Table 5 Functional annotations (GO, KEGG, Biocarta) enriched in transcripts downregulated* in BMP2+ cells compared to control cells in seven-day-old EBs
Category | Term | Count | p value |
|---|---|---|---|
GOTERM_BP_5 | Development | 82 | 3.6E-20 |
GOTERM_BP_5 | Organ development | 57 | 5.1E-19 |
GOTERM_BP_5 | Morphogenesis | 56 | 1.6E-16 |
GOTERM_BP_5 | Cell differentiation | 37 | 2.1E-11 |
GOTERM_BP_5 | Blood vessel morphogenesis | 25 | 1.7E-10 |
GOTERM_BP_5 | Embryonic development | 25 | 1.2E-8 |
GOTERM_BP_5 | System development | 30 | 1.9E-8 |
GOTERM_BP_5 | Organ morphogenesis | 27 | 2.3E-8 |
GOTERM_BP_5 | Vasculature development | 17 | 2.8E-8 |
GOTERM_BP_5 | Tube development | 18 | 5.8E-8 |
GOTERM_BP_5 | Enzyme linked receptor protein signaling pathway | 27 | 6.1E-8 |
GOTERM_BP_5 | Cell migration | 28 | 1.0E-7 |
GOTERM_BP_5 | Blood vessel development | 16 | 1.3E-7 |
GOTERM_BP_5 | Nervous system development | 25 | 5.5E-7 |
GOTERM_BP_5 | Embryonic limb morphogenesis | 12 | 1.8E-6 |
GOTERM_BP_5 | Angiogenesis | 17 | 3.7E-6 |
GOTERM_BP_5 | Embryonic morphogenesis | 14 | 6.7E-6 |
GOTERM_BP_5 | Cell motility | 21 | 7.3E-6 |
GOTERM_BP_5 | Locomotion | 21 | 8.7E-6 |
GOTERM_BP_5 | Localization of cell | 21 | 8.7E-6 |
GOTERM_BP_5 | Neuron differentiation | 24 | 1.1E-5 |
GOTERM_BP_5 | Steroid biosynthesis | 12 | 1.2E-5 |
GOTERM_BP_5 | Brain development | 16 | 1.9E-5 |
GOTERM_BP_5 | Cell development | 15 | 2.0E-5 |
GOTERM_BP_5 | Alcohol catabolism | 11 | 3.2E-5 |
GOTERM_BP_5 | Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 100 | 3.3E-5 |
GOTERM_BP_5 | Tissue development | 12 | 6.8E-5 |
GOTERM_BP_5 | Axon guidance | 12 | 6.8E-5 |
GOTERM_BP_5 | Tube morphogenesis | 10 | 7.1E-5 |
GOTERM_BP_5 | Central nervous system development | 10 | 8.5E-5 |
GOTERM_BP_5 | Lipid biosynthesis | 20 | 9.8E-5 |
GOTERM_BP_5 | Monosaccharide metabolism | 15 | 1.1E-4 |
GOTERM_BP_5 | Regulation of biological process | 41 | 1.4E-4 |
GOTERM_BP_5 | Ossification | 12 | 1.5E-4 |
GOTERM_BP_5 | Transcription | 99 | 1.6E-4 |
GOTERM_BP_5 | Carbohydrate catabolism | 11 | 2.2E-4 |
GOTERM_CC_5 | Cell | 203 | 2.6E-4 |
GOTERM_BP_5 | Neural crest cell development | 6 | 2.7E-4 |
GOTERM_BP_5 | Regulation of development | 11 | 2.9E-4 |
GOTERM_BP_5 | Regulation of cellular process | 35 | 3.1E-4 |
GOTERM_BP_5 | DNA metabolism | 34 | 3.4E-4 |
GOTERM_BP_5 | Neuron morphogenesis during differentiation | 16 | 3.4E-4 |
GOTERM_BP_5 | Cellular macromolecule catabolism | 21 | 3.5E-4 |
GOTERM_BP_5 | Branching morphogenesis of a tube | 7 | 4.1E-4 |
GOTERM_BP_5 | Morphogenesis of a branching structure | 7 | 4.1E-4 |
GOTERM_BP_5 | Neurogenesis | 15 | 4.3E-4 |
GOTERM_CC_5 | Anchored to plasma membrane | 5 | 4.8E-4 |
GOTERM_CC_5 | Anchored to membrane | 5 | 4.8E-4 |
GOTERM_BP_5 | Cellular morphogenesis during differentiation | 17 | 4.9E-4 |
GOTERM_BP_5 | Pattern specification | 10 | 4.9E-4 |
GOTERM_BP_5 | Skeletal development | 8 | 5.0E-4 |
