Table 2 |
||||||
|
MAPPFinder results for genes significantly increased and significantly decreased in 12.5-day embryos versus adult mice |
||||||
|
GO name |
Number changed |
Number measured |
Number in GO |
% Changed |
% Present |
z score |
|
|
||||||
|
Significantly increased |
||||||
|
Process |
||||||
|
Mitotic cell cycle |
44 |
70 |
89 |
62.9 |
78.7 |
8.1631 |
|
DNA metabolism |
67 |
135 |
163 |
49.6 |
82.8 |
7.6807 |
|
mRNA splicing |
19 |
21 |
30 |
90.5 |
70 |
7.4868 |
|
RNA processing |
29 |
41 |
60 |
70.7 |
68.3 |
7.4411 |
|
RNA metabolism |
30 |
44 |
66 |
68.2 |
66.7 |
7.3038 |
|
Cell cycle |
98 |
240 |
291 |
40.8 |
82.5 |
7.0096 |
|
mRNA processing |
24 |
33 |
45 |
72.7 |
73.3 |
6.9456 |
|
Protein biosynthesis |
52 |
104 |
152 |
50 |
68.4 |
6.8095 |
|
Macromolecule biosynthesis |
57 |
121 |
172 |
47.1 |
70.3 |
6.5863 |
|
DNA replication |
28 |
46 |
55 |
60.9 |
83.6 |
6.2752 |
|
DNA replication and chromosome cycle |
29 |
49 |
62 |
59.2 |
79 |
6.1944 |
|
Ribosome biogenesis |
19 |
28 |
37 |
67.9 |
75.7 |
5.7749 |
|
Biosynthesis |
89 |
242 |
334 |
36.8 |
72.5 |
5.4866 |
|
DNA dependent DNA replication |
13 |
18 |
22 |
72.2 |
81.8 |
5.0697 |
|
Mitosis |
13 |
18 |
24 |
72.2 |
75 |
5.0697 |
|
Nuclear division |
14 |
21 |
30 |
66.7 |
70 |
4.8663 |
|
DNA packaging |
20 |
36 |
46 |
55.6 |
78.3 |
4.7782 |
|
Cell organization and biogenesis |
74 |
207 |
294 |
35.7 |
70.4 |
4.6913 |
|
M phase |
15 |
25 |
36 |
60 |
69.4 |
4.5110 |
|
mRNA splice site selection |
7 |
8 |
8 |
87.5 |
100 |
4.4125 |
|
DNA replication initiation |
6 |
7 |
7 |
85.7 |
100 |
4.0138 |
|
Chromosome organization and biogenesis (sensu Eukarya) |
18 |
37 |
51 |
48.6 |
72.5 |
3.8338 |
|
DNA repair |
21 |
46 |
53 |
45.7 |
86.8 |
3.7895 |
|
Protein folding |
12 |
22 |
31 |
54.5 |
71 |
3.6157 |
|
Cytoplasm organization and biogenesis |
56 |
169 |
241 |
33.1 |
70.1 |
3.3912 |
|
Establishment and/or maintenance of chromatin architecture |
13 |
27 |
35 |
48.1 |
77.1 |
3.2089 |
|
Protein synthesis elongation |
6 |
9 |
37 |
66.7 |
24.3 |
3.1815 |
|
Chromatin assembly/disassembly |
10 |
20 |
25 |
50 |
80 |
2.9585 |
|
Biological process unknown |
34 |
98 |
250 |
34.7 |
39.2 |
2.9354 |
|
Protein-ligand dependent protein degradation |
17 |
43 |
58 |
39.5 |
74.1 |
2.6968 |
|
Ubiquitin-dependent protein degradation |
16 |
42 |
57 |
38.1 |
73.7 |
2.4404 |
|
Protein-nucleus import |
5 |
9 |
10 |
55.6 |
90 |
2.3820 |
|
Ubiquitin cycle |
6 |
12 |
16 |
50 |
75 |
2.2896 |
|
Nucleocytoplasmic transport |
6 |
12 |
17 |
50 |
70.6 |
2.2896 |
|
Actin cytoskeleton organization and biogenesis |
6 |
12 |
19 |
50 |
63.2 |
2.2896 |
|
