Download a compressed file (GO_Compressed.zip (35.5 MB)) including all of the individual GO files. This zip file contains every raw and intermediate files, some of which are available on this web page.

Gene Ontology Enrichment Section is composed of 9 results. For the three Gene Ontology categories (Biological Processes, Molecular Functions, and Cellular Components), three different sets of Gene Ontology terms are used.
   Explicit GO: Only use GO terms that are explicitly assigned to the target gene.
   Full GO: Use both explicitly assigned GO terms and implicitly assigned terms. Implicit terms are all the parent terms of explicity GO terms from the GO tree structure.
   Level 2~5: Use only the highest 4 levels of GO terms. These can generally provide functional categories due to their broad meanings. GO assignements are based on the full GO.

Biological Processes

Top 10 most enriched GO terms (Biological Process -- Level 2~5) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level4	GO:0006800	oxygen and reactive oxygen species metabolic process	13	40	49	25205	2.33e-23	0.25	0.00	126.4
2	Level5	GO:0006801	superoxide metabolic process	11	42	21	25233	1.40e-22	0.21	0.00	249.6
3	Level3	GO:0006950	response to stress	28	25	1572	23682	4.09e-20	0.53	0.06	8.5
4	Level2	GO:0050896	response to stimulus	35	18	3524	21730	6.21e-18	0.66	0.14	4.7
5	Level3	GO:0042221	response to chemical stimulus	19	34	827	24427	3.04e-15	0.36	0.03	10.9
6	Level5	GO:0000302	response to reactive oxygen species	8	45	36	25218	3.56e-14	0.15	0.00	105.9
7	Level4	GO:0003013	circulatory system process	12	41	240	25014	1.36e-13	0.23	0.01	23.8
8	Level5	GO:0008015	blood circulation	12	41	240	25014	1.36e-13	0.23	0.01	23.8
9	Level3	GO:0009605	response to external stimulus	18	35	962	24292	5.91e-13	0.34	0.04	8.9
10	Level3	GO:0006118	electron transport	13	40	386	24868	1.46e-12	0.25	0.02	16.0

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Top 10 most enriched GO terms (Biological Process -- Full GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0006800	oxygen and reactive oxygen species metabolic process	13	40	49	25205	2.33e-23	0.25	0.00	126.4
2		GO:0006801	superoxide metabolic process	11	42	21	25233	1.40e-22	0.21	0.00	249.6
3		GO:0006950	response to stress	28	25	1572	23682	4.09e-20	0.53	0.06	8.5
4		GO:0050896	response to stimulus	35	18	3524	21730	6.21e-18	0.66	0.14	4.7
5		GO:0042221	response to chemical stimulus	19	34	827	24427	3.04e-15	0.36	0.03	10.9
6		GO:0000302	response to reactive oxygen species	8	45	36	25218	3.56e-14	0.15	0.00	105.9
7		GO:0008015	blood circulation	12	41	240	25014	1.36e-13	0.23	0.01	23.8
8		GO:0003013	circulatory system process	12	41	240	25014	1.36e-13	0.23	0.01	23.8
9		GO:0009605	response to external stimulus	18	35	962	24292	5.91e-13	0.34	0.04	8.9
10		GO:0006118	electron transport	13	40	386	24868	1.46e-12	0.25	0.02	16.0

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Top 10 most enriched GO terms (Biological Process -- Explicit GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0006801	superoxide metabolic process	7	46	11	25243	3.66e-15	0.13	0.00	303.2
2		GO:0006118	electron transport	13	40	386	24868	1.46e-12	0.25	0.02	16.0
3		GO:0042554	superoxide release	5	48	8	25246	4.22e-11	0.09	0.00	297.8
4		GO:0008217	regulation of blood pressure	7	46	61	25193	1.03e-10	0.13	0.00	54.7
5		GO:0000303	response to superoxide	4	49	5	25249	2.14e-09	0.08	0.00	381.2
6		GO:0001666	response to hypoxia	6	47	74	25180	1.68e-08	0.11	0.00	38.6
7		GO:0006809	nitric oxide biosynthetic process	4	49	17	25237	9.99e-08	0.08	0.00	112.1
8		GO:0015992	proton transport	5	48	80	25174	9.59e-07	0.09	0.00	29.8
9		GO:0006091	generation of precursor metabolites and energy	5	48	101	25153	2.87e-06	0.09	0.00	23.6
10		GO:0006979	response to oxidative stress	5	48	104	25150	3.29e-06	0.09	0.00	22.9

