Signaling pathways enriched in Ldb1+/+ and Ldb1−/− derived Flk1+ cells
| . | Column A . | Column B . | Column C . | Column D . | Column E . |
|---|---|---|---|---|---|
| Pathways . | Signaling pathways enriched with genes expressed in Flk1+ cells . | Signaling pathways enriched with genes expressed in Flk1+ cells (and bound by Ldb1) . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells (and bound by Ldb1) (Set1*) . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells (and not bound by Ldb1) (Set3) . |
| Focal adhesion | ✓ | ✓ | ✓ | ✓ | ✓ |
| Adherens junction | ✓ | ✓ | ✓ | ✓ | ✓ |
| Angiogenesis | ✓ | ✓ | ✓ | ✓ | ✓ |
| Colorectal cancer | ✓ | ✓ | ✓ | ✓ | ✓ |
| Hedgehog signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| ErbB signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Insulin signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Integrin signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Leukocyte transendothelial migration | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pathways in cancer | ✓ | ✓ | ✓ | ✓ | ✓ |
| MAPK signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Regulation of actin cytoskeleton | ✓ | ✓ | ✓ | ✓ | ✓ |
| WNT signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Acute myeloid leukemia | ✓ | ✓ | ✓ | ✓ | |
| Basal cell carcinoma | ✓ | ✓ | ✓ | ||
| Interleukin signaling pathway | ✓* | ✓* | ✓* | ✓ | |
| Melanoma | ✓ | ✓ | ✓ | ✓ | |
| T-cell–receptor signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| VEGF signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Apoptosis | ✓ | ✓ | ✓ | ✓ | |
| Axon guidance | ✓ | ✓ | ✓ | ✓ | |
| Chronic myeloid leukemia | ✓ | ✓ | ✓ | ✓ | |
| PDGF signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Small-cell lung cancer | ✓ | ✓ | ✓ | ✓ | |
| EGF signaling pathway | ✓* | ✓ | ✓ | ✓ | |
| Endocytosis | ✓ | ✓ | ✓ | ✓ | |
| Glioma | ✓ | ✓ | ✓ | ✓ | |
| Neurotrophin signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| TGF-β signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Prostate cancer | ✓ | ✓ | ✓ | ||
| Pancreatic cancer | ✓ | ✓ | ✓ | ||
| uCalpain and friends in Cell spread | ✓ | ✓ | |||
| Bladder cancer | ✓ | ✓ | ✓ | ||
| Dopamine receptor–mediated signaling pathway | ✓* | ✓ | ✓ | ||
| Tight junction | ✓ | ✓ | ✓ | ||
| Oxidative stress response | ✓ | ✓ | ✓ | ||
| Melanogenesis | ✓ | ✓ | |||
| B-cell activation | ✓ | ✓ | |||
| Telomeres, telomerase, cellular aging, and immortality | ✓ | ✓ | |||
| Cell cycle | ✓ | ✓ | ✓ | ||
| mTOR signaling pathway | ✓ | ✓ | ✓ | ||
| Ras pathway | ✓ | ✓ | ✓ | ||
| Glutathione metabolism | ✓ | ✓ | |||
| Control of gene expression by vitamin D receptor | ✓* | ✓ | |||
| Aminoacyl-tRNA biosynthesis | ✓ | ✓ | |||
| Amyotrophic lateral sclerosis | ✓ | ✓ | |||
| B-cell–receptor signaling pathway | ✓ | ✓ | |||
| Basal transcription factors | ✓ | ✓ | |||
| Endometrial cancer | ✓ | ✓ | |||
| Glyoxylate and dicarboxylate metabolism | ✓ | ✓ | |||
| Heme biosynthesis | ✓ | ✓ | |||
| Huntington disease | ✓ | ✓ | |||
| Interferon-γ signaling pathway | ✓ | ✓ | |||
| JAK/STAT signaling pathway | ✓ | ✓ | |||
| Lysosome | ✓ | ✓ | |||
| Transcription regulation by bZIP transcription factor | ✓ | ✓ | |||
| Adipocytokine signaling pathway | ✓ | ✓ | |||
| Alzheimer disease | ✓ | ✓ | |||
