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Table 2 Differentially regulated GO categories

From: Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis

Up-regulated GO categories       
GO ID GO Name GO Type Number Changed Number Measured Percent Changed z Score corrected P
6955 immune response BP 106 346 30.64 7.84 0
9607 response to biotic stimulus BP 130 456 28.51 7.77 0
6952 defense response BP 113 381 29.66 7.71 0
50874 organismal physiological process BP 208 859 24.21 7.30 0
50896 response to stimulus BP 215 941 22.85 6.45 0
43207 response to external biotic stimulus BP 71 235 30.21 6.24 0
9613 response to pest\, pathogen or parasite BP 69 228 30.26 6.16 0
9605 response to external stimulus BP 134 563 23.80 5.51 0.01
4871 signal transducer activity MF 251 1199 20.93 5.44 0.011
9596 detection of pest\, pathogen or parasite BP 5 5 100.00 5.19 0.047
2453 probes met the [fold-change]>=1.2 criterion.
1782 probes meeting the filter linked to an Ensembl ID.
1323 genes meeting the criterion linked to a GO term.
The z score is based on an N of 8457 and an R of 1323 distinct genes in the GO.
Down-regulated GO categories       
GO ID GO Name GO Type Number Changed Number Measured Percent Changed z Score corrected P
15077 monovalent inorganic cation transporter activity MF 86 120 71.67 13.88 0
15078 hydrogen ion transporter activity MF 80 111 72.07 13.44 0
15399 primary active transporter activity MF 88 131 67.18 13.23 0
16655 oxidoreductase activity\, acting on NADH or NADPH\, quinone or similar compound as acceptor MF 37 42 88.10 10.81 0
5739 mitochondrion CC 186 459 40.52 10.78 0
3954 NADH dehydrogenase activity MF 34 38 89.47 10.49 0
6119 oxidative phosphorylation BP 47 64 73.44 10.45 0
50136 NADH dehydrogenase (quinone) activity MF 33 37 89.19 10.30 0
8137 NADH dehydrogenase (ubiquinone) activity MF 33 37 89.19 10.30 0
16651 oxidoreductase activity\, acting on NADH or NADPH MF 43 57 75.44 10.23 0
15081 sodium ion transporter activity MF 34 40 85.00 10.06 0
19866 inner membrane CC 62 114 54.39 8.94 0
42775 ATP synthesis coupled electron transport (sensu Eukaryota) BP 22 24 91.67 8.59 0
5737 cytoplasm CC 547 1987 27.53 8.58 0
6091 generation of precursor metabolites and energy BP 143 375 38.13 8.52 0
8324 cation transporter activity MF 127 324 39.20 8.38 0
42773 ATP synthesis coupled electron transport BP 22 25 88.00 8.32 0
5740 mitochondrial membrane CC 59 115 51.30 8.15 0
46873 metal ion transporter activity MF 42 70 60.00 8.15 0
15075 ion transporter activity MF 146 397 36.78 8.10 0
5386 carrier activity MF 109 271 40.22 8.06 0
6120 mitochondrial electron transport\, NADH to ubiquinone BP 19 21 90.48 7.90 0
5743 mitochondrial inner membrane CC 48 89 53.93 7.78 0
6096 glycolysis BP 22 30 73.33 7.13 0
6754 ATP biosynthesis BP 26 41 63.41 6.77 0
6753 nucleoside phosphate metabolism BP 26 41 63.41 6.77 0
9206 purine ribonucleoside triphosphate biosynthesis BP 30 51 58.82 6.74 0
9145 purine nucleoside triphosphate biosynthesis BP 30 51 58.82 6.74 0
9201 ribonucleoside triphosphate biosynthesis BP 30 51 58.82 6.74 0
6092 main pathways of carbohydrate metabolism BP 35 64 54.69 6.74 0
15992 proton transport BP 31 54 57.41 6.68 0
16818 hydrolase activity\, acting on acid anhydrides\, in phosphorus-containing anhydrides MF 124 358 34.64 6.65 0
16817 hydrolase activity\, acting on acid anhydrides MF 124 358 34.64 6.65 0
9142 nucleoside triphosphate biosynthesis BP 30 52 57.69 6.60 0
15405 P-P-bond-hydrolysis-driven transporter activity MF 36 68 52.94 6.59 0
9199 ribonucleoside triphosphate metabolism BP 31 55 56.36 6.55 0
9144 purine nucleoside triphosphate metabolism BP 31 55 56.36 6.55 0
6818 hydrogen transport BP 31 55 56.36 6.55 0
9205 purine ribonucleoside triphosphate metabolism BP 31 55 56.36 6.55 0
46034 ATP metabolism BP 27 45 60.00 6.52 0
16462 pyrophosphatase activity MF 122 356 34.27 6.45 0
46961 hydrogen-transporting ATPase activity\, rotational mechanism MF 23 36 63.89 6.41 0
16469 proton-transporting two-sector ATPase complex CC 23 36 63.89 6.41 0