GOTERM_BP_5 | Limb morphogenesis | 7 | 6.2E-4 |
GOTERM_BP_5 | Appendage morphogenesis | 7 | 6.2E-4 |
GOTERM_BP_5 | Appendage development | 7 | 6.2E-4 |
GOTERM_BP_5 | Regulation of cell differentiation | 9 | 8.5E-4 |
GOTERM_BP_5 | Patterning of blood vessels | 6 | 8.5E-4 |
GOTERM_BP_5 | Vasculogenesis | 6 | 8.5E-4 |
GOTERM_BP_5 | Regulation of myeloid cell differentiation | 4 | 1.1E-3 |
GOTERM_BP_5 | Cellular carbohydrate metabolism | 21 | 1.2E-3 |
GOTERM_BP_5 | Neural crest cell migration | 5 | 1.2E-3 |
GOTERM_BP_5 | Steroid metabolism | 14 | 1.5E-3 |
KEGG_PATHWAY | Focal adhesion | 25 | 1.5E-3 |
KEGG_PATHWAY | TGF-β signaling pathway | 14 | 1.7E-3 |
GOTERM_BP_5 | Exocrine system development | 4 | 1.8E-3 |
GOTERM_BP_5 | Salivary gland morphogenesis | 4 | 1.8E-3 |
GOTERM_BP_5 | Salivary gland development | 4 | 1.8E-3 |
GOTERM_BP_5 | Negative regulation of cell differentiation | 6 | 2.0E-3 |
KEGG_PATHWAY | ECM-receptor interaction | 14 | 2.1E-3 |
GOTERM_BP_5 | Biomineral formation | 7 | 2.1E-3 |
GOTERM_BP_5 | Ureteric bud branching | 5 | 2.2E-3 |
GOTERM_CC_5 | Intracellular | 183 | 2.3E-3 |
GOTERM_BP_5 | Negative regulation of signal transduction | 10 | 2.3E-3 |
GOTERM_MF_5 | Heparin binding | 8 | 2.4E-3 |
GOTERM_BP_5 | Ureteric bud development | 6 | 2.5E-3 |
GOTERM_BP_5 | Lung development | 7 | 2.9E-3 |
GOTERM_BP_5 | Gland development | 4 | 2.9E-3 |
GOTERM_BP_5 | Mesenchymal cell differentiation | 5 | 2.9E-3 |
GOTERM_BP_5 | Mesenchymal cell development | 5 | 2.9E-3 |
KEGG_PATHWAY | Hedgehog signaling pathway | 10 | 3.4E-3 |
GOTERM_BP_5 | Embryonic appendage morphogenesis | 6 | 3.5E-3 |
GOTERM_BP_5 | Embryonic development (sensu Metazoa) | 10 | 3.6E-3 |
GOTERM_BP_5 | Bone remodeling | 7 | 4.9E-3 |
GOTERM_BP_5 | Alcohol biosynthesis | 6 | 4.9E-3 |
GOTERM_BP_5 | Negative regulation of development | 6 | 4.9E-3 |
GOTERM_MF_5 | Nucleic acid binding | 8 | 5.4E-3 |
GOTERM_CC_5 | Transcription factor complex | 28 | 5.4E-3 |
KEGG_PATHWAY | Glycolysis/gluconeogenesis | 10 | 5.7E-3 |
GOTERM_BP_5 | Neural crest cell differentiation | 4 | 5.8E-3 |
GOTERM_BP_5 | Cartilage development | 4 | 5.8E-3 |
GOTERM_BP_5 | Cartilage condensation | 4 | 5.8E-3 |
GOTERM_BP_5 | Axonogenesis | 8 | 5.9E-3 |
GOTERM_BP_5 | Tissue remodeling | 7 | 6.2E-3 |
GOTERM_BP_5 | Regulation of cell migration | 7 | 6.2E-3 |
GOTERM_BP_5 | Neurite morphogenesis | 8 | 6.5E-3 |
GOTERM_BP_5 | Sterol metabolism | 8 | 6.5E-3 |
GOTERM_BP_5 | Cellular morphogenesis | 14 | 7.0E-3 |
GOTERM_BP_5 | Regulation of physiological process | 28 | 7.0E-3 |
GOTERM_BP_5 | Positive regulation of cellular metabolism | 18 | 7.5E-3 |
GOTERM_BP_5 | Regulation of cell motility | 7 | 7.7E-3 |
GOTERM_BP_5 | Hindlimb morphogenesis | 4 | 7.7E-3 |
GOTERM_BP_5 | Carboxylic acid metabolism | 27 | 8.0E-3 |
GOTERM_BP_5 | Carbohydrate biosynthesis | 9 | 8.1E-3 |
GOTERM_BP_5 | Somitogenesis | 5 | 8.1E-3 |
