Table 1

Functional annotations enriched among genes upregulated* in BMP2+ cells compared to control cells in seven-day-old EBs
Category
 Term
 Count
 p value
GOTERM_MF_5
 Zinc ion binding
 142
 3.2E-16
GOTERM_CC_5
 Nucleus
 279
 3.6E-12
GOTERM_BP_5
 Transcription
 128
 2.5E-10
GOTERM_BP_5
 Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
 121
 5.5E-9
GOTERM_BP_5
 Cellular protein metabolism
 147
 4.9E-8
GOTERM_MF_5
 Binding
 143
 2.9E-7
GOTERM_MF_5
 Metal ion binding
 61
 6.8E-7
GOTERM_MF_5
 Transition metal ion binding
 74
 4.1E-6
GOTERM_MF_5
 Cation binding
 74
 4.6E-6
GOTERM_MF_5
 Ion binding
 74
 4.6E-6
GOTERM_BP_5
 Biopolymer modification
 83
 1.3E-5
GOTERM_BP_5
 Response to unfolded protein
 12
 2.5E-5
GOTERM_MF_5
 ATP binding
 84
 6.8E-5
GOTERM_BP_5
 Apoptosis
 38
 1.2E-4
GOTERM_CC_5
 Intracellular membrane-bound organelle
 225
 2.4E-4
GOTERM_CC_5
 Membrane-bound organelle
 225
 2.4E-4
GOTERM_BP_5
 Regulation of protein kinase activity
 12
 3.1E-4
GOTERM_MF_5
 Protein kinase activity
 44
 4.9E-4
KEGG_PATHWAY
 MAPK signaling pathway
 24
 7.1E-4
GOTERM_BP_5
 Nucleobase, nucleoside, nucleotide and nucleic acid metabolism
 18
 1.7E-3
GOTERM_BP_5
 Regulation of programmed cell death
 24
 1.9E-3
GOTERM_CC_5
 Intracellular
 244
 3.3E-3
GOTERM_BP_5
 Response to protein stimulus
 6
 3.4E-3
GOTERM_CC_5
 Vacuole
 17
 3.4E-3
GOTERM_BP_5
 Phosphate metabolism
 45
 3.7E-3
GOTERM_BP_5
 Cell death
 16
 4.1E-3
GOTERM_BP_5
 Death
 16
 4.1E-3
GOTERM_BP_5
 Programmed cell death
 16
 4.1E-3
GOTERM_BP_5
 Negative regulation of cellular metabolism
 17
 5.6E-3
BIOCARTA
 The information-processing pathway at the IFN-β enhancer
 4
 6.2E-3
GOTERM_BP_5
 Regulation of apoptosis
 22
 6.7E-3
GOTERM_BP_5
 Protein kinase cascade
 17
 6.8E-3
GOTERM_BP_5
 Embryonic development
 15
 7.2E-3
GOTERM_MF_5
 Nucleotide binding
 41
 8.9E-3
GOTERM_CC_5
 Intracellular organelle
 243
 9.0E-3
GOTERM_CC_5
 Organelle
 243
 9.0E-3
GOTERM_BP_5
 Negative regulation of progression through cell cycle
 10
 9.3E-3
GOTERM_BP_5
 Regulation of progression through cell cycle
 24
 9.7E-3
GOTERM_BP_5
 Positive regulation of programmed cell death
 12
 1.2E-2
GOTERM_BP_5
 Embryonic limb morphogenesis
 7
 1.5E-2
GOTERM_MF_5
 Pyrophosphatase activity
 29
 2.1E-2
BIOCARTA
 Regulation of transcriptional activity by PML
 4
 2.2E-2
GOTERM_BP_5
 Cellular physiological process
 112
 2.3E-2
GOTERM_MF_5
 Purine nucleotide binding
 52
 2.4E-2
GOTERM_BP_5
 Embryonic development (sensu Mammalia)
 7
 2.7E-2
GOTERM_CC_5
 Lytic vacuole
 13
 2.8E-2
GOTERM_BP_5
 Negative regulation of protein kinase activity
 5
 2.8E-2
GOTERM_BP_5
 Regulation of biological process
