SciMiner Analysis Result Report Page

Enriched Biological Functions of 1026 ROS-Diabetes Targets

Here are the enriched biological functions of 1026 ROS-Diabetes targets in terms of Gene Ontology, pathways, and protein-protein interactions. Comparison was done against the all human genes in the HUGO Gene Nomenclature Committee (HGNC) database.
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Gene Ontology Enrichment

Download a compressed file (GO_Compressed.zip (44.6 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.

	Corpus size	# of targets (total)	# of targets (used)
ROS-Diabetes set	1154	1026	1026
Background set		25254	25254

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

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level2	GO:0009987	cellular process	920	106	12581	12673	1.84e-158	0.90	0.50	1.8
2	Level2	GO:0008152	metabolic process	768	258	8925	16329	1.17e-140	0.75	0.35	2.1
3	Level3	GO:0044237	cellular metabolic process	721	305	8197	17057	1.16e-129	0.70	0.32	2.2
4	Level2	GO:0032502	developmental process	462	564	3683	21571	4.01e-114	0.45	0.15	3.1
5	Level3	GO:0044238	primary metabolic process	691	335	8164	17090	1.74e-111	0.67	0.32	2.1
6	Level2	GO:0065007	biological regulation	557	469	5705	19549	5.03e-102	0.54	0.23	2.4
7	Level2	GO:0050896	response to stimulus	432	594	3524	21730	1.49e-101	0.42	0.14	3.0
8	Level3	GO:0007154	cell communication	484	542	4781	20473	1.08e-88	0.47	0.19	2.5
9	Level2	GO:0032501	multicellular organismal process	462	564	4429	20825	1.83e-87	0.45	0.18	2.6
10	Level3	GO:0006950	response to stress	268	758	1572	23682	6.81e-85	0.26	0.06	4.2

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0009987	cellular process	920	106	12581	12673	1.84e-158	0.90	0.50	1.8
2	GO:0008152	metabolic process	768	258	8925	16329	1.17e-140	0.75	0.35	2.1
3	GO:0044237	cellular metabolic process	721	305	8197	17057	1.16e-129	0.70	0.32	2.2
4	GO:0032502	developmental process	462	564	3683	21571	4.01e-114	0.45	0.15	3.1
5	GO:0044238	primary metabolic process	691	335	8164	17090	1.74e-111	0.67	0.32	2.1
6	GO:0065007	biological regulation	557	469	5705	19549	5.03e-102	0.54	0.23	2.4
7	GO:0050896	response to stimulus	432	594	3524	21730	1.49e-101	0.42	0.14	3.0
8	GO:0007154	cell communication	484	542	4781	20473	1.08e-88	0.47	0.19	2.5
9	GO:0032501	multicellular organismal process	462	564	4429	20825	1.83e-87	0.45	0.18	2.6
10	GO:0006950	response to stress	268	758	1572	23682	6.81e-85	0.26	0.06	4.2

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0008152	metabolic process	113	913	843	24411	3.41e-26	0.11	0.03	3.3
2	GO:0006468	protein amino acid phosphorylation	98	928	694	24560	2.86e-24	0.10	0.03	3.5
3	GO:0001666	response to hypoxia	36	990	74	25180	8.79e-24	0.04	0.00	12.0
4	GO:0007165	signal transduction	200	826	2316	22938	5.01e-23	0.19	0.09	2.1
5	GO:0006118	electron transport	70	956	386	24868	7.05e-23	0.07	0.02	4.5
6	GO:0006915	apoptosis	73	953	421	24833	8.36e-23	0.07	0.02	4.3
7	GO:0006954	inflammatory response	58	968	282	24972	1.96e-21	0.06	0.01	5.1
8	GO:0008284	positive regulation of cell proliferation	53	973	242	25012	9.53e-21	0.05	0.01	5.4
9	GO:0008283	cell proliferation	63	963	353	24901	2.17e-20	0.06	0.01	4.4
10	GO:0006091	generation of precursor metabolites and energy	36	990	101	25153	3.55e-20	0.04	0.00	8.8

Molecular Functions

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level2	GO:0005488	binding	919	107	12737	12517	3.18e-153	0.90	0.50	1.8
2	Level3	GO:0005515	protein binding	717	309	7817	17437	3.81e-138	0.70	0.31	2.3
3	Level2	GO:0003824	catalytic activity	581	445	5927	19327	2.47e-109	0.57	0.23	2.4
4	Level3	GO:0016491	oxidoreductase activity	164	862	950	24304	8.34e-51	0.16	0.04	4.2
5	Level4	GO:0005102	receptor binding	161	865	968	24286	5.69e-48	0.16	0.04	4.1
6	Level5	GO:0030554	adenyl nucleotide binding	197	829	1799	23455	7.88e-35	0.19	0.07	2.7
7	Level3	GO:0016740	transferase activity	210	816	2049	23205	1.71e-33	0.20	0.08	2.5
8	Level4	GO:0046872	metal ion binding	346	680	4562	20692	1.13e-31	0.34	0.18	1.9
9	Level4	GO:0017076	purine nucleotide binding	213	813	2163	23091	1.25e-31	0.21	0.09	2.4
10	Level4	GO:0009055	electron carrier activity	77	949	330	24924	3.30e-31	0.08	0.01	5.7