| Ubiquitin mediated proteolysis | ✓ | ✓ | |||
| Non–small-cell lung cancer | ✓ | ✓ | |||
| Nucleotide excision repair | ✓ | ✓ | |||
| Oxidative phosphorylation | ✓ | ✓ | |||
| p38 MAPK signaling pathway | ✓ | ✓ | |||
| p53 signaling pathway | ✓ | ✓ | |||
| Parkinson disease | ✓ | ✓ | |||
| Proteasome | ✓ | ✓ | |||
| Renal cell carcinoma | ✓ | ✓ | |||
| Ribosome | ✓ | ✓ | |||
| RNA degradation | ✓ | ✓ | |||
| Spliceosome | ✓ | ✓ | |||
| Apoptotic signaling in response to DNA damage | ✓ | ||||
| Arginine and proline metabolism | ✓ | ||||
| Base excision repair | ✓ | ||||
| Biosynthesis of unsaturated fatty acids | ✓ | ||||
| Chemokine signaling pathway | ✓ | ||||
| Chondroitin sulfate biosynthesis | ✓ | ||||
| Circadian clock system | ✓ | ||||
| Citrate cycle (TCA cycle) | ✓ | ||||
| CXCR4 signaling pathway | ✓ | ||||
| Cysteine and methionine metabolism | ✓ | ||||
| DNA replication | ✓ | ||||
| Dorsoventral axis formation | ✓ | ||||
| Endothelin signaling pathway | ✓ | ||||
| Fatty acid metabolism | ✓ | ||||
| Fc γ R–mediated phagocytosis | ✓ | ||||
| fMLP-induced chemokine gene expression in HMC-1 cells | ✓ | ||||
| Fructose and mannose metabolism | ✓ | ||||
| Gap junction | ✓ | ||||
| General transcription regulation | ✓ | ||||
| Glycerophospholipid metabolism | ✓ | ||||
| Glycosylphosphatidylinositol-anchor biosynthesis | ✓ | ||||
| Gonadotropin-releasing hormone signaling pathway | ✓ | ||||
| HIV-I Nef: negative effector of Fas and tumor necrosis factor | ✓ | ||||
| Homologous recombination | ✓ | ||||
| Hypoxia response via HIF activation | ✓ | ||||
| Influence of Ras and Rho proteins on G1 to S transition | ✓ | ||||
| Inositol phosphate metabolism | ✓ | ||||
| Keratan sulfate biosynthesis | ✓ | ||||
| Limonene and pinene degradation | ✓ | ||||
| Links between Pyk2 and MAP kinases | ✓ | ||||
| Long-term depression | ✓ | ||||
| Long-term potentiation | ✓ | ||||
| Lysine degradation | ✓ | ||||
| Mismatch repair | ✓ | ||||
| N-glycan biosynthesis | ✓ | ||||
| Notch signaling pathway | ✓ | ||||
| One carbon pool by folate | ✓ | ||||
| Oocyte meiosis | ✓ | ||||
| Other glycan degradation | ✓ | ||||
| Phosphatidylinositol signaling system | ✓ | ||||
| Phospholipids as signaling intermediaries | ✓ | ||||
| Progesterone-mediated oocyte maturation | ✓ | ||||
| Propanoate metabolism | ✓ | ||||
| Purine metabolism | ✓ | ||||
| Pyrimidine metabolism | ✓ | ||||
| Pyruvate metabolism | ✓ | ||||
| Ras-signaling pathway | ✓ | ||||
| Regulation of eIF4e and p7 S6 kinase | ✓ | ||||
| RNA polymerase | ✓ | ||||
| Role of BRCA1, BRCA2, and ATR in cancer susceptibility | ✓ | ||||
| Role of mitochondria in apoptotic signaling | ✓ | ||||
| Selenoamino acid metabolism | ✓ | ||||
| Signaling of hepatocyte growth factor receptor | ✓ | ||||
| Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway | ✓ | ||||
| SNARE interactions in vesicular transport | ✓ | ||||
| Steroid biosynthesis | ✓ | ||||
| Amino sugar and nucleotide sugar metabolism | ✓ | ||||
| Valine, leucine, and isoleucine degradation | ✓ | ||||
| Thyroid cancer | ✓ |
| . | Column A . | Column B . | Column C . | Column D . | Column E . |
|---|---|---|---|---|---|
