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Analysis Option Summary

Analysis ID #	5
Email	juhur@umich.edu
Target Query #	15 (Name: 'ALS ROS', # of PMIDs: '172', # of genes: '399') (Result Page) MinPaperCount (1)
Background Query #	16 (Name: 'ALS INF', # of PMIDs: '168', # of genes: '555') (Result Page) MinPaperCount (1)
P-value Threshold	0.05
Enrichment tests	Gene Ontology, Gene list, MeSH term, Protein-Protein Interaction, Pathway (PPI Selection: FullHUGO)

Target Enrichment

Here is summary of the targets (genes and proteins) from each query (search) result. Please note that Tested set refers to the identified targets from the Target Query and Background set refers to the identified targets from the Background Query. If no background query number is specified above, then the background set is full HUGO gene set (for Gene Ontology terms, pathways, and protein-protein intearctions) and full PubMed (for MeSH terms)

Corpus size # of targets (total) # of targets (used)

Tested set 172 399 399

Background set 168 555 555

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

Here are the top 10 most enriched targets in the tested set.

Switch table detail

Rank	HUGOID	Symbol	Name	t+	t-	t+ uniq	com mon	b+ uniq	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	6018	IL6	interleukin 6 (interferon, beta 2)	1	171	1	0	25	25	143	1.30e-07	0.01	0.15	0.0
2	11892	TNF	tumor necrosis factor (TNF superfamily, member 2)	10	162	6	4	39	43	125	3.90e-07	0.06	0.26	0.2
3	9605	PTGS2	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	2	170	2	0	26	26	142	5.10e-07	0.01	0.15	0.1
4	1516	CAT	catalase	30	142	28	2	3	5	163	8.70e-06	0.17	0.03	5.9
5	4235	GFAP	glial fibrillary acidic protein	6	166	4	2	20	22	146	1.36e-03	0.03	0.13	0.3
6	31395	COX8B	cytochrome c oxidase, subunit 8B pseudogene	13	159	13	0	1	1	167	1.51e-03	0.08	0.01	12.7
7	5992	IL1B	interleukin 1, beta	4	168	2	2	16	18	150	1.70e-03	0.02	0.11	0.2
8	5438	IFNG	interferon, gamma	3	169	2	1	15	16	152	1.78e-03	0.02	0.10	0.2
9	11180	SOD2	superoxide dismutase 2, mitochondrial	19	153	17	2	2	4	164	1.88e-03	0.11	0.02	4.6
10	11179	SOD1	superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))	91	81	88	3	59	62	106	3.30e-03	0.53	0.37	1.4

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Gene Ontology Enrichment

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level3	GO:0006974	response to DNA damage stimulus	40	359	19	536	5.50e-05	0.10	0.03	2.9
2	Level5	GO:0007166	cell surface receptor linked signal transduction	61	338	144	411	8.48e-05	0.15	0.26	0.6
3	Level5	GO:0006259	DNA metabolic process	56	343	36	519	1.36e-04	0.14	0.06	2.2
4	Level3	GO:0006955	immune response	31	368	85	470	4.12e-04	0.08	0.15	0.5
5	Level4	GO:0009611	response to wounding	38	361	93	462	1.58e-03	0.10	0.17	0.6
6	Level3	GO:0009605	response to external stimulus	58	341	124	431	2.60e-03	0.15	0.22	0.7
7	Level4	GO:0007165	signal transduction	153	246	266	289	3.61e-03	0.38	0.48	0.8
8	Level2	GO:0002376	immune system process	51	348	108	447	6.35e-03	0.13	0.19	0.7
9	Level5	GO:0006631	fatty acid metabolic process	8	391	30	525	7.29e-03	0.02	0.05	0.4
10	Level4	GO:0006629	lipid metabolic process	32	367	75	480	9.10e-03	0.08	0.14	0.6

