyzing the upstream transcriptional regulators. The regulatory analysis helps in identifying significantly activated or inhibited transcriptional regulators based on upregulation or downregulation of its target genes. The significance of transcriptional regulators activation/inhibition was determined using one-tailed Fisher’s exact test. The regulators with a p-value <0.01 and absolute z-score 2 were considered statistically significant.

To further characterize the T-ALL BME and understand the molecular mechanism of disease progression, we performed pathways and systems biology analysis on the transcripts that are significantly overexpressed in the blast cells as well as in the immune cells of the T-ALL BME. Pathways and systems biology analysis was performed using the Ingenuity Pathway Analysis software package (IPA 9.0) (Qiagen). A detailed description of IPA analysis is available at the Ingenuity Systems’ website (http//www.ingenuity.com). Systems biology analysis was performed using upstream regulators enrichment approach to identify upstream transcriptional regulators that can explain observed transcriptome changes. Regulatory analysis helps in identifying significantly activated or inhibited transcriptional regulators based on upregulation or downregulation of their target genes. The significance of transcriptional regulator activation/inhibition was determined using one-tailed Fisher’s Exact test. Regulators with a P value < 0.01 and absolute Z-score ≥ 1 were considered statistically significant.

To precisely characterize the AML blast cells and understand the molecular mechanism of disease progression, we performed pathways enrichment and systems biology analysis. Pathways and systems biology analysis was performed using the Ingenuity Pathway Analysis software package (IPA 9.0) (Qiagen). A detailed description of IPA analysis is available at the Ingenuity Systems’ website (https://www.ingenuity.com). Furthermore, systems biology analysis was performed using upstream regulators enrichment approach to identify the upstream transcriptional regulators that can explain observed transcriptome changes. Regulatory analysis helps in identifying significantly activated or inhibited transcriptional regulators based on upregulation or downregulation of its target genes. The significance of transcriptional regulators activation/inhibition was determined using one-tailed Fisher’s Exact test. The regulators with P < 0.01 and absolute Z-score of ±1.5 were considered statistically significant.