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Molecular Functions

Top 10 most enriched GO terms (Molecular Function -- Level 2~5) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level3	GO:0016491	oxidoreductase activity	25	28	950	24304	1.05e-21	0.47	0.04	12.5
2	Level4	GO:0009055	electron carrier activity	17	36	330	24924	2.99e-19	0.32	0.01	24.5
3	Level5	GO:0050660	FAD binding	10	43	89	25165	8.93e-15	0.19	0.00	53.5
4	Level3	GO:0046906	tetrapyrrole binding	11	42	178	25076	1.74e-13	0.21	0.01	29.4
5	Level4	GO:0020037	heme binding	11	42	178	25076	1.74e-13	0.21	0.01	29.4
6	Level2	GO:0005488	binding	51	2	12737	12517	3.45e-13	0.96	0.50	1.9
7	Level4	GO:0050662	coenzyme binding	11	42	196	25058	4.74e-13	0.21	0.01	26.7
8	Level3	GO:0048037	cofactor binding	12	41	276	24978	6.61e-13	0.23	0.01	20.7
9	Level2	GO:0003824	catalytic activity	36	17	5927	19327	9.23e-12	0.68	0.23	2.9
10	Level5	GO:0046914	transition metal ion binding	26	27	2996	22258	3.41e-11	0.49	0.12	4.1

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Top 10 most enriched GO terms (Molecular Function -- Full GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0016491	oxidoreductase activity	25	28	950	24304	1.05e-21	0.47	0.04	12.5
2		GO:0009055	electron carrier activity	17	36	330	24924	2.99e-19	0.32	0.01	24.5
3		GO:0005506	iron ion binding	15	38	355	24899	8.49e-16	0.28	0.01	20.1
4		GO:0050660	FAD binding	10	43	89	25165	8.93e-15	0.19	0.00	53.5
5		GO:0020037	heme binding	11	42	178	25076	1.74e-13	0.21	0.01	29.4
6		GO:0046906	tetrapyrrole binding	11	42	178	25076	1.74e-13	0.21	0.01	29.4
7		GO:0005488	binding	51	2	12737	12517	3.45e-13	0.96	0.50	1.9
8		GO:0050662	coenzyme binding	11	42	196	25058	4.74e-13	0.21	0.01	26.7
9		GO:0048037	cofactor binding	12	41	276	24978	6.61e-13	0.23	0.01	20.7
10		GO:0003824	catalytic activity	36	17	5927	19327	9.23e-12	0.68	0.23	2.9

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Top 10 most enriched GO terms (Molecular Function -- Explicit GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0009055	electron carrier activity	15	38	270	24984	1.75e-17	0.28	0.01	26.5
2		GO:0016491	oxidoreductase activity	18	35	600	24654	2.18e-16	0.34	0.02	14.3
3		GO:0005506	iron ion binding	15	38	338	24916	4.23e-16	0.28	0.01	21.1
4		GO:0050660	FAD binding	10	43	89	25165	8.93e-15	0.19	0.00	53.5
5		GO:0020037	heme binding	11	42	178	25076	1.74e-13	0.21	0.01	29.4
6		GO:0050661	NADP binding	6	47	30	25224	1.17e-10	0.11	0.00	95.3
7		GO:0004784	superoxide dismutase activity	3	50	4	25250	3.02e-07	0.06	0.00	357.4
8		GO:0046872	metal ion binding	19	34	2537	22717	4.56e-07	0.36	0.10	3.6
9		GO:0004517	nitric\-oxide synthase activity	3	50	7	25247	1.03e-06	0.06	0.00	204.2
10		GO:0010181	FMN binding	3	50	15	25239	6.92e-06	0.06	0.00	95.3

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Cellular Components

Top 10 most enriched GO terms (Cellular Component -- Level 2~5) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level4	GO:0000267	cell fraction	14	39	1154	24100	8.18e-08	0.26	0.05	5.8
2	Level3	GO:0044421	extracellular region part	13	40	976	24278	9.03e-08	0.25	0.04	6.3
3	Level3	GO:0044464	cell part	48	5	14508	10746	1.82e-07	0.91	0.57	1.6
4	Level2	GO:0005623	cell	48	5	14509	10745	1.82e-07	0.91	0.57	1.6
5	Level2	GO:0005576	extracellular region	17	36	2112	23142	8.50e-07	0.32	0.08	3.8
6	Level4	GO:0005615	extracellular space	10	43	649	24605	9.51e-07	0.19	0.03	7.3
7	Level5	GO:0005625	soluble fraction	7	46	297	24957	3.23e-06	0.13	0.01	11.2
8	Level2	GO:0031975	envelope	9	44	627	24627	6.24e-06	0.17	0.02	6.8
9	Level4	GO:0016020	membrane	32	21	7607	17647	6.54e-06	0.60	0.30	2.0
10	Level5	GO:0044424	intracellular part	37	16	10247	15007	2.97e-05	0.70	0.41	1.7