Transmembrane receptor protein Ser/Thr kinase signaling pathway |
10 |
25 |
31 |
40 |
80.6 |
2.1081 |
|
Induction of apoptosis |
7 |
16 |
24 |
43.8 |
66.7 |
2.0449 |
|
Component |
||||||
|
Spliceosome |
17 |
20 |
42 |
85 |
47.6 |
6.7175 |
|
Cytosolic ribosome (sensu Eukarya) |
19 |
26 |
33 |
73.1 |
78.8 |
6.2032 |
|
Cytosol |
40 |
85 |
112 |
47.1 |
75.9 |
5.4872 |
|
Ribosome |
35 |
71 |
93 |
49.3 |
76.3 |
5.4624 |
|
Chromosome |
19 |
36 |
55 |
52.8 |
65.5 |
4.3772 |
|
Nuclear envelope-endoplasmic reticulum network |
9 |
12 |
17 |
75 |
70.6 |
4.3676 |
|
Adherens junction |
6 |
7 |
14 |
85.7 |
50 |
4.0138 |
|
Endoplasmic reticulum membrane |
7 |
9 |
13 |
77.8 |
69.2 |
3.9811 |
|
Chromatin |
15 |
28 |
41 |
53.6 |
68.3 |
3.9579 |
|
Cellular component unknown |
41 |
117 |
291 |
35 |
40.2 |
3.3057 |
|
Nucleolus |
10 |
19 |
34 |
52.6 |
55.9 |
3.1587 |
|
26S proteasome |
11 |
22 |
23 |
50 |
95.7 |
3.1036 |
|
Endoplasmic reticulum |
39 |
117 |
141 |
33.3 |
83 |
2.8569 |
|
20S core proteasome |
9 |
19 |
19 |
47.4 |
100 |
2.6078 |
|
Nuclear membrane |
6 |
11 |
18 |
54.5 |
61.1 |
2.5536 |
|
Cytoskeleton |
64 |
223 |
306 |
28.7 |
72.9 |
2.2918 |
|
Collagen |
10 |
25 |
31 |
40 |
80.6 |
2.1081 |
|
Golgi membrane |
7 |
16 |
18 |
43.8 |
88.9 |
2.0449 |
|
Actin cytoskeleton |
16 |
46 |
63 |
34.8 |
73 |
2.0140 |
|
Function |
||||||
|
RNA binding |
51 |
113 |
155 |
45.1 |
72.9 |
5.8498 |
|
Cyclin-dependent protein kinase |
17 |
24 |
33 |
70.8 |
72.7 |
5.6944 |
|
Structural constituent of ribosome |
39 |
83 |
101 |
47 |
82.2 |
5.4055 |
|
Cyclin-dependent protein kinase, regulator |
12 |
17 |
24 |
70.6 |
70.8 |
4.7646 |
|
Structural molecule |
77 |
223 |
278 |
34.5 |
80.2 |
4.4306 |
|
Pre-mRNA splicing factor |
7 |
8 |
12 |
87.5 |
66.7 |
4.4125 |
|
mRNA binding |
10 |
14 |
19 |
71.4 |
73.7 |
4.3979 |
|
Protein serine/threonine kinase |
62 |
181 |
243 |
34.3 |
74.5 |
3.8821 |
|
Actin binding |
25 |
58 |
83 |
43.1 |
69.9 |
3.7927 |
|
Proteasome endopeptidase |
11 |
19 |
19 |
57.9 |
100 |
3.7096 |
|
DNA-directed DNA polymerase |
7 |
10 |
15 |
70 |
66.7 |
3.6069 |
|
RHO small monomeric GTPase |
7 |
10 |
10 |
70 |
100 |
3.6069 |
|
Nucleotidyltransferase |
16 |
33 |
41 |
48.5 |
80.5 |
3.5964 |
|
Kinase regulator |
15 |
33 |
42 |
45.5 |
78.6 |
3.1777 |
|
DNA dependent adenosinetriphosphatase |
8 |
14 |
16 |
57.1 |
87.5 |
3.1151 |
|
Cytoskeletal protein binding |
33 |
93 |
144 |
35.5 |
64.6 |
3.0423 |
|
DNA repair protein |
11 |
23 |
27 |
47.8 |
85.2 |
2.9232 |
|
Translation factor, nucleic acid binding |
14 |
32 |
43 |
43.8 |
74.4 |
2.8970 |
|
Transcription co-activator |
6 |
10 |
14 |
60 |
71.4 |
2.8483 |
|
