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|---|---|---|---|
A monocyte chemoattractant protein-1 gene polymorphism is associated with occult ischemia in a high-risk asymptomatic population. | NA | {
"id": 6347,
"name": "CCL2",
"pos": [
2,
34
]
} | {
"id": "C0231221",
"name": "Asymptomatic",
"pos": [
105,
12
]
} |
This study examined the effects of Her2 blockade on tumor angiogenesis, vascular architecture, and hypoxia in Her2(+) and Her2(-) MCF7 xenograft tumors. | NA | {
"id": 2064,
"name": "ERBB2",
"pos": [
122,
4
]
} | {
"id": "C0242184",
"name": "Hypoxia",
"pos": [
99,
7
]
} |
Eleven deleterious variants, six nonsense and five missense, were identified in seven genes: four LCA-associated genes (CEP290, IQCB1, NMNAT1, and RPGRIP1), one gene responsible for syndromic LCA (ALMS1), and two IRDs-related genes (CTNNA1 and CYP4V2). | genomic_alterations | {
"id": 80184,
"name": "CEP290",
"pos": [
120,
6
]
} | {
"id": "C2931258",
"name": "Amaurosis congenita of Leber, type 1",
"pos": [
98,
3
]
} |
However, neither rhs-TM pretreated with an anti-rhs-TM monoclonal antibody (MAb) F2H5, which inhibits thrombin binding to rhs-TM, nor those pretreated with MAb R5G12, which selectively inhibits protein C activation by rhs-TM, prevented the motor disturbances. | NA | {
"id": 5624,
"name": "PROC",
"pos": [
194,
9
]
} | {
"id": "C2220255",
"name": "Motor disturbances",
"pos": [
240,
18
]
} |
In tissue specimens from normal brain and lung, as well as in glioma and lung carcinoma cell lines, com1 expression was barely detectable. | NA | {
"id": 26471,
"name": "NUPR1",
"pos": [
100,
4
]
} | {
"id": "C0017638",
"name": "Glioma",
"pos": [
62,
6
]
} |
FLG mutation carriers were also more likely to have eczema by 3 months of age (OR 4·26, 95% CI 1·34-13·57, P = 0·014). | NA | {
"id": 2260,
"name": "FGFR1",
"pos": [
0,
3
]
} | {
"id": "C0013595",
"name": "Eczema",
"pos": [
52,
6
]
} |
Life-threatening episodes of coma and hypoglycemia induced by fasting are a common presenting feature in most of the fatty acid oxidation disorders (MCAD, LCAD, and HMG-CoA lyase deficiencies, the infantile form of CPT deficiency, the mild form of MAD deficiency, and in some cases of primary carnitine deficiency). | NA | {
"id": 270,
"name": "AMPD1",
"pos": [
248,
3
]
} | {
"id": "C0009421",
"name": "Comatose",
"pos": [
29,
4
]
} |
These results reveal a leukemic pathway involving FAK/Tiam1/Rac1/PAK1 and demonstrate an essential role for these signaling molecules in regulating the nuclear translocation of Stat5 in leukemogenesis. | NA | {
"id": 5747,
"name": "PTK2",
"pos": [
50,
3
]
} | {
"id": "C0598766",
"name": "Leukemogenesis",
"pos": [
186,
14
]
} |
In addition, silencing of HLJ1 partially reverses the inhibition of cancer-cell invasion by andrographolide. | biomarker | {
"id": 11080,
"name": "DNAJB4",
"pos": [
26,
4
]
} | {
"id": "C1269955",
"name": "Tumor Cell Invasion",
"pos": [
80,
8
]
} |
Patients carrying JARID2 deletion manifested with cognitive impairment, gait disturbance and a characteristic facial appearance, whereas patients with deletion of ATXN1 seemed to be characterized by intellectual disability and behavioural abnormalities. | NA | {
"id": 3720,
"name": "JARID2",
"pos": [
18,
6
]
} | {
"id": "C0000768",
"name": "Congenital Abnormality",
"pos": [
239,
13
]
} |
The identification of ApoB loss-of-function mutations in type 1 diabetic patients presents innovative cases to study the interaction between hypobetalipoproteinemia and insulin deficiency. | genomic_alterations | {
"id": 338,
"name": "APOB",
"pos": [
22,
4
]
} | {
"id": "C0020597",
"name": "Hypobetalipoproteinemias",
"pos": [
141,
23
]
} |
These findings indicate that deregulation of KLF6, together with genetic abnormalities of allelic imbalance and mutations, may play a role in HCC pathogenesis. | NA | {
