Table 1.
Pathway terms ranked by methods (left) and LRM. *is for cancer specific terms.
| DESeq | LRM |
| *ECM-Receptor Interaction Collagen Formation, Assembly of Collagen Fibrils, Collagen Biosynthesis Cytokine-Cytokine Receptor Interaction *Cell Adhesion Molecules ( CAMs ) *PI3K-Akt Signaling Pathway Protein Digestion and Absorption | *Cancer Specific Terms (FDR-corrected P-value) |
| Cell Adhesion Molecules (6.53E-10)ECM-Receptor Interaction (5.68E-06)Focal Adhesion (1.54E-05)PI3K-Akt Signaling Pathway (2.52E-03)p53 Signaling Pathway (9.31E-03)ECM Organization (3.41E-02) | |
| NOISeq | Top Scored Terms (FDR-corrected P-value) |
| * ECM-Receptor Interaction Collagen formation, Assembly of Collagen Fibrils, Collagen Biosynthesis, Protein Digestion and Absorption *Cell adhesion molecules ( CAMs )Leishmaniasis, Interferon Gamma Signaling | Phagosome (7.42E-12)Complement System (8.09E-11)Protein Digestion and Absorption (6.53E-10)Leishmaniasis (3.59-08)Collagen Formation (1.26E-08)Allograft Rejection (1.24E-07)Viral myocarditis (1.55E-07)Graft-versus-host disease (1.75E-07)Type I diabetes mellitus (3.19-07)Asthma (1.45E-07)Rheumatoid Arthritis (6.46E-06)Cell Cycle (5.68E-06)Autoimmune thyroid disease (4.02E-05)IgA Intestinal Immune Network Production (1.31E-05)Tuberculosis (4.31E-05)Hematopoietic cell lineage (2.02E-04)Pertussis (2.12E-04)Systemic Lupus Erythematosus (2.60E-04)HTLV-I infection (2.88E-03)Spinal Cord Injury (1.19E-03)Inflammatory Bowel Disease (IBD) (2.16E-03)Toxoplasmosis (5.02E-03)Natural killer cell mediated cytotoxicity (6.95E-03)Insulin Processing (2.43E-03)Leukocyte transendothelial migration (1.27E-02) |
| CuffDiff | |
| *ECM-Receptor Interaction Immunoregulatory Interactions between a Lymphoid and a non-Lymphoid cell *Cell adhesion molecules ( CAMs )Collagen formation, Hemostasis Assembly of Collagen Fibrils Natural killer Cell Mediated Cytotoxicity *Rap1 signaling pathway | |
| Limma | |
| *ECM-Receptor Interaction Hemostasis, Complement and Coagulation Cascades, Collagen formation, Cyclin B2 Mediated Events, Cytokine-Cytokine Receptor Interaction, Collagen Biosynthesis | |
| GeneSpring | |
| Cell Cycle, Mitotic Prometaphase, Mitotic Metaphase and Anaphase, Separation of Sister Chromatids, Mitotic Anaphase, Resolution of Sister Chromatid Cohesion | |
| PCA | |
| Rheumatoid Arthritis, Phosphorylation CD3 and TCR, Hematopoietic Cell Lineage, TCR Signaling, ZAP-70 Translocation, Cytokine-cytokine receptor interaction *PD-1 signaling |