GOTERM_BP_5 | Hemopoiesis | 7 | 8.6E-3 |
GOTERM_BP_5 | Hemopoietic or lymphoid organ development | 7 | 9.5E-3 |
GOTERM_BP_5 | Regulation of cellular physiological process | 24 | 9.6E-3 |
GOTERM_BP_5 | Neuron development | 8 | 1.0E-2 |
GOTERM_BP_5 | Respiratory tube development | 6 | 1.1E-2 |
GOTERM_BP_5 | Embryonic pattern specification | 5 | 1.1E-2 |
GOTERM_BP_5 | Metanephros development | 6 | 1.2E-2 |
GOTERM_BP_5 | Cellular lipid metabolism | 26 | 1.3E-2 |
GOTERM_BP_5 | Anterior/posterior pattern formation | 5 | 1.3E-2 |
GOTERM_BP_5 | Protein complex assembly | 11 | 1.5E-2 |
KEGG_PATHWAY | Pentose phosphate pathway | 6 | 1.5E-2 |
GOTERM_CC_5 | Organelle | 179 | 1.5E-2 |
GOTERM_CC_5 | Intracellular organelle | 179 | 1.5E-2 |
GOTERM_BP_5 | Glial cell differentiation | 4 | 1.6E-2 |
GOTERM_BP_5 | Wnt receptor signaling pathway | 10 | 1.6E-2 |
GOTERM_CC_5 | Membrane-bound organelle | 157 | 1.8E-2 |
GOTERM_CC_5 | Intracellular membrane-bound organelle | 157 | 1.8E-2 |
GOTERM_MF_5 | Catalytic activity | 63 | 1.9E-2 |
BIOCARTA | Pertussis toxin-insensitive CCR5 signaling in macrophage | 5 | 2.0E-2 |
GOTERM_BP_5 | Genitalia morphogenesis | 3 | 2.1E-2 |
GOTERM_BP_5 | Placenta development | 3 | 2.1E-2 |
GOTERM_CC_5 | Nucleoplasm | 31 | 2.1E-2 |
GOTERM_MF_5 | Iron ion binding | 16 | 2.1E-2 |
GOTERM_BP_5 | Positive regulation of biological process | 12 | 2.1E-2 |
GOTERM_BP_5 | Odontogenesis | 4 | 2.3E-2 |
GOTERM_BP_5 | Positive regulation of cell proliferation | 10 | 2.4E-2 |
KEGG_PATHWAY | Axon guidance | 15 | 2.5E-2 |
GOTERM_BP_5 | Positive regulation of cellular process | 10 | 2.7E-2 |
GOTERM_BP_5 | Embryonic placenta development | 3 | 2.8E-2 |
GOTERM_BP_5 | Cell proliferation | 11 | 2.8E-2 |
GOTERM_BP_5 | Negative regulation of cellular process | 11 | 3.0E-2 |
GOTERM_BP_5 | Inner ear morphogenesis | 5 | 3.1E-2 |
GOTERM_BP_5 | Negative regulation of biological process | 12 | 3.2E-2 |
GOTERM_BP_5 | Base-excision repair | 4 | 3.6E-2 |
GOTERM_BP_5 | Negative regulation of neuron differentiation | 3 | 3.7E-2 |
GOTERM_MF_5 | DNA N-glycosylase activity | 3 | 3.7E-2 |
KEGG_PATHWAY | Fructose and mannose metabolism | 8 | 3.8E-2 |
GOTERM_BP_5 | Amino acid derivative metabolism | 7 | 3.8E-2 |
GOTERM_CC_5 | Nucleosome | 7 | 4.1E-2 |
GOTERM_BP_5 | Positive regulation of cellular physiological process | 7 | 4.1E-2 |
GOTERM_CC_5 | Chromosome | 19 | 4.1E-2 |
GOTERM_MF_5 | Oxidoreductase activity | 11 | 4.2E-2 |
GOTERM_BP_5 | Morphogenesis of an epithelium | 5 | 4.2E-2 |
GOTERM_MF_5 | Protein kinase activity | 27 | 4.6E-2 |
GOTERM_CC_5 | Nuclear lumen | 35 | 4.6E-2 |
GOTERM_BP_5 | Hormone metabolism | 4 | 4.7E-2 |
GOTERM_MF_5 | Pyrophosphatase activity | 21 | 4.8E-2 |
GOTERM_CC_5 | Plasma membrane | 17 | 5.0E-2 |
GOTERM_BP_5 | Regulation of progression through cell cycle | 20 | 5.0E-2 |
GOTERM_BP_5 | Odontogenesis (sensu Vertebrata) | 4 | 5.3E-2 |
GOTERM_CC_5 | Membrane-bound vesicle | 8 | 5.3E-2 |