"id": 1316,
"name": "KLF6",
"pos": [
45,
4
]
} | {
"id": "C0000768",
"name": "Congenital Abnormality",
"pos": [
73,
13
]
} |
In most of the classic Philadelphia-negative MPNs-polycythemia vera (PV), essential thrombocythemia (ET), and MPN-associated myelofibrosis (MPN-MF)-oncogenic mutations affecting JAK2 or MPL lead to constitutive activation of cytokine-regulated intracellular signalling pathways. | genomic_alterations | {
"id": 4352,
"name": "MPL",
"pos": [
186,
3
]
} | {
"id": "C1292778",
"name": "Chronic myeloproliferative disorder",
"pos": [
110,
3
]
} |
] (RVA/Human-wt/CHN/E931/2008/G4P[6], RVA/Human-wt/CHN/R1954/2013/G4P[6]), one G3P[6] (RVA/Human-wt/CHN/R946/2006/G3P[6]) and one G4P[8] (RVA/Human-wt/CHN/E2484/2011/G4P[8]) group A rotavirus (RVA) strains detected in sporadic cases of diarrhea in humans in the city of Wuhan, China. | NA | {
"id": 1123,
"name": "CHN1",
"pos": [
151,
3
]
} | {
"id": "C0011991",
"name": "Diarrhea",
"pos": [
236,
8
]
} |
Collectively, these observations suggest a potential sex-dependent link between abnormalities in IMPA2 expression and calcium homeostasis in the pathophysiology of BD. | NA | {
"id": 3613,
"name": "IMPA2",
"pos": [
97,
5
]
} | {
"id": "C0000768",
"name": "Congenital Abnormality",
"pos": [
80,
13
]
} |
Three apoptosis-related genes (NOD2, DUSP1, and ADM) and 8 genes overexpressed in AD skin lesions (CCDC109B, CCL5, CCL8, IFI35, LYN, RAB31, IFITM1, and IFITM2) were induced by IFN-γ in primary keratinocytes. | NA | {
"id": 8519,
"name": "IFITM1",
"pos": [
140,
6
]
} | {
"id": "C0037284",
"name": "Skin lesion",
"pos": [
85,
12
]
} |
We analyzed for PIK3CA and KRAS mutations and LINE-1 methylation by Pyrosequencing, microsatellite instability (MSI), and DNA methylation (epigenetic changes) in eight CpG island methylator phenotype (CIMP)-specific promoters [CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1] by MethyLight (real-time PCR). | NA | {
"id": 1381,
"name": "CRABP1",
"pos": [
250,
6
]
} | {
"id": "C0920269",
"name": "Microsatellite Instability",
"pos": [
84,
26
]
} |
These analyses demonstrate that ATX is highly expressed in a variety of carcinomas and sarcomas, whereas LIPI is almost exclusively overexpressed in highly aggressive Ewing's sarcomas, which underscores the potential contribution of LPA in metastatic disease. | NA | {
"id": 149998,
"name": "LIPI",
"pos": [
105,
4
]
} | {
"id": "C0007097",
"name": "Carcinoma",
"pos": [
72,
10
]
} |
We identified a BCR/ABL-dependent increase in expression of multiple genes involved in pre-mRNA splicing (eg SRPK1, RNA Helicase II/Gu, and hnRNPA2/B1) by subtractive hybridization of cDNA from p210BCR/ABL-eGFP vs eGFP-transduced umbilical cord blood CD34+ cells. beta1-integrin signaling is important to HSC maintenance and proliferation/differentiation, and is abnormal in CML. | biomarker | {
"id": 6732,
"name": "SRPK1",
"pos": [
109,
5
]
} | {
"id": "C0023473",
"name": "Myeloid Leukemia, Chronic",
"pos": [
375,
3
]
} |
The severity of MEN1-related biochemical and clinical findings did not significantly differ from that for other affected family members lacking the BRCA1 mutation, except for the development of an extremely large visceral lipoma; the proband has not developed any BRCA1-related malignancies. | genomic_alterations | {
"id": 4221,
"name": "MEN1",
"pos": [
16,
4
]
} | {
"id": "C0006826",
"name": "Malignant Neoplasms",
"pos": [
278,
12
]
} |
However, the Cockayne syndrome caused by the ERCC6 defect has not been linked to cancer predisposition; likely due to the fact that cells with severe disruption of the ERCC6 function are sensitive to lesion-induced apoptosis, thus reducing the chance of tumorigenesis. | NA | {
