Table 2.
IPA Canonical Pathways Affected by Cdc7 Suppressiona
| canonical pathway | BH p-value | no. mapped to pathway/total available for pathway | no. differentially expressed/no. mapped to pathway | differentially expressed molecules |
|---|---|---|---|---|
| Nrf2-mediated oxidative stress response | 4.97 × 10−8 | 68/181 | 18/68 (26.4%) | MGST1, FTL, DNAJC9, DNAJB4, GCLC, DNAJC10, TXNRD1, HMOX1, DNAJC8, ABCC1, DNAJB1, TXN, SQSTM1, DNAJB6, MGST3, EPHX1, FTH1, AKR1B1 |
| synthesis and degradation of ketone bodies | 5.13 × 10−8 | 9/19 | 6/9 (66.6%) | HADHB, ACAA1, ACAT1, HMGCL, HMGCS1, HADHA |
| butanoate metabolism | 1.89 × 10−5 | 25/128 | 8/25 (32%) | HADHB, PPME1, ACAA1, SUCLG2, ACAT1, HMGCL, HMGCS1, HADHA |
| bile acid biosynthesis | 2.29 × 10−4 | 11/97 | 6/11 (54.5%) | ADH5, HADHB, AKR1C1, ACAA1, PTGR1, HADHA |
| valine, leucine, and isoleucine degradation | 2.55 × 10−4 | 25/105 | 7/25 (28%) | HADHB, ACAA1, ACAT1, HMGCL, IVD, HMGCS1, HADHA |
| biosynthesis of steroids | 2.95 × 10−4 | 7/126 | 5/7 (71.4%) | MVD, FDPS, FDFT1, IDI1, LSS |
| granzyme A signaling | 3.06 × 10−4 | 10/18 | 4/10 (40%) | H1F0, HIST1H1C, HIST1H1B, HMGB2 |
| oxidative phosphorylation | 5.47 × 10−4 | 42/156 | 10/42 (23.8%) | ATP6 V1E1, NDUFS1, ATP6 V1C1, NDUFB7, NDUFS2, ATP6 V1G1, ATP6 V1A, ATP6 V1B2, NDUFA8, NDUFS4 |
| glutathione metabolism | 1.14 × 10−3 | 23/92 | 6/23 (26%) | MGST1, PGD, GPX1, GCLC, MGST3, IDH1 |
| propanoate metabolism | 1.74 × 10−3 | 23/128 | 6/23 (26%) | HADHB, ACAA1, SUCLG2, ACAT1, IVD, HADHA |
2,045 quantified proteins were uploaded into Ingenuity Pathway Analysis (IPA) software using REFSEQ identifiers, fold changes, and Significance B p-values. The expression value cut-off was set to 0.05. This resulted in 2,023 molecules being mapped to the Ingenuity knowledge base, of which 270 qualified as function/pathway eligible molecules (molecules that meet the expression value criteria and have at least one functional annotation in the IPA knowledge base). Shown are the top ranking 10 canonical pathways associated with this data set. A Benjamini–Hochberg test was used to test for significance of the over-representation of each pathway (BH p-value). A ratio value is given for the number of proteins identified within the pathway (no. mapped) divided by the total number of molecules for the pathway within the IPA library (total available). Another ratio is given for the number of significantly altered molecules (no. differentially expressed) divided by the number of proteins identified in the pathway (no. mapped). The differentially expressed proteins associated with each pathway are also listed. All proteins mapped to these 10 pathways are detailed in Supplementary Table S3 and proteins are overlaid onto each pathway in Supplementary Figures S3–S12.