Table 2.
Annotations for six DE fundamental components with the highest absolute expression change.*
| Component (Δexpr)** |
Annotation | P-Value |
|---|---|---|
| 66 | Ingenuity Canonical Pathways | |
| (+3.11) | NF-κB Signaling | 8.51E-03 |
| T Cell Receptor Signaling | 8.51E-03 | |
| Type I Diabetes Mellitus Signaling | 8.51E-03 | |
| IL-6 Signaling | 1.51E-02 | |
| Glucocorticoid Receptor Signaling | 1.51E-02 | |
| GO Categories | ||
| regulation of transcription, DNA-dependent | 2.76E-06 | |
| negative regulation of biological process | 4.23E-02 | |
| GEO experiments with high expression of this component | ||
| GSE10609 | the recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-ALL | |
| GSE7440 | Early Response and Outcome in High-Risk Childhood Acute Lymphoblastic Leukemia: A Children's Oncology Group Study | |
| GSE10358 | Discovery and validation of expression data for the Genomics of Acute Myeloid Leukemia Program at Washington University. | |
| GSE10792 | Genome wide genotyping and gene expression data of childhood B-cell precursor ALL without known genetic aberration | |
| GSE7757 | Robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures |
|
| 362 | Ingenuity Canonical Pathways | |
| (+2.34) | NRF2-mediated Oxidative Stress Response | 1.05E-04 |
| Complement System | 1.23E-02 | |
| Aryl Hydrocarbon Receptor Signaling | 1.23E-02 | |
| Glucocorticoid Receptor Signaling | 2.40E-02 | |
| Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses | 2.40E-02 | |
| GO Categories | ||
| response to unfolded protein | 1.67E-15 | |
| protein folding | 2.86E-15 | |
| organ development | 4.48E-02 | |
| GEO experiments with high expression of this component | ||
| GSE7307 | Human body index - transcriptional profiling | |
| GSE7621 | Expression data of substantia nigra from postmortem human brain of Parkinson's disease patients (PD) | |
| GSE10315 | Multipotent mesenchymal stromal cells: identification of pathways common to TGFβ3/BMP2-induced chondrogene |
|
| GSE8977 | Bone-marrow-derived mesenchymal stem cells promote breast cancer metastasis | |
| GSE2816 | cMyb and vMyb in human monocytes | |
| 84 | Ingenuity Canonical Pathways | |
| (+1.53) | N-Glycan Biosynthesis | 3.38E-10 |
| Endoplasmic Reticulum Stress Pathway | 1.23E-04 | |
| NRF2-mediated Oxidative Stress Response | 1.23E-02 | |
| Antigen Presentation Pathway | 1.72E-02 | |
| Lipid Antigen Presentation by CD1 | 3.03E-02 | |
| GO Categories | ||
| protein folding | 4.92E-10 | |
| protein amino acid N-linked glycosylation | 2.46E-07 | |
| secretion | 6.40E-05 | |
| intracellular protein transport | 2.26E-04 | |
| cell redox homeostasis | 2.90E-04 | |
| GEO experiments with high expression of this component | ||
| GSE10315 | Multipotent mesenchymal stromal cells: identification of pathways common to TGFβ3/BMP2-induced chondrogene |
|
| GSE6283 | Specific transcriptional changes in human fetus with autosomal trisomies | |
| GSE6400 | Cultured A549 lung cancer cells treated with actinomycin D and sapphyrin PCI-2050 | |
| GSE6241 | The effects of Serum Amyloid A on gene expression profile in HUVECs | |
| GSE7846 | Differentially expressed genes in HEECs of eutopic endometrium of patients with endometriosis compared with control | |
| 208 | Ingenuity Canonical Pathways | |
| (−1.73) | none | |
| GO Categories | ||
| none | ||
| GEO experiments with high expression of this component | ||
| GSE2109 | Expression Project for Oncology (expO) | |
| GSE10609 | the recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-ALL | |
| GSE9891 | Expression profile of 285 ovarian tumour samples | |
| GSE6532 | Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade | |
| GSE9151 | Allergen induced gene expression of airway epithelial cells shows a possible role for TNF-α | |
| 62 | Ingenuity Canonical Pathways | |
| (−1.95) | EIF2 Signaling | 1.91E-10 |
| Regulation of eIF4 and p70S6K Signaling | 3.89E-08 | |
| mTOR Signaling | 3.72E-04 | |
| GO Categories | ||
| translation | <1E-30 | |
| translational elongation | 3.99E-05 | |
| regulation of translational initiation | 4.18E-04 | |
| ribonucleoprotein complex biogenesis | 3.64E-03 | |
| GEO experiments with high expression of this component | ||
| GSE10358 | Discovery and validation of expression data for the Genomics of Acute Myeloid Leukemia Program at Washington University. | |
| GSE10609 | the recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-ALL | |
| GSE2109 | Expression Project for Oncology (expO) | |
| GSE10792 | Genome wide genotyping and gene expression data of childhood B-cell precursor ALL without known genetic aberrations | |
| GSE7307 | Human body index - transcriptional profiling | |
| 101 | Ingenuity Canonical Pathways | |
| (−2.68) | none | |
| GO Categories | ||
| defense response | 2.22E-03 | |
| icosanoid biosynthetic process | 5.91E-03 | |
| immune system process | 8.37E-03 | |
| GEO experiments with high expression of this component | ||
| GSE10358 | Discovery and validation of expression data for the Genomics of Acute Myeloid Leukemia Program at Washington University. | |
| GSE7757 | Robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures. |
|
| GSE8023 | AML1-ETO transduced human cord blood cells, CD34 selected, compared to normal cord blood cells, CD34 selected |
|
*
Only the top five annotations in each category are shown. For a full list, see Supplementary Table 4. P-values for Ingenuity Canonical Pathways have Benjamini-Hochberg correction applied. P-values for GO categories have Bonferroni correction applied.
**
A positive expression change indicates that the component is up-regulated in PTL-treated compared to untreated.