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

Lederer, Carsten W; Torrisi, Antonietta; Pantelidou, Maria; Santama, Niovi; Cavallaro, Sebastiano

doi:10.1186/1471-2164-8-26

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.

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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ISSN: 1471-2164

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