"id": 2074,
"name": "ERCC6",
"pos": [
168,
5
]
} | {
"id": "C0007621",
"name": "Neoplastic Cell Transformation",
"pos": [
254,
13
]
} |
Sequential trypsinization of layers of cells from HT-29 multicellular spheroids and analysis of gene expression by reverse transcription-polymerase chain reaction demonstrate that NQO1 expression is elevated in cells close to the necrotic center. | NA | {
"id": 1728,
"name": "NQO1",
"pos": [
180,
4
]
} | {
"id": "C0027540",
"name": "Necrosis",
"pos": [
230,
8
]
} |
We investigated the association between the polymorphisms of the GAD2 and DRD2 genes and obesity with a higher body mass index (BMI) in Taiwanese patients. | NA | {
"id": 1813,
"name": "DRD2",
"pos": [
74,
4
]
} | {
"id": "C1305855",
"name": "Body mass index",
"pos": [
111,
15
]
} |
Although both conditions occur most often with reduced blood CD4+ T-cell numbers, oral warts and OHL rarely occur simultaneously, suggesting that dysfunctions in other secondary local immune parameters are also involved. | NA | {
"id": 920,
"name": "CD4",
"pos": [
61,
3
]
} | {
"id": "C1262299",
"name": "Oral wart",
"pos": [
82,
10
]
} |
Our results shed new light on our understanding of TREM-1 and its role in the innate inflammatory response in infections and might contribute to the development of future concepts to treat sepsis. | NA | {
"id": 54210,
"name": "TREM1",
"pos": [
51,
6
]
} | {
"id": "C3714514",
"name": "Infection",
"pos": [
110,
10
]
} |
The objective of the present study was to review previous investigations on the association of haplotypes in the G-protein β3 subunit (GNB3) gene with representative cardiovascular risk factors/phenotypes: hypertension, overweight, and variation in the systolic and diastolic blood pressures (SBP and DBP, respectively) and as well as body mass index (BMI). | NA | {
"id": 1628,
"name": "DBP",
"pos": [
301,
3
]
} | {
"id": "C1305855",
"name": "Body mass index",
"pos": [
335,
15
]
} |
Somatic MYH7, MYBPC3, TPM1, TNNT2 and TNNI3 mutations in sporadic hypertrophic cardiomyopathy. | NA | {
"id": 7139,
"name": "TNNT2",
"pos": [
28,
5
]
} | {
"id": "C1853237",
"name": "Isolated cases",
"pos": [
57,
8
]
} |
Knockdown of PTEN (phosphatase and tensin homologue deleted on chromosome 10) and PTP1B (protein tyrosine phosphatase 1B) gene expression by siRNA (small interfering RNA) treatment significantly increased GLUT4 translocation only in cells treated with palmitate but not in untreated cells. | NA | {
"id": 6517,
"name": "SLC2A4",
"pos": [
205,
5
]
} | {
"id": "C0040715",
"name": "Chromosomal translocation",
"pos": [
211,
13
]
} |
Translocation (8;16)(p11;p13), though rare, may be of primary importance in the process of leukemogenesis in some cases of histiocytic/monocytic malignancies. | NA | {
"id": 51013,
"name": "EXOSC1",
"pos": [
25,
3
]
} | {
"id": "C0006826",
"name": "Malignant Neoplasms",
"pos": [
145,
12
]
} |
These findings suggest a role of UCP2-UCP3 gene cluster haplotypes in diabetes; in particular, the effects of the high-risk haplotypes were more apparent in overweight Caucasian women. | NA | {
"id": 7351,
"name": "UCP2",
"pos": [
33,
4
]
} | {
"id": "C0497406",
"name": "Overweight",
"pos": [
157,
10
]
} |
Genetic polymorphisms of TGF-beta, PAI-1, and COL1A-1, and determination of bone mineral density in Caucasian females. | NA | {
"id": 7040,
"name": "TGFB1",
"pos": [
25,
8
]
} | {
"id": "C0005938",
"name": "Bone Density",
"pos": [
76,
20
]
} |
This finding suggests that the choice of poly/monoclonal antibody for Caveolin 1 in the differential diagnosis of malignant pleural mesothelioma and pulmonary adenocarcinoma is important. | biomarker | {
"id": 857,
"name": "CAV1",
"pos": [
70,
10
]
} | {
"id": "C0001418",
