Table 3.
Predicted upstream regulators in select molecule types generated in IPA based on observed proteins that were differentially expressed and their corresponding genes in the data set in relation to the saline (S) control treatment. Proteins were derived from the intestinal tract of day of hatch chicks that were inoculated at 18 embryonic days with either Citrobacter freundii (C) Citrobacter spp. (C2), or lactic acid bacteria (L) in ovo.
|
Molecule type |
Upstream regulator | Z-score1,2 |
P-value of overlap3 |
||||
|---|---|---|---|---|---|---|---|
| C | C2 | L | C | C2 | L | ||
| Complex | TCR | --4 (--)2 | -- (--) | 1.91 (--) | -- | -- | <0.01 |
| NF-kβ | 1.98 (1.98) | -- (--) | -- (-1.98) | 0.01 | -- | -- | |
| Membrane receptor | PDGF BB | 1.49 (--) | -- (--) | -- (--) | <0.01 | -- | -- |
| CD3 | – | 1.63 (--) | -- (--) | -- | <0.01 | -- | |
| Cytokines | TNFα | -- (2.08) | -- (--) | -- (--) | -- | -- | -- |
| IL1β | -- (--) | 1.96 (1.53) | -- (--) | -- | <0.01 | -- | |
| OSM | -- | 1.88 (--) | -- (-1.55) | -- | 0.002 | -- | |
| IL6 | -- (--) | 2.57 (2.28) | -- (--) | -- | <0.01 | -- | |
| IL13 | -- (--) | -- (--) | 2.00 (--) | -- | -- | 0.001 | |
| Group | Vegf | -- (--) | 2.00 (2.23) | -- (--) | -- | 0.03 | -- |
| Pkc(s) | -- (--) | -- (2.00) | -- (--) | -- | -- | -- | |
| ERK | 1.98 (--) | -- (--) | -- (--) | <0.01 | -- | -- | |
| Growth factor | FGF2 | -- (--) | -- (--) | 1.92 (--) | -- | -- | 0.01 |
| Ligand nuclear receptor | PPARα | -- (--) | −1.94 (--) | -- (--) | -- | <0.01 | -- |
| Kinase | ERBB2 | 1.82 (--) | -- (1.97) | -- (--) | <0.01 | -- | -- |
| MKNK1 | −2.00 (--) | – | -- (--) | <0.01 | -- | -- | |
| Transcription regulators | XBP1 | -- (--) | -- (−1.55) | 2.40 (--) | <0.01 | -- | -- |
| FOS | -- (--) | -- (--) | 1.73 (--) | -- | -- | <0.01 | |
| GATA6 | −2.16 (−1.63) | -- (1.63) | −2.00 (--) | <0.01 | -- | <0.01 | |
| STAT3 | -- (−2.42) | 1.50 (2.42) | -- (−1.62) | -- | <0.01 | -- | |
| PRDM1 | -- (--) | 1.98 (--) | -- (--) | -- | <0.01 | -- | |
| RB1 | −1.38 (--) | -- (−1.96) | -- (1.96) | 0.01 | -- | -- | |
| NFE2L2 | 1.73 (--) | -- (−1.95) | 2.91 (1.95) | <0.01 | -- | <0.01 | |
| MYCN | -- (--) | -- (--) | 1.50 (1.81) | -- | -- | <0.01 | |
| MYC | −1.86 (−2.73) | -- (−1.69) | 1.82 (2.73) | <0.01 | -- | <0.01 | |
| SMAD3 | -- (--) | -- (1.96) | -- (−1.96) | -- | -- | -- | |
| SMAD7 | -- (--) | -- (−1.96) | -- (1.96) | -- | -- | -- | |
| HNF1α | −2.00 (--) | 1.92 (--) | -- (--) | <0.01 | 0.027 | -- | |
| HNF4α | −1.96 (−1.96) | -- (--) | 1.94 (--) | <0.01 | -- | <0.01 | |
| MKL1 | -- (--) | -- (--) | −1.95 (--) | -- | -- | <0.01 | |
The top Z-score value represents the up-regulator prediction in relation to S. The scores that were activated (Z-score ≥ 2.00) or inhibited (Z-score ≤ −2.00). Qualified predictions were ranked as (Z-score ≥ |1.90| or more) medium (Z-score = |1.70 – 1.90|) or low (Z-score = |1.50 – 1.70|).
The Z-score in ( ) represents the prediction of the corresponding up-regulator among the C, C2 and L treatments, all P-value of overlap ≤ 0.05.
P-value of overlap generated in IPA observed the significant statistical overlap between the samples in the data set and the genes that are regulated by the corresponding transcriptional regulator. The values represent treatment difference in relation to S. All values presented had a Fisher's exact test significant value of P ≤ 0.05.
-- = Z-score or P-value of overlap was not provided so no prediction could not be obtained.