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005488	binding	919	107	12737	12517	3.18e-153	0.90	0.50	1.8
2	GO:0005515	protein binding	717	309	7817	17437	3.81e-138	0.70	0.31	2.3
3	GO:0003824	catalytic activity	581	445	5927	19327	2.47e-109	0.57	0.23	2.4
4	GO:0016491	oxidoreductase activity	164	862	950	24304	8.34e-51	0.16	0.04	4.2
5	GO:0005102	receptor binding	161	865	968	24286	5.69e-48	0.16	0.04	4.1
6	GO:0030554	adenyl nucleotide binding	197	829	1799	23455	7.88e-35	0.19	0.07	2.7
7	GO:0016740	transferase activity	210	816	2049	23205	1.71e-33	0.20	0.08	2.5
8	GO:0046872	metal ion binding	346	680	4562	20692	1.13e-31	0.34	0.18	1.9
9	GO:0017076	purine nucleotide binding	213	813	2163	23091	1.25e-31	0.21	0.09	2.4
10	GO:0009055	electron carrier activity	77	949	330	24924	3.30e-31	0.08	0.01	5.7

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005515	protein binding	514	512	5992	19262	2.82e-71	0.50	0.24	2.1
2	GO:0016491	oxidoreductase activity	103	923	600	24654	1.51e-31	0.10	0.02	4.2
3	GO:0016740	transferase activity	148	878	1325	23929	1.65e-26	0.14	0.05	2.7
4	GO:0005506	iron ion binding	70	956	338	24916	8.60e-26	0.07	0.01	5.1
5	GO:0005524	ATP binding	169	857	1690	23564	1.54e-25	0.16	0.07	2.5
6	GO:0009055	electron carrier activity	60	966	270	24984	1.32e-23	0.06	0.01	5.5
7	GO:0004672	protein kinase activity	78	948	524	24730	1.06e-20	0.08	0.02	3.7
8	GO:0000166	nucleotide binding	177	849	2047	23207	2.88e-20	0.17	0.08	2.1
9	GO:0004713	protein\-tyrosine kinase activity	73	953	496	24758	3.41e-19	0.07	0.02	3.6
10	GO:0020037	heme binding	44	982	178	25076	3.80e-19	0.04	0.01	6.1

Cellular Components

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level2	GO:0005623	cell	897	129	14509	10745	6.90e-94	0.87	0.57	1.5
2	Level3	GO:0044464	cell part	896	130	14508	10746	3.13e-93	0.87	0.57	1.5
3	Level5	GO:0044424	intracellular part	735	291	10247	15007	2.31e-86	0.72	0.41	1.8
4	Level4	GO:0005622	intracellular	744	282	10722	14532	3.82e-81	0.73	0.42	1.7
5	Level2	GO:0043226	organelle	598	428	8636	16618	2.20e-53	0.58	0.34	1.7
6	Level3	GO:0043227	membrane\-bounded organelle	546	480	7613	17641	5.16e-51	0.53	0.30	1.8
7	Level4	GO:0000267	cell fraction	178	848	1154	24100	4.20e-49	0.17	0.05	3.8
8	Level2	GO:0005576	extracellular region	245	781	2112	23142	3.96e-48	0.24	0.08	2.9
9	Level3	GO:0044421	extracellular region part	149	877	976	24278	2.27e-40	0.15	0.04	3.8
10	Level4	GO:0005615	extracellular space	117	909	649	24605	1.36e-37	0.11	0.03	4.4

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005737	cytoplasm	621	405	6740	18514	4.51e-109	0.61	0.27	2.3
2	GO:0005623	cell	897	129	14509	10745	6.90e-94	0.87	0.57	1.5
3	GO:0044464	cell part	896	130	14508	10746	3.13e-93	0.87	0.57	1.5
4	GO:0044424	intracellular part	735	291	10247	15007	2.31e-86	0.72	0.41	1.8
5	GO:0005622	intracellular	744	282	10722	14532	3.82e-81	0.73	0.42	1.7
6	GO:0044444	cytoplasmic part	417	609	4034	21220	1.78e-75	0.41	0.16	2.5
7	GO:0043226	organelle	598	428	8636	16618	2.20e-53	0.58	0.34	1.7
8	GO:0043229	intracellular organelle	597	429	8634	16620	4.01e-53	0.58	0.34	1.7
9	GO:0043227	membrane\-bounded organelle	546	480	7613	17641	5.16e-51	0.53	0.30	1.8
10	GO:0043231	intracellular membrane\-bounded organelle	545	481	7612	17642	1.42e-50	0.53	0.30	1.8