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0006281	DNA repair	34	365	13	542	2.47e-05	0.09	0.02	3.6
2	GO:0006974	response to DNA damage stimulus	40	359	19	536	5.50e-05	0.10	0.03	2.9
3	GO:0007166	cell surface receptor linked signal transduction	61	338	144	411	8.48e-05	0.15	0.26	0.6
4	GO:0006259	DNA metabolic process	56	343	36	519	1.36e-04	0.14	0.06	2.2
5	GO:0006955	immune response	31	368	85	470	4.12e-04	0.08	0.15	0.5
6	GO:0006260	DNA replication	24	375	10	545	6.54e-04	0.06	0.02	3.3
7	GO:0007186	G\-protein coupled receptor protein signaling pathway	20	379	63	492	6.54e-04	0.05	0.11	0.4
8	GO:0009611	response to wounding	38	361	93	462	1.58e-03	0.10	0.17	0.6
9	GO:0006310	DNA recombination	19	380	7	548	1.86e-03	0.05	0.01	3.8
10	GO:0007187	G\-protein signaling\, coupled to cyclic nucleotide second messenger	1	398	16	539	1.93e-03	0.00	0.03	0.1

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0006310	DNA recombination	11	388	0	555	6.32e-05	0.03	0.00	bZero
2	GO:0006955	immune response	18	381	62	493	2.11e-04	0.05	0.11	0.4
3	GO:0006281	DNA repair	21	378	7	548	3.64e-04	0.05	0.01	4.2
4	GO:0006629	lipid metabolic process	5	394	30	525	6.78e-04	0.01	0.05	0.2
5	GO:0006508	proteolysis	10	389	41	514	7.24e-04	0.03	0.07	0.3
6	GO:0007267	cell\-cell signaling	18	381	55	500	1.91e-03	0.05	0.10	0.5
7	GO:0007186	G\-protein coupled receptor protein signaling pathway	15	384	46	509	4.68e-03	0.04	0.08	0.5
8	GO:0007165	signal transduction	66	333	133	422	5.96e-03	0.17	0.24	0.7
9	GO:0007131	meiotic recombination	5	394	0	555	1.26e-02	0.01	0.00	bZero
10	GO:0000724	double\-strand break repair via homologous recombination	5	394	0	555	1.26e-02	0.01	0.00	bZero

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level2	GO:0060089	molecular transducer activity	54	345	154	401	1.27e-07	0.14	0.28	0.5
2	Level3	GO:0004871	signal transducer activity	54	345	154	401	1.27e-07	0.14	0.28	0.5
3	Level4	GO:0004872	receptor activity	36	363	111	444	2.92e-06	0.09	0.20	0.5
4	Level5	GO:0004888	transmembrane receptor activity	25	374	79	476	8.50e-05	0.06	0.14	0.4
5	Level4	GO:0005102	receptor binding	44	355	114	441	9.46e-05	0.11	0.21	0.5
6	Level3	GO:0000166	nucleotide binding	109	290	100	455	8.34e-04	0.27	0.18	1.5
7	Level4	GO:0008026	ATP\-dependent helicase activity	10	389	1	554	1.05e-03	0.03	0.00	13.9
8	Level4	GO:0019955	cytokine binding	2	397	18	537	2.57e-03	0.01	0.03	0.2
9	Level5	GO:0043566	structure\-specific DNA binding	14	385	4	551	2.71e-03	0.04	0.01	4.9
10	Level2	GO:0003824	catalytic activity	228	171	264	291	3.86e-03	0.57	0.48	1.2

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0004871	signal transducer activity	54	345	154	401	1.27e-07	0.14	0.28	0.5
2	GO:0060089	molecular transducer activity	54	345	154	401	1.27e-07	0.14	0.28	0.5
3	GO:0004872	receptor activity	36	363	111	444	2.92e-06	0.09	0.20	0.5
4	GO:0004888	transmembrane receptor activity	25	374	79	476	8.50e-05	0.06	0.14	0.4
5	GO:0005102	receptor binding	44	355	114	441	9.46e-05	0.11	0.21	0.5
6	GO:0000166	nucleotide binding	109	290	100	455	8.34e-04	0.27	0.18	1.5
7	GO:0008026	ATP\-dependent helicase activity	10	389	1	554	1.05e-03	0.03	0.00	13.9
8	GO:0019955	cytokine binding	2	397	18	537	2.57e-03	0.01	0.03	0.2
9	GO:0043566	structure\-specific DNA binding	14	385	4	551	2.71e-03	0.04	0.01	4.9
10	GO:0003824	catalytic activity	228	171	264	291	3.86e-03	0.57	0.48	1.2