GOTERM_CC_5 | Vesicle | 8 | 5.3E-2 |
GOTERM_CC_5 | Cytoplasmic vesicle | 8 | 5.3E-2 |
KEGG_PATHWAY | WNT signaling pathway | 15 | 5.5E-2 |
GOTERM_CC_5 | Protein complex | 36 | 5.5E-2 |
GOTERM_BP_5 | Nucleoside metabolism | 4 | 5.9E-2 |
GOTERM_BP_5 | Segmentation | 4 | 5.9E-2 |
GOTERM_BP_5 | Morphogenesis of embryonic epithelium | 4 | 5.9E-2 |
GOTERM_BP_5 | Sex differentiation | 5 | 6.0E-2 |
GOTERM_MF_5 | Interleukin-11 receptor activity | 2 | 6.1E-2 |
GOTERM_MF_5 | Interleukin-11 binding | 2 | 6.1E-2 |
GOTERM_CC_5 | Chromatin | 11 | 6.2E-2 |
GOTERM_CC_5 | Heterotrimeric G-protein complex | 5 | 6.3E-2 |
BIOCARTA | Sonic hedgehog (shh) pathway | 4 | 6.4E-2 |
GOTERM_CC_5 | Cytosol | 6 | 6.5E-2 |
GOTERM_BP_5 | Regulation of enzyme activity | 4 | 6.5E-2 |
GOTERM_CC_5 | Intrinsic to Golgi membrane | 4 | 6.6E-2 |
KEGG_PATHWAY | Biosynthesis of steroids | 4 | 6.8E-2 |
KEGG_PATHWAY | Huntington's disease | 5 | 6.8E-2 |
GOTERM_BP_5 | Eye development | 5 | 7.0E-2 |
GOTERM_BP_5 | Regulation of cell proliferation | 9 | 7.2E-2 |
GOTERM_BP_5 | Biopolymer modification | 59 | 7.2E-2 |
GOTERM_BP_5 | Physiological process | 117 | 7.2E-2 |
GOTERM_BP_5 | Cellular physiological process | 100 | 7.7E-2 |
GOTERM_BP_5 | Astrocyte differentiation | 2 | 7.7E-2 |
GOTERM_BP_5 | Regulation of astrocyte differentiation | 2 | 7.7E-2 |
GOTERM_BP_5 | Mesoderm morphogenesis | 3 | 7.8E-2 |
GOTERM_BP_5 | Mesoderm formation | 3 | 7.8E-2 |
GOTERM_BP_5 | Mesoderm development | 3 | 7.8E-2 |
GOTERM_BP_5 | T cell activation | 3 | 7.8E-2 |
GOTERM_BP_5 | Embryonic heart tube development | 3 | 7.8E-2 |
GOTERM_BP_5 | Negative regulation of Wnt receptor signaling pathway | 3 | 7.8E-2 |
GOTERM_BP_5 | Negative regulation of BMP signaling pathway | 3 | 7.8E-2 |
GOTERM_BP_5 | M phase of mitotic cell cycle | 9 | 7.8E-2 |
GOTERM_BP_5 | Regulation of signal transduction | 8 | 7.8E-2 |
GOTERM_BP_5 | Neural plate morphogenesis | 4 | 7.9E-2 |
GOTERM_BP_5 | Ear morphogenesis | 4 | 7.9E-2 |
GOTERM_BP_5 | Ear development | 4 | 7.9E-2 |
KEGG_PATHWAY | Synthesis and degradation of ketone bodies | 3 | 8.0E-2 |
GOTERM_BP_5 | Eye development (sensu Mammalia) | 5 | 8.6E-2 |
GOTERM_MF_5 | Acyltransferase activity | 9 | 8.7E-2 |
BIOCARTA | Repression of pain sensation by the transcriptional regulator DREAM | 3 | 8.7E-2 |
BIOCARTA | IL12 and Stat4 dependent signaling pathway in Th1 development | 4 | 8.8E-2 |
GOTERM_BP_5 | Anatomical structure formation | 3 | 9.0E-2 |
GOTERM_BP_5 | Formation of primary germ layer | 3 | 9.0E-2 |
GOTERM_MF_5 | Bisphosphoglycerate mutase activity | 2 | 9.0E-2 |
GOTERM_MF_5 | Phosphoglycerate mutase activity | 2 | 9.0E-2 |
GOTERM_BP_5 | Phosphate metabolism | 35 | 9.6E-2 |
BIOCARTA | Rho-selective guanine exchange factor akap13 mediates stress fiber formation | 3 | 9.7E-2 |
KEGG_PATHWAY | Pyruvate metabolism | 6 | 9.8E-2 |
KEGG_PATHWAY | Regulation regulation of actin cytoskeleton | 18 | 9.9E-2 |