| Pathways . | Signaling pathways enriched with genes expressed in Flk1+ cells . | Signaling pathways enriched with genes expressed in Flk1+ cells (and bound by Ldb1) . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells (and bound by Ldb1) (Set1*) . | Signaling pathways perturbed in Ldb1−/− Flk1+ cells (and not bound by Ldb1) (Set3) . |
| Focal adhesion | ✓ | ✓ | ✓ | ✓ | ✓ |
| Adherens junction | ✓ | ✓ | ✓ | ✓ | ✓ |
| Angiogenesis | ✓ | ✓ | ✓ | ✓ | ✓ |
| Colorectal cancer | ✓ | ✓ | ✓ | ✓ | ✓ |
| Hedgehog signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| ErbB signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Insulin signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Integrin signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Leukocyte transendothelial migration | ✓ | ✓ | ✓ | ✓ | ✓ |
| Pathways in cancer | ✓ | ✓ | ✓ | ✓ | ✓ |
| MAPK signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Regulation of actin cytoskeleton | ✓ | ✓ | ✓ | ✓ | ✓ |
| WNT signaling pathway | ✓ | ✓ | ✓ | ✓ | ✓ |
| Acute myeloid leukemia | ✓ | ✓ | ✓ | ✓ | |
| Basal cell carcinoma | ✓ | ✓ | ✓ | ||
| Interleukin signaling pathway | ✓* | ✓* | ✓* | ✓ | |
| Melanoma | ✓ | ✓ | ✓ | ✓ | |
| T-cell–receptor signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| VEGF signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Apoptosis | ✓ | ✓ | ✓ | ✓ | |
| Axon guidance | ✓ | ✓ | ✓ | ✓ | |
| Chronic myeloid leukemia | ✓ | ✓ | ✓ | ✓ | |
| PDGF signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Small-cell lung cancer | ✓ | ✓ | ✓ | ✓ | |
| EGF signaling pathway | ✓* | ✓ | ✓ | ✓ | |
| Endocytosis | ✓ | ✓ | ✓ | ✓ | |
| Glioma | ✓ | ✓ | ✓ | ✓ | |
| Neurotrophin signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| TGF-β signaling pathway | ✓ | ✓ | ✓ | ✓ | |
| Prostate cancer | ✓ | ✓ | ✓ | ||
| Pancreatic cancer | ✓ | ✓ | ✓ | ||
| uCalpain and friends in Cell spread | ✓ | ✓ | |||
| Bladder cancer | ✓ | ✓ | ✓ | ||
| Dopamine receptor–mediated signaling pathway | ✓* | ✓ | ✓ | ||
| Tight junction | ✓ | ✓ | ✓ | ||
| Oxidative stress response | ✓ | ✓ | ✓ | ||
| Melanogenesis | ✓ | ✓ | |||
| B-cell activation | ✓ | ✓ | |||
| Telomeres, telomerase, cellular aging, and immortality | ✓ | ✓ | |||
| Cell cycle | ✓ | ✓ | ✓ | ||
| mTOR signaling pathway | ✓ | ✓ | ✓ | ||
| Ras pathway | ✓ | ✓ | ✓ | ||
| Glutathione metabolism | ✓ | ✓ | |||
| Control of gene expression by vitamin D receptor | ✓* | ✓ | |||
| Aminoacyl-tRNA biosynthesis | ✓ | ✓ | |||
| Amyotrophic lateral sclerosis | ✓ | ✓ | |||
| B-cell–receptor signaling pathway | ✓ | ✓ | |||
| Basal transcription factors | ✓ | ✓ | |||
| Endometrial cancer | ✓ | ✓ | |||
| Glyoxylate and dicarboxylate metabolism | ✓ | ✓ | |||
| Heme biosynthesis | ✓ | ✓ | |||
| Huntington disease | ✓ | ✓ | |||
| Interferon-γ signaling pathway | ✓ | ✓ | |||
| JAK/STAT signaling pathway | ✓ | ✓ | |||
| Lysosome | ✓ | ✓ | |||
| Transcription regulation by bZIP transcription factor | ✓ | ✓ | |||
| Adipocytokine signaling pathway | ✓ | ✓ | |||
| Alzheimer disease | ✓ | ✓ | |||
| Ubiquitin mediated proteolysis | ✓ | ✓ | |||
| Non–small-cell lung cancer | ✓ | ✓ | |||
| Nucleotide excision repair | ✓ | ✓ | |||
| Oxidative phosphorylation | ✓ | ✓ | |||
| p38 MAPK signaling pathway | ✓ | ✓ | |||
| p53 signaling pathway | ✓ | ✓ | |||
| Parkinson disease | ✓ | ✓ | |||
| Proteasome | ✓ | ✓ | |||
| Renal cell carcinoma | ✓ | ✓ | |||