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0004872	receptor activity	23	376	73	482	1.81e-04	0.06	0.13	0.4
2	GO:0000166	nucleotide binding	80	319	70	485	2.14e-03	0.20	0.13	1.6
3	GO:0004386	helicase activity	7	392	0	555	2.17e-03	0.02	0.00	bZero
4	GO:0003684	damaged DNA binding	8	391	1	554	5.11e-03	0.02	0.00	11.1
5	GO:0005319	lipid transporter activity	1	398	12	543	1.06e-02	0.00	0.02	0.1
6	GO:0008026	ATP\-dependent helicase activity	7	392	1	554	1.11e-02	0.02	0.00	9.7
7	GO:0008408	3'\-5' exonuclease activity	5	394	0	555	1.26e-02	0.01	0.00	bZero
8	GO:0003677	DNA binding	66	333	61	494	1.55e-02	0.17	0.11	1.5
9	GO:0005102	receptor binding	1	398	11	544	1.80e-02	0.00	0.02	0.1
10	GO:0008009	chemokine activity	1	398	11	544	1.80e-02	0.00	0.02	0.1

Rank	Level	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Level2	GO:0005576	extracellular region	67	332	150	405	2.23e-04	0.17	0.27	0.6
2	Level5	GO:0005886	plasma membrane	82	317	173	382	2.72e-04	0.21	0.31	0.7
3	Level4	GO:0016020	membrane	152	247	275	280	4.70e-04	0.38	0.50	0.8
4	Level5	GO:0044425	membrane part	121	278	220	335	3.24e-03	0.30	0.40	0.8
5	Level5	GO:0044424	intracellular part	303	96	380	175	1.33e-02	0.76	0.68	1.1
6	Level3	GO:0043227	membrane\-bounded organelle	236	163	283	272	1.47e-02	0.59	0.51	1.2
7	Level4	GO:0005622	intracellular	306	93	386	169	1.53e-02	0.77	0.70	1.1
8	Level4	GO:0005615	extracellular space	36	363	77	478	2.52e-02	0.09	0.14	0.7
9	Level3	GO:0044421	extracellular region part	42	357	86	469	2.70e-02	0.11	0.15	0.7
10	Level3	GO:0044422	organelle part	129	270	145	410	4.22e-02	0.32	0.26	1.2

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005576	extracellular region	67	332	150	405	2.23e-04	0.17	0.27	0.6
2	GO:0005886	plasma membrane	82	317	173	382	2.72e-04	0.21	0.31	0.7
3	GO:0016020	membrane	152	247	275	280	4.70e-04	0.38	0.50	0.8
4	GO:0031224	intrinsic to membrane	94	305	189	366	5.50e-04	0.24	0.34	0.7
5	GO:0016021	integral to membrane	93	306	183	372	1.14e-03	0.23	0.33	0.7
6	GO:0044459	plasma membrane part	62	337	133	422	1.48e-03	0.16	0.24	0.6
7	GO:0005887	integral to plasma membrane	41	358	97	458	2.00e-03	0.10	0.17	0.6
8	GO:0031226	intrinsic to plasma membrane	42	357	98	457	2.16e-03	0.11	0.18	0.6
9	GO:0044425	membrane part	121	278	220	335	3.24e-03	0.30	0.40	0.8
10	GO:0005739	mitochondrion	72	327	65	490	6.63e-03	0.18	0.12	1.5

Rank	GO ID	GO Term	t+	t-	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	GO:0005886	plasma membrane	39	360	113	442	9.55e-06	0.10	0.20	0.5
2	GO:0005576	extracellular region	59	340	140	415	9.92e-05	0.15	0.25	0.6
3	GO:0016020	membrane	111	288	216	339	4.14e-04	0.28	0.39	0.7
4	GO:0005739	mitochondrion	72	327	61	494	2.36e-03	0.18	0.11	1.6
5	GO:0005887	integral to plasma membrane	37	362	87	468	4.50e-03	0.09	0.16	0.6
6	GO:0016021	integral to membrane	73	326	137	418	2.15e-02	0.18	0.25	0.7
7	GO:0005829	cytosol	43	356	38	517	3.43e-02	0.11	0.07	1.6
8	GO:0000781	chromosome\, telomeric region	3	396	0	555	7.28e-02	0.01	0.00	bZero
9	GO:0016607	nuclear speck	3	396	0	555	7.28e-02	0.01	0.00	bZero
10	GO:0005615	extracellular space	35	364	70	485	7.43e-02	0.09	0.13	0.7