"name": "Adenocarcinoma",
"pos": [
159,
14
]
} |
Modulatory role of DR4- to DQ8-restricted CD4 T-cell responses and type 1 diabetes susceptibility. | NA | {
"id": 8797,
"name": "TNFRSF10A",
"pos": [
19,
3
]
} | {
"id": "C0011854",
"name": "Diabetes Mellitus, Insulin-Dependent",
"pos": [
67,
15
]
} |
In patients with mutations of PRSS1 (N29I, R122H) and SPINK1 (N34S) the parameters such as calcification, dilatation of the main pancreatic duct, diabetes mellitus, hospital treatments, and surgery were recorded. | NA | {
"id": 5644,
"name": "PRSS1",
"pos": [
30,
5
]
} | {
"id": "C0002940",
"name": "Aneurysm",
"pos": [
106,
10
]
} |
For these PM, IBM, and unclassifiable patients, their mean ages at diagnosis were 63, 70, and 64 years; autoimmune disease was present in 7 (41%), 13 (19%), and 4 (67%); hepatitis C virus infection was detected in 0%, 13 (20%), and 2 (33%); and p62 was immunopositive in 0%, 66 (94%), and 2 (33%), respectively. | biomarker | {
"id": 2965,
"name": "GTF2H1",
"pos": [
245,
3
]
} | {
"id": "C0019196",
"name": "Hepatitis C",
"pos": [
170,
27
]
} |
This C/EBP delta binding site in aromatase promoters I.3/II seems to act as a positive regulatory element in non-p65-overexpressing breast cancer epithelial cells, whereas it is possibly inactive in p65 overexpressing cancer epithelial cells, such as estrogen receptor-negative breast cancer cells. | biomarker | {
"id": 10682,
"name": "EBP",
"pos": [
7,
3
]
} | {
"id": "C0678222",
"name": "Breast Carcinoma",
"pos": [
132,
13
]
} |
The proband presented with proteinuria aged 50 and a family history of amyloidosis, and underwent renal biopsy, whole-body serum amyloid P component (SAP) scintigraphy, and sequencing of the lysozyme gene. | NA | {
"id": 325,
"name": "APCS",
"pos": [
150,
3
]
} | {
"id": "C0033687",
"name": "Proteinuria",
"pos": [
27,
11
]
} |
The disease loci for X-linked Retinoschisis (RS), Keratosis follicularis spinulosa decalvans (KFSD), and Coffin-Lowry syndrome (CLS) have been localized to the same, small region in Xp22 on the human X Chromosome (Chr). | genomic_alterations | {
"id": 51360,
"name": "MBTPS2",
"pos": [
50,
42
]
} | {
"id": "C0271091",
"name": "Retinoschisis, Juvenile, X-Linked",
"pos": [
21,
22
]
} |
There was a clear-cut clinical difference between the 28 patients having a balanced 11q23 anomaly/MLL rearrangement and the 17 patients having an unbalanced chromosomal anomaly: AML with unbalanced 11q23 anomalies occurred in older patients (P = 0.07) tended to be less frequently associated with previous exposure to topoisomerase II-active drugs and with M4/M5 FAB cytological subtypes, were always associated with other chromosomal anomalies (P < 0.0001), expressed more frequently the CD34 antigen (P = 0.05) and were of considerably poorer prognosis for achievement of CR (P = 0.005) and survival (P = 0.0005). | genomic_alterations | {
"id": 947,
"name": "CD34",
"pos": [
492,
12
]
} | {
"id": "C0023467",
"name": "Leukemia, Myelocytic, Acute",
"pos": [
178,
3
]
} |
RPE and MCF-7 cells (as a positive control) were initially infected with replication deficient adenovirus, to overexpress beta-galactosidase (RAdLacZ) or TIMP-3 (RAdTIMP-3). | NA | {
"id": 6120,
"name": "RPE",
"pos": [
0,
3
]
} | {
"id": "C0001486",
"name": "Adenovirus Infections",
"pos": [
95,
10
]
} |
These results increase understanding of the biology of these disorders and suggest that patterns of atrophy on MRI may be useful to aid in the differentiation of groups of PGRN and MAPT mutation carriers. | NA | {
"id": 78996,
"name": "CYREN",
"pos": [
111,
3
]
} | {
"id": "C0333641",
"name": "Atrophic",
"pos": [
100,
7
]
} |