Chromatin binding |
5 |
8 |
11 |
62.5 |
72.7 |
2.7166 |
|
Kinase |
89 |
311 |
394 |
28.6 |
78.9 |
2.6983 |
|
Phosphotransferase, alcohol group as acceptor |
87 |
305 |
386 |
28.5 |
79 |
2.6301 |
|
Protein kinase |
76 |
263 |
336 |
28.9 |
78.3 |
2.5796 |
|
Exonuclease |
6 |
11 |
15 |
54.5 |
73.3 |
2.5536 |
|
Small monomeric GTPase |
15 |
38 |
46 |
39.5 |
82.6 |
2.5247 |
|
GTP binding |
43 |
141 |
201 |
30.5 |
70.1 |
2.3248 |
|
Peptidylprolyl cis-trans isomerase |
6 |
12 |
16 |
50 |
75 |
2.2896 |
|
Translation elongation factor |
6 |
12 |
16 |
50 |
75 |
2.2896 |
|
Transcription factor binding |
11 |
27 |
43 |
40.7 |
62.8 |
2.2838 |
|
Guanyl nucleotide binding |
46 |
155 |
219 |
29.7 |
70.8 |
2.1927 |
|
Adenosinetriphosphatase |
12 |
31 |
38 |
38.7 |
81.6 |
2.1763 |
|
Molecular_function unknown |
29 |
91 |
230 |
31.9 |
39.6 |
2.1739 |
|
Protein binding |
99 |
368 |
539 |
26.9 |
68.3 |
2.1328 |
|
Chaperone |
16 |
45 |
62 |
35.6 |
72.6 |
2.1166 |
|
Extracellular matrix structural constituent conferring tensile strength |
10 |
25 |
31 |
40 |
80.6 |
2.1081 |
|
DNA-directed RNA polymerase |
5 |
10 |
11 |
50 |
90.9 |
2.0897 |
|
Structural constituent of cytoskeleton |
21 |
63 |
79 |
33.3 |
79.7 |
2.0838 |
|
Transferase, transferring one-carbon groups |
8 |
19 |
29 |
42.1 |
65.5 |
2.0570 |
|
GTPase |
25 |
78 |
95 |
32.1 |
82.1 |
2.0488 |
|
Isomerase |
12 |
32 |
42 |
37.5 |
76.2 |
2.0468 |
|
Significantly decreased |
||||||
|
Process |
||||||
|
Fatty acid metabolism |
19 |
30 |
41 |
63.3 |
73.2 |
5.9082 |
|
Main pathways of carbohydrate metabolism |
20 |
39 |
50 |
51.3 |
78 |
4.8600 |
|
Energy derivation by oxidation of organic compounds |
23 |
50 |
66 |
46 |
75.8 |
4.5739 |
|
Catabolic carbohydrate metabolism |
18 |
36 |
45 |
50 |
80 |
4.4754 |
|
Tricarboxylic acid cycle |
6 |
8 |
10 |
75 |
80 |
3.8664 |
|
Hexose metabolism |
18 |
41 |
49 |
43.9 |
83.7 |
3.8016 |
|
Lipid metabolism |
42 |
127 |
167 |
33.1 |
76 |
3.6708 |
|
Lipid transport |
5 |
7 |
11 |
71.4 |
63.6 |
3.3807 |
|
Glycolysis |
12 |
26 |
32 |
46.2 |
81.2 |
3.3091 |
|
Peroxisome organization and biogenesis |
7 |
12 |
15 |
58.3 |
80 |
3.2972 |
|
Glucose metabolism |
15 |
36 |
42 |
41.7 |
85.7 |
3.2247 |
|
Lymph gland development |
8 |
15 |
17 |
53.3 |
88.2 |
3.2043 |
|
Cell proliferation |
10 |
21 |
34 |
47.6 |
61.8 |
3.1400 |
|
Humoral immune response |
15 |
37 |
79 |
40.5 |
46.8 |
3.0982 |
|
Carbohydrate metabolism |
31 |
95 |
135 |
32.6 |
70.4 |
3.0557 |
|
Regulation of cell proliferation |
5 |
8 |
15 |
62.5 |
53.3 |
2.9848 |
|
Muscle contraction |
9 |
20 |
28 |
45 |
71.4 |
2.7716 |
|
Muscle development |
13 |
34 |
43 |
38.2 |
79.1 |