MeSH Terms Enrichment

corpus size :	172	Background :	168	Switch table detail

Rank	MeSH Term	t+	t-	t+ uniq	com mon	b+ uniq	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	Reactive Oxygen Species	104	68	103	1	0	1	167	1.63e-39	0.60	0.01	101.6
2	Mitochondria	33	139	33	0	3	3	165	5.80e-08	0.19	0.02	10.7
3	Oxidation-Reduction	27	145	26	1	2	3	165	3.60e-06	0.16	0.02	8.8
4	Oxidative Stress	59	113	56	3	19	22	146	3.99e-06	0.34	0.13	2.6
5	Superoxide Dismutase	69	103	69	0	35	35	133	1.52e-04	0.40	0.21	1.9
6	Microglia	4	168	3	1	21	22	146	1.59e-04	0.02	0.13	0.2
7	Lipid Peroxidation	13	159	0	0	0	0	168	1.95e-04	0.08	0.00	bZero
8	Inflammation Mediators	1	171	0	1	12	13	155	6.97e-04	0.01	0.08	0.1
9	Disease Models, Animal	12	160	11	1	30	31	137	1.74e-03	0.07	0.18	0.4
10	Antioxidants	24	148	23	1	6	7	161	2.16e-03	0.14	0.04	3.3

Pathway Enrichment

	# of targets	# of Targets with pathway info	# of unique pathways
Tested set	399	276	534
Background set	555	392	496

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

# of targets in test set	399	# of targets in background set	555	Switch table detail

Rank	PathwayID	Title	t+	t-	t+ uniq	com mon	b+ uniq	b+	b-	p-value	t-ratio	b-ratio	enrichment folds
1	73894	DNA Repair	18	381	18	0	1	1	554	1.42e-06	0.05	0.00	25.0
2	73890	Double-Strand Break Repair	8	391	8	0	0	0	555	8.98e-04	0.02	0.00	bZero
3	hsa04080	Neuroactive ligand-receptor interaction - Homo sapiens (human)	8	391	3	5	29	34	521	2.08e-03	0.02	0.06	0.3
4	hsa04060	Cytokine-cytokine receptor interaction - Homo sapiens (human)	20	379	2	18	39	57	498	3.61e-03	0.05	0.10	0.5
5	73951	Homologous recombination repair of replication-independent double-strand breaks	6	393	6	0	0	0	555	5.24e-03	0.02	0.00	bZero
6	157579	Telomere Maintenance	6	393	6	0	0	0	555	5.24e-03	0.02	0.00	bZero
7	73888	Homologous Recombination Repair	6	393	6	0	0	0	555	5.24e-03	0.02	0.00	bZero
8	hsa04514	Cell adhesion molecules (CAMs) - Homo sapiens (human)	3	396	0	3	13	16	539	1.95e-02	0.01	0.03	0.3
9	hsa00620	Pyruvate metabolism - Homo sapiens (human)	8	391	8	0	2	2	553	2.05e-02	0.02	0.00	5.6
10	hsa04610	Complement and coagulation cascades - Homo sapiens (human)	1	398	0	1	9	10	545	3.05e-02	0.00	0.02	0.1

Protein-Protein Interaction Network

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.

	Corpus size	# of targets (total)	# of targets (used)
Tested set	172	399	399
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	172
Num of genes (total)	399
Num of genes (used)	399
Num of targets with any interaction	368
Num of targets interacting within corpus	289
Num of direct interaction within corpus	1042
Maximum degree target	MYC (Degree = 56)
Minimum degree target	PRPF3 (Degree = 1)

[TABLE] Top 10 interacting targets within the test set

Rank	Target Symbol	Num of Direct Interactions
1	MYC	56
2	TP53	48
3	JUN	46
4	CASP3	32
5	MAPK1	31
6	BCL2	30
7	NFKB1	29
8	ATF2	29
9	MAPK3	27
10	MAPK8	25

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 399 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 399 targets. Thus 399 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	368	289	1042	56
Mean	206.56	34.91	27.18	6.35
STDEV	9.41	12.46	14.51	10.74
Z-Score	17.2	20.4	69.9	4.6
P-value(Z)	0.0e+00 (0.000)	0.0e+00 (0.000)	0.0e+00 (0.000)	1.9e-06 (0.000)
T-Stat	-171.6	-203.9	-699.5	-46.2
P-value(T)	2.5e-124 (0.000)	9.9e-132 (0.000)	1.1e-184 (0.000)	7.9e-69 (0.000)

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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