Overall, 61 significant associations (P < or = 0.01) were found between SNPs belonging to cytokine receptor genes regulating T helper (Th)1 (IL12RB2, IL2RA and B) and Th2 (IL4R and IL10RB) immunity, and cytokine (IL1B, TNFA, IL6 and IFNB1) and cytokine receptor (IL1RA, IFNAR2, IL18R1, TNFRSF1A and B) genes regulating innate immunity and variations in antibody levels to measles, mumps and/or rubella. | NA | {
"id": 3554,
"name": "IL1R1",
"pos": [
263,
5
]
} | {
"id": "C0025007",
"name": "Measles",
"pos": [
372,
7
]
} |
We demonstrate that exposure of pDCs to HCV-infected hepatoma cells surprisingly did not induce phosphorylation of NF-κB or cell surface expression of CD40, CCR7, CD86, or TRAIL or secretion of TNF-α and IL-6. | NA | {
"id": 942,
"name": "CD86",
"pos": [
163,
4
]
} | {
"id": "C0023903",
"name": "Liver neoplasms",
"pos": [
53,
8
]
} |
Mononuclear cells expressing IFN-gamma and IL-4 mRNA were aggregated in inflamed portal tracts in PBC livers, but were rarely present in extrahepatic biliary obstruction, alcoholic fibrosis, or normal liver sections. | NA | {
"id": 3565,
"name": "IL4",
"pos": [
43,
4
]
} | {
"id": "C0005398",
"name": "Cholestasis, Extrahepatic",
"pos": [
137,
32
]
} |
Using the cell-based reporter assay, we identified several oncogenic pathways modulated by sulforaphane in hypoxia by activating anticancer responses (p53, ARE, IRF-1, Pax-6 and XRE) and suppressing responses supporting tumor progression (AP-1 and HIF-1). | biomarker | {
"id": 5080,
"name": "PAX6",
"pos": [
168,
5
]
} | {
"id": "C0178874",
"name": "Tumor Progression",
"pos": [
220,
17
]
} |
Furthermore, there may be two distinct subtypes of cerebral SVD, isolated lacunar infarction (ILI) and ischaemic leukoaraiosis (ILA). | NA | {
"id": 3604,
"name": "TNFRSF9",
"pos": [
129,
3
]
} | {
"id": "C0333559",
"name": "Infarction, Lacunar",
"pos": [
75,
18
]
} |
Although leukemia with t(11;19) has been classified as ANLL, most commonly M5 of FAB classification, the patient with this chromosomal abnormality may have a mixed leukemia in which cells with lymphoid features and those with monocytic ones exist. | genomic_alterations | {
"id": 2187,
"name": "FANCB",
"pos": [
81,
3
]
} | {
"id": "C0023418",
"name": "leukemia",
"pos": [
9,
8
]
} |
HLA-DRB1 alleles may influence disease phenotype in patients with inflammatory bowel disease: a critical reappraisal with review of the literature. | genomic_alterations | {
"id": 3123,
"name": "HLA-DRB1",
"pos": [
0,
8
]
} | {
"id": "C0021390",
"name": "Inflammatory Bowel Diseases",
"pos": [
66,
26
]
} |
Diffuse alveolar damage score and gene expression of markers associated with lung inflammation (interleukin-6), alveolar-stretch (amphiregulin), epithelial cell damage (club cell protein 16), and fibrogenesis (metalloproteinase-9 and type III procollagen), as well as diaphragm inflammation (tumor necrosis factor-α) and proteolysis (muscle RING-finger-1) were comparable between groups. | genomic_alterations | {
"id": 3569,
"name": "IL6",
"pos": [
96,
13
]
} | {
"id": "C0032285",
"name": "Pneumonia",
"pos": [
77,
17
]
} |
This study aimed to demonstrate the role of miR-144-3p in HCMV-positive glioblastoma. | biomarker | {
"id": 406936,
"name": "MIR144",
"pos": [
44,
7
]
} | {
"id": "C0017636",
"name": "Glioblastoma",
"pos": [
72,
12
]
} |
In three cases tested for both ALK and the t(2;5), ALK protein was detected in the absence of the t(2;5) translocation but no cases showed the reverse pattern, consistent with ALK fusion to genes other than NPM or activation of the ALK gene by another mechanism. | NA | {
"id": 238,
"name": "ALK",
"pos": [
232,
8
]
} | {
"id": "C0040715",
"name": "Chromosomal translocation",
"pos": [
105,
13
]
} |
Lung tumorigenesis promoted by anti-apoptotic effects of cotinine, a nicotine metabolite through activation of PI3K/Akt pathway. | NA | {