| Ribosome | ✓ | ✓ | |||
| RNA degradation | ✓ | ✓ | |||
| Spliceosome | ✓ | ✓ | |||
| Apoptotic signaling in response to DNA damage | ✓ | ||||
| Arginine and proline metabolism | ✓ | ||||
| Base excision repair | ✓ | ||||
| Biosynthesis of unsaturated fatty acids | ✓ | ||||
| Chemokine signaling pathway | ✓ | ||||
| Chondroitin sulfate biosynthesis | ✓ | ||||
| Circadian clock system | ✓ | ||||
| Citrate cycle (TCA cycle) | ✓ | ||||
| CXCR4 signaling pathway | ✓ | ||||
| Cysteine and methionine metabolism | ✓ | ||||
| DNA replication | ✓ | ||||
| Dorsoventral axis formation | ✓ | ||||
| Endothelin signaling pathway | ✓ | ||||
| Fatty acid metabolism | ✓ | ||||
| Fc γ R–mediated phagocytosis | ✓ | ||||
| fMLP-induced chemokine gene expression in HMC-1 cells | ✓ | ||||
| Fructose and mannose metabolism | ✓ | ||||
| Gap junction | ✓ | ||||
| General transcription regulation | ✓ | ||||
| Glycerophospholipid metabolism | ✓ | ||||
| Glycosylphosphatidylinositol-anchor biosynthesis | ✓ | ||||
| Gonadotropin-releasing hormone signaling pathway | ✓ | ||||
| HIV-I Nef: negative effector of Fas and tumor necrosis factor | ✓ | ||||
| Homologous recombination | ✓ | ||||
| Hypoxia response via HIF activation | ✓ | ||||
| Influence of Ras and Rho proteins on G1 to S transition | ✓ | ||||
| Inositol phosphate metabolism | ✓ | ||||
| Keratan sulfate biosynthesis | ✓ | ||||
| Limonene and pinene degradation | ✓ | ||||
| Links between Pyk2 and MAP kinases | ✓ | ||||
| Long-term depression | ✓ | ||||
| Long-term potentiation | ✓ | ||||
| Lysine degradation | ✓ | ||||
| Mismatch repair | ✓ | ||||
| N-glycan biosynthesis | ✓ | ||||
| Notch signaling pathway | ✓ | ||||
| One carbon pool by folate | ✓ | ||||
| Oocyte meiosis | ✓ | ||||
| Other glycan degradation | ✓ | ||||
| Phosphatidylinositol signaling system | ✓ | ||||
| Phospholipids as signaling intermediaries | ✓ | ||||
| Progesterone-mediated oocyte maturation | ✓ | ||||
| Propanoate metabolism | ✓ | ||||
| Purine metabolism | ✓ | ||||
| Pyrimidine metabolism | ✓ | ||||
| Pyruvate metabolism | ✓ | ||||
| Ras-signaling pathway | ✓ | ||||
| Regulation of eIF4e and p7 S6 kinase | ✓ | ||||
| RNA polymerase | ✓ | ||||
| Role of BRCA1, BRCA2, and ATR in cancer susceptibility | ✓ | ||||
| Role of mitochondria in apoptotic signaling | ✓ | ||||
| Selenoamino acid metabolism | ✓ | ||||
| Signaling of hepatocyte growth factor receptor | ✓ | ||||
| Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway | ✓ | ||||
| SNARE interactions in vesicular transport | ✓ | ||||
| Steroid biosynthesis | ✓ | ||||
| Amino sugar and nucleotide sugar metabolism | ✓ | ||||
| Valine, leucine, and isoleucine degradation | ✓ | ||||
| Thyroid cancer | ✓ |
Column A: Signaling pathways enriched for genes expressed in Flk1+ cells. Column B: Signaling pathways enriched for genes expressed in Flk1+ cells and bound by Ldb1. Column C: Signaling pathways perturbed in Ldb1−/− Flk1+ cells. Column D: Signaling pathways enriched with genes differentially expressed in Ldb1−/− Flk1+ cells and bound by Ldb1 (Set1*). Column E: Signaling pathways enriched with genes differentially expressed in Ldb1−/− Flk1+ cells and not bound by Ldb1 (Set3). Signaling pathways were selected based on significance (P ≤ .05) unless stated otherwise.
*P = .07 to .09.