9152 purine ribonucleotide biosynthesis BP 33 62 53.23 6.34 0
9141 nucleoside triphosphate metabolism BP 31 57 54.39 6.30 0
15985 energy coupled proton transport\, down electrochemical gradient BP 23 37 62.16 6.24 0
6007 glucose catabolism BP 23 37 62.16 6.24 0
15986 ATP synthesis coupled proton transport BP 23 37 62.16 6.24 0
15980 energy derivation by oxidation of organic compounds BP 46 101 45.54 6.20 0
5489 electron transporter activity MF 67 168 39.88 6.20 0
45259 proton-transporting ATP synthase complex CC 10 10 100.00 6.19 0
45255 hydrogen-translocating F-type ATPase complex CC 10 10 100.00 6.19 0
5753 proton-transporting ATP synthase complex (sensu Eukaryota) CC 10 10 100.00 6.19 0
46933 hydrogen-transporting ATP synthase activity\, rotational mechanism MF 22 35 62.86 6.17 0
42625 ATPase activity\, coupled to transmembrane movement of ions MF 32 61 52.46 6.14 0
19829 cation-transporting ATPase activity MF 23 38 60.53 6.07 0
17111 nucleoside-triphosphatase activity MF 114 338 33.73 6.03 0
9150 purine ribonucleotide metabolism BP 33 65 50.77 6.01 0
6164 purine nucleotide biosynthesis BP 33 65 50.77 6.01 0
45298 tubulin BP 15 20 75.00 6.00 0
46785 microtubule polymerization CC 15 20 75.00 6.00 0
9260 ribonucleotide biosynthesis BP 33 66 50.00 5.90 0
31109 microtubule polymerization or depolymerization BP 17 25 68.00 5.84 0
9259 ribonucleotide metabolism BP 34 70 48.57 5.78 0
46164 alcohol catabolism BP 23 40 57.50 5.76 0
46365 monosaccharide catabolism BP 23 40 57.50 5.76 0
19320 hexose catabolism BP 23 40 57.50 5.76 0
6752 group transfer coenzyme metabolism BP 27 51 52.94 5.70 0
6163 purine nucleotide metabolism BP 33 68 48.53 5.69 0
15002 heme-copper terminal oxidase activity MF 13 17 76.47 5.68 0
16676 oxidoreductase activity\, acting on heme group of donors\, oxygen as acceptor MF 13 17 76.47 5.68 0
16675 oxidoreductase activity\, acting on heme group of donors MF 13 17 76.47 5.68 0
4129 cytochrome-c oxidase activity MF 13 17 76.47 5.68 0
6732 coenzyme metabolism BP 45 107 42.06 5.49 0
42626 ATPase activity\, coupled to transmembrane movement of substances MF 36 79 45.57 5.48 0
16820 hydrolase activity\, acting on acid anhydrides\, catalyzing transmembrane movement of substances MF 36 79 45.57 5.48 0
43234 protein complex CC 313 1175 26.64 5.41 0
51186 cofactor metabolism BP 50 125 40.00 5.36 0
6006 glucose metabolism BP 27 54 50.00 5.33 0
5215 transporter activity MF 240 871 27.55 5.27 0
45333 cellular respiration BP 17 28 60.71 5.23 0
51258 protein polymerization BP 18 31 58.06 5.14 0.002
226 microtubule cytoskeleton organization and biogenesis BP 25 50 50.00 5.13 0.004
31090 organelle membrane CC 89 270 32.96 5.05 0.004
7017 microtubule-based process BP 38 93 40.86 4.82 0.01
502 proteasome complex (sensu Eukaryota) CC 18 33 54.55 4.81 0.016
16052 carbohydrate catabolism BP 24 50 48.00 4.78 0.025
44275 cellular carbohydrate catabolism BP 24 50 48.00 4.78 0.025
9117 nucleotide metabolism BP 48 128 37.50 4.73 0.026
6118 electron transport BP 73 220 33.18 4.63 0.043
3924 GTPase activity MF 44 116 37.93 4.61 0.043
16491 oxidoreductase activity MF 115 383 30.03 4.61 0.044
5829 cytosol CC 69 207 33.33 4.54 0.045
9165 nucleotide biosynthesis BP 38 97 39.18 4.52 0.045
3059 probes met the [fold-change]<=(1/1.2) criterion.
2522 probes meeting the filter linked to an Ensembl ID.
1751 genes meeting the criterion linked to a GO term.
The z score is based on an N of 8457 and an R of 1751 distinct genes in the GO.
  1. Shown are all GO nodes differentially regulated between SALS motor-cortex-patient samples and controls for the comprehensive dataset. Of 19,431 probes in the dataset, 8,457 were linked to a GO term. Nodes are sorted by up- or down-regulation (top and bottom sub-tables, respectively), then sorted by corrected P value (lowest first) and z value (highest first). CC – cellular component; MF – molecular function; BP – biological process
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