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Top 10 most enriched GO terms (Cellular Component -- Full GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0005737	cytoplasm	35	18	6740	18514	2.57e-09	0.66	0.27	2.5
2		GO:0044444	cytoplasmic part	26	27	4034	21220	2.22e-08	0.49	0.16	3.1
3		GO:0000267	cell fraction	14	39	1154	24100	8.18e-08	0.26	0.05	5.8
4		GO:0044421	extracellular region part	13	40	976	24278	9.03e-08	0.25	0.04	6.3
5		GO:0005739	mitochondrion	13	40	1019	24235	1.48e-07	0.25	0.04	6.1
6		GO:0044464	cell part	48	5	14508	10746	1.82e-07	0.91	0.57	1.6
7		GO:0005623	cell	48	5	14509	10745	1.82e-07	0.91	0.57	1.6
8		GO:0005576	extracellular region	17	36	2112	23142	8.50e-07	0.32	0.08	3.8
9		GO:0005615	extracellular space	10	43	649	24605	9.51e-07	0.19	0.03	7.3
10		GO:0031966	mitochondrial membrane	8	45	390	24864	1.67e-06	0.15	0.02	9.8

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Top 10 most enriched GO terms (Cellular Component -- Explicit GO) (sorted by p-value)

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Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1		GO:0005739	mitochondrion	13	40	984	24270	9.91e-08	0.25	0.04	6.3
2		GO:0005615	extracellular space	10	43	623	24631	6.61e-07	0.19	0.02	7.6
3		GO:0005625	soluble fraction	7	46	297	24957	3.23e-06	0.13	0.01	11.2
4		GO:0005576	extracellular region	15	38	1867	23387	4.64e-06	0.28	0.07	3.8
5		GO:0005743	mitochondrial inner membrane	6	47	236	25018	1.13e-05	0.11	0.01	12.1
6		GO:0005624	membrane fraction	8	45	631	24623	5.15e-05	0.15	0.02	6.0
7		GO:0005829	cytosol	7	46	486	24768	7.25e-05	0.13	0.02	6.9
8		GO:0005777	peroxisome	4	49	106	25148	8.40e-05	0.08	0.00	18.0
9		GO:0005737	cytoplasm	19	34	4032	21222	4.41e-04	0.36	0.16	2.2
10		GO:0005833	hemoglobin complex	2	51	17	25237	7.19e-04	0.04	0.00	56.1

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The following table summarizes those targets that were used in this pathway enrichment analysis. Pathway information are derived from KEGG and Reactome databases for each target.

More full results are available.

Test set (all in text file format)	Pathway assignment	Matrix_Type1	Matrix_Type2
Background set (all in text file format)	Pathway assignment	Matrix_Type1	Matrix_Type2

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Top 10 most enriched Pathways (sorted by p-value)

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The following table summarizes the targets (from the tested set) that were used in this PPI network analysis. Background set is the source of the target frequency information for random network generation. For more detail, refer to the Network Significance Test below.

Interaction Network Within Corpus (sorted by degree)

[TABLE] Here is a summary table of the Protein-Protein Interaction network data of the test set. This table basically shows how many targets are interacting each other within the test set.

[TABLE] Top 10 interacting targets within the test set

Rank	Target Symbol	Num of Direct Interactions	MiMI Network
1	RAC1	10
2	NFKB1	9
3	NCF1	8
4	UCP2	6
5	CYBA	6
6	NCF4	5
7	CYBB	5
8	NOS3	5
9	NCF2	5
10	PRKCA	4

View your full list in a TEXT or EXCEL file.

View the full merged network in cytoscape SIF (MiMI Network File). This file has to be downloaded first and imported into a Cytoscape program.

Network Significance Test (100 iteration of random genes with size of 1026 from total of 25254 genes)

This Network Significance Test section will test the integrity of the Protein-Protein Interaction network among the test set targets. This is based on the assumption that targets commonly related to a certain topic will be more likely to have frequent protein-protein interaction with each others. Therefore, if a set of targets identified by text-mining (SciMiner) from a certain query have more frequent direct interactions among the targets compared to randomly generated sets, it can, in part, support the validity of using text-mining method to identify related targets from a set of related papers. 100 random network of the same number of target in the test set will be generated from the background set. The test set had 1026 targets. Thus 1026 are randomly selected from the background which had a total of 25254 targets. If the background set was full HUGO set, all the targets will have an equal chance of being selected. If the background set was either Selected background above or Whole document in SciMinerDB, the probability of each target begin selected is determined by the observed frequency of each target as in (# of papers with the target / # of all papers).Two statistical measures are given below; standard Z-test and one-sample T-test.

Distrubution of randomly generated networks

This section will histograms of the random network samples. Red bars represent the targets from the tested set (target query) being tested.

Targets with any interaction	Targets interacting within corpus	Direct interactions within corpus	Max degree

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