 34
 2.9E-2
GOTERM_CC_5
 Cell
 256
 3.0E-2
GOTERM_BP_5
 Regulation of cellular process
 29
 3.4E-2
GOTERM_BP_5
 Regulation of protein biosynthesis
 9
 3.8E-2
GOTERM_MF_5
 Transcription cofactor activity
 9
 3.8E-2
GOTERM_MF_5
 Transcription factor binding
 9
 4.0E-2
GOTERM_BP_5
 Negative regulation of programmed cell death
 9
 4.2E-2
GOTERM_BP_5
 Protein catabolism
 13
 4.2E-2
GOTERM_BP_5
 Regulation of gene expression, epigenetic
 3
 4.2E-2
GOTERM_MF_5
 Protein kinase binding
 6
 4.3E-2
GOTERM_BP_5
 Primary metabolism
 35
 4.5E-2
GOTERM_BP_5
 RNA metabolism
 22
 4.5E-2
GOTERM_BP_5
 Regulation of cellular biosynthesis
 9
 4.7E-2
GOTERM_MF_5
 Guanyl nucleotide binding
 14
 4.8E-2
GOTERM_BP_5
 Reproduction
 11
 4.8E-2
GOTERM_BP_5
 Response to abiotic stimulus
 13
 4.8E-2
GOTERM_BP_5
 Gene silencing
 4
 5.0E-2
KEGG_PATHWAY
 Pantothenate and CoA biosynthesis
 4
 5.0E-2
GOTERM_BP_5
 Physiological process
 127
 5.1E-2
GOTERM_BP_5
 Bone resorption
 3
 5.2E-2
GOTERM_MF_5
 Cysteine-type peptidase activity
 9
 5.2E-2
GOTERM_MF_5
 Ligase activity
 17
 5.4E-2
GOTERM_BP_5
 Response to chemical stimulus
 11
 5.4E-2
GOTERM_BP_5
 Regulation of bone remodeling
 4
 5.6E-2
GOTERM_BP_5
 Biopolymer catabolism
 13
 6.1E-2
KEGG_PATHWAY
 Nitrogen metabolism
 4
 6.3E-2
GOTERM_BP_5
 ER-nuclear signaling pathway
 3
 6.4E-2
GOTERM_BP_5
 Regulation of protein metabolism
 13
 6.4E-2
GOTERM_CC_5
 Nucleolus
 12
 7.1E-2
GOTERM_BP_5
 Protein biosynthesis
 30
 7.3E-2
GOTERM_MF_5
 Transcription corepressor activity
 6
 7.3E-2
GOTERM_BP_5
 Intracellular receptor-mediated signaling pathway
 3
 7.6E-2
GOTERM_MF_5
 Transcription regulator activity
 9
 7.7E-2
GOTERM_BP_5
 Macromolecule biosynthesis
 33
 8.0E-2
GOTERM_BP_5
 Positive regulation of cell proliferation
 9
 8.1E-2
GOTERM_BP_5
 Embryonic hemopoiesis
 2
 8.2E-2
GOTERM_BP_5
 Posttranscriptional gene silencing
 2
 8.2E-2
GOTERM_BP_5
 RNA-mediated gene silencing
 2
 8.2E-2
GOTERM_BP_5
 RNA-mediated posttranscriptional gene silencing
 2
 8.2E-2
GOTERM_MF_5
 Glutaminase activity
 2
 8.4E-2
GOTERM_MF_5
 Ubiquitin-protein ligase activity
 16
 8.4E-2
GOTERM_BP_5
 Eye development
 5
 8.6E-2
BIOCARTA
 Eukaryotic protein translation
 3
 9.0E-2
GOTERM_BP_5
 Amino acid transport
 6
 9.1E-2
GOTERM_BP_5
 Positive regulation of cell activation
 5
 9.2E-2
GOTERM_BP_5
 Development
 37
 9.3E-2

*Change fold >2, Student's t-test p value < 0.01. Count indicates the number of genes in the functional annotation category. The p value is from gene enrichment in annotation terms calculated by the Fisher's exact t-test.

Doss et al. Genome Biology 2007 8:R184   doi:10.1186/gb-2007-8-9-r184

Open Data