2.6328 |
|
Mesoderm development |
28 |
90 |
111 |
31.1 |
81.1 |
2.6096 |
|
Potassium transport |
17 |
49 |
60 |
34.7 |
81.7 |
2.5450 |
|
Metal ion transport |
24 |
77 |
100 |
31.2 |
77 |
2.4230 |
|
Monovalent inorganic cation transport |
21 |
67 |
88 |
31.3 |
76.1 |
2.2935 |
|
Complement activation |
8 |
20 |
23 |
40 |
87 |
2.2132 |
|
Cation transport |
28 |
98 |
135 |
28.6 |
72.6 |
2.0923 |
|
Electron transport |
25 |
87 |
113 |
28.7 |
77 |
2.0075 |
|
Component |
||||||
|
Mitochondrion |
88 |
187 |
293 |
47.1 |
63.8 |
9.3508 |
|
Peroxisome |
18 |
29 |
42 |
62.1 |
69 |
5.6381 |
|
Mitochondrial inner membrane |
19 |
36 |
60 |
52.8 |
60 |
4.8922 |
|
Mitochondrial electron transport chain complex |
10 |
14 |
32 |
71.4 |
43.8 |
4.7848 |
|
Mitochondrial membrane |
20 |
40 |
72 |
50 |
55.6 |
4.7195 |
|
Cytochrome C oxidase |
6 |
8 |
16 |
75 |
50 |
3.8664 |
|
Mitochondrial matrix |
9 |
22 |
33 |
40.9 |
66.7 |
2.4283 |
|
Basement lamina |
5 |
11 |
11 |
45.5 |
100 |
2.0910 |
|
Cytoskeleton |
57 |
223 |
306 |
25.6 |
72.9 |
2.0527 |
|
Function |
||||||
|
Hydrogen ion transporter |
11 |
15 |
33 |
73.3 |
45.5 |
5.1373 |
|
Primary active transporter |
27 |
64 |
107 |
42.2 |
59.8 |
4.4175 |
|
Cation transporter |
17 |
36 |
61 |
47.2 |
59 |
4.0585 |
|
Ion transporter |
19 |
43 |
79 |
44.2 |
54.4 |
3.9406 |
|
Cytochrome c oxidase |
6 |
8 |
16 |
75 |
50 |
3.8664 |
|
Oxidoreductase |
48 |
149 |
207 |
32.2 |
72 |
3.7213 |
|
Major histocompatibility complex antigen |
13 |
30 |
54 |
43.3 |
55.6 |
3.1700 |
|
Oxidoreductase, acting on the aldehyde or oxo group of donors |
7 |
13 |
16 |
53.8 |
81.2 |
3.0285 |
|
Carrier |
40 |
131 |
196 |
30.5 |
66.8 |
2.9960 |
|
Complement component |
8 |
16 |
19 |
50 |
84.2 |
2.9770 |
|
P-type ATPase |
5 |
9 |
11 |
55.6 |
81.8 |
2.6467 |
|
Hydrolase, acting on acid anhydrides, catalyzing transmembrane movement of substances |
15 |
42 |
67 |
35.7 |
62.7 |
2.5199 |
|
Nucleobase, nucleoside, nucleotide kinase |
7 |
16 |
19 |
43.8 |
84.2 |
2.3531 |
|
Phosphotransferase, phosphate group as acceptor |
5 |
10 |
13 |
50 |
76.9 |
2.3520 |
|
Glutathione transferase |
5 |
10 |
13 |
50 |
76.9 |
2.3520 |
|
P-P-bond-hydrolysis-driven transporter |
17 |
52 |
78 |
32.7 |
66.7 |
2.2609 |
|
ATP-binding cassette (ABC) transporter |
11 |
30 |
50 |
36.7 |
60 |
2.2573 |
|
Potassium channel |
15 |
45 |
56 |
33.3 |
80.4 |
2.2093 |
|
Carbon-carbon lyase |
5 |
11 |
18 |
45.5 |
61.1 |
2.0910 |
|
|
||||||
|
All terms with a z score of 2 and at least 5, but less than 100 genes meeting the criterion are shown. |
||||||
|
Doniger et al. Genome Biology 2003 4:R7 doi:10.1186/gb-2003-4-1-r7 |
||||||