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005737	cytoplasm	381	645	4032	21222	1.54e-57	0.37	0.16	2.3
2	GO:0005576	extracellular region	220	806	1867	23387	9.10e-44	0.21	0.07	2.9
3	GO:0005739	mitochondrion	154	872	984	24270	6.27e-43	0.15	0.04	3.9
4	GO:0005615	extracellular space	112	914	623	24631	6.88e-36	0.11	0.02	4.4
5	GO:0005887	integral to plasma membrane	142	884	1282	23972	3.26e-25	0.14	0.05	2.7
6	GO:0005829	cytosol	77	949	486	24768	6.96e-22	0.08	0.02	3.9
7	GO:0005624	membrane fraction	86	940	631	24623	1.67e-20	0.08	0.02	3.4
8	GO:0005625	soluble fraction	55	971	297	24957	1.40e-18	0.05	0.01	4.6
9	GO:0005743	mitochondrial inner membrane	48	978	236	25018	8.71e-18	0.05	0.01	5.0
10	GO:0016020	membrane	369	657	6061	19193	4.91e-17	0.36	0.24	1.5

Pathway Enrichment

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.

	# of targets	# of Targets with pathway info	# of unique pathways
ROS-Diabetes set	1026	759	697
Background set	25254	5116	942

More full results are available.

ROS-Diabetes 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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ROS-Diabetes 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

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

# of targets in ROS-Diabetes	1026	# of targets in HUGO gene set	25254	Switch table detail

Rank	PathwayID	Title	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	hsa04510	Focal adhesion - Homo sapiens (human)	75	951	197	25057	2.36e-42	0.07	0.01	9.4
2	hsa04210	Apoptosis - Homo sapiens (human)	49	977	83	25171	6.68e-35	0.05	0.00	14.5
3	hsa04010	MAPK signaling pathway - Homo sapiens (human)	73	953	259	24995	4.29e-34	0.07	0.01	6.9
4	109582	Hemostasis	62	964	172	25082	4.54e-34	0.06	0.01	8.9
5	hsa05215	Prostate cancer - Homo sapiens (human)	49	977	93	25161	3.78e-33	0.05	0.00	13.0
6	hsa04920	Adipocytokine signaling pathway - Homo sapiens (human)	45	981	72	25182	5.99e-33	0.04	0.00	15.4
7	hsa04910	Insulin signaling pathway - Homo sapiens (human)	53	973	137	25117	1.68e-30	0.05	0.01	9.5
8	hsa05212	Pancreatic cancer - Homo sapiens (human)	42	984	74	25180	1.42e-29	0.04	0.00	14.0
9	168256	Signaling in Immune system	72	954	312	24942	5.52e-29	0.07	0.01	5.7
10	hsa05222	Small cell lung cancer - Homo sapiens (human)	43	983	87	25167	2.28e-28	0.04	0.00	12.2

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Protein-Protein Interaction Network

The following table summarizes the targets (from the ROS-Diabetes 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.

	Corpus size	# of targets (total)	# of targets (used)
ROS-Diabetes	1154	1026	1026
Background set		25254	25254

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.

Num of PMIDs	1154
Num of genes (total)	1026
Num of genes (used)	1026
Num of targets with any interaction	983
Num of targets interacting within corpus	879
Num of direct interaction within corpus	5002
Maximum degree target	HNF4A (Degree = 173)
Minimum degree target	SLC7A2 (Degree = 1)

[TABLE] Top 10 interacting targets within the test set

Rank	Target Symbol	Num of Direct Interactions
1	HNF4A	173
2	JUN	106
3	MYC	102
4	TP53	82
5	MAPK1	77
6	SRC	75
7	RELA	74
8	PRKCA	72
9	EGFR	70
10	MAPK3	62

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.

	Targets with any interaction	Targets interacting within corpus	Direct interactions within corpus	Max degree
Tested	983	879	5002	173
Mean	529.75	158.59	171.41	25.10
STDEV	14.76	34.00	51.47	35.93
Z-Score	30.7	21.2	93.9	4.1
P-value(Z)	0.0e+00 (0.000)	0.0e+00 (0.000)	0.0e+00 (0.000)	1.9e-05 (0.000)
T-Stat	-307.0	-211.9	-938.5	-41.2
P-value(T)	2.7e-149 (0.000)	2.3e-133 (0.000)	2.6e-197 (0.000)	4.4e-64 (0.000)

Distrubution of randomly generated networks

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

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

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