"id": 5290,
"name": "PIK3CA",
"pos": [
111,
4
]
} | {
"id": "C0007621",
"name": "Neoplastic Cell Transformation",
"pos": [
5,
13
]
} |
Plasma MMP-9, and urine NGAL and MMP-9 concentrations were measured in 121 T1DM and 55 control subjects and examined relative to indicators of glycemia, renal function, and degree of albuminuria. | NA | {
"id": 3934,
"name": "LCN2",
"pos": [
24,
4
]
} | {
"id": "C0001925",
"name": "Albuminuria",
"pos": [
183,
11
]
} |
Ubiquitous and tenacious methylation of the CpG site in codon 248 of the p53 gene may explain its frequent appearance as a mutational hot spot in human cancer. | genomic_alterations | {
"id": 7157,
"name": "TP53",
"pos": [
73,
3
]
} | {
"id": "C1306459",
"name": "Primary malignant neoplasm",
"pos": [
152,
6
]
} |
Molecular characterisation of six patients with prolidase deficiency: identification of the first small duplication in the prolidase gene and of a mutation generating symptomatic and asymptomatic outcomes within the same family. | NA | {
"id": 5184,
"name": "PEPD",
"pos": [
123,
9
]
} | {
"id": "C0231221",
"name": "Asymptomatic",
"pos": [
183,
12
]
} |
The extraordinary induction of type 1 cytokines and the preferential activation of CD8(+) T cells by S. mutans offers an explanation for the etiology of the CD8(+) T-cell-dominant lesion in early pulpitis and suggests that S. mutans may have a major impact on the initial lesion and pulpal pathology. | NA | {
"id": 925,
"name": "CD8A",
"pos": [
157,
3
]
} | {
"id": "C0034103",
"name": "Pulpitis",
"pos": [
196,
8
]
} |
Among six genes whose induction by hypoxia was newly defined in this way, three were of known function, encoding the glucose transporter isoform 3 (Glut-3), adenylate kinase isoenzyme 3 (AK-3), and tissue factor, two were expressed sequence tags (ESTs), and one corresponded to a new sequence. | NA | {
"id": 2152,
"name": "F3",
"pos": [
198,
13
]
} | {
"id": "C0242184",
"name": "Hypoxia",
"pos": [
35,
7
]
} |
Long noncoding RNA BLACAT1 is overexpressed in hepatocellular carcinoma and its downregulation suppressed cancer cell development through endogenously competing against hsa-miR-485-5p. | biomarker | {
"id": 574436,
"name": "MIR485",
"pos": [
169,
11
]
} | {
"id": "C1306459",
"name": "Primary malignant neoplasm",
"pos": [
106,
6
]
} |
The CB1 oncolytic adenovirus induces a potent antiglioma effect and could ultimately demonstrate clinical relevance and therapeutic utility. | NA | {
"id": 1268,
"name": "CNR1",
"pos": [
4,
3
]
} | {
"id": "C0001486",
"name": "Adenovirus Infections",
"pos": [
18,
10
]
} |
A new study examines the question of pleiotropic effects acting on both electro-encephalographic (EEG) abnormalities and speech sound disorder in rolandic epilepsy families - another study questions the rationale for EEG recording in patients with specific language impairment (SLI) - whereas two studies examine the effect of anti-epileptic drug treatment on speech and language. | NA | {
"id": 25759,
"name": "SHC2",
"pos": [
278,
3
]
} | {
"id": "C0000768",
"name": "Congenital Abnormality",
"pos": [
103,
13
]
} |
Within PSMD9, we reported a linkage to T2D and to MODY3 in Italian families. | genomic_alterations | {
"id": 6927,
"name": "HNF1A",
"pos": [
50,
5
]
} | {
"id": "C0011860",
"name": "Diabetes Mellitus, Non-Insulin-Dependent",
"pos": [
39,
3
]
} |
Knockdown of HIF-1α attenuated the increasing protein levels of both Btg2 and Ndrg1 by hypoxia or L-mimosine in LNCaP cells. | NA | {
"id": 7832,
"name": "BTG2",
"pos": [
69,
4
]
} | {
"id": "C0242184",
"name": "Hypoxia",
"pos": [
87,
7
]
} |
Somatic mutations of LKB1 and beta-catenin genes in gastrointestinal polyps from patients with Peutz-Jeghers syndrome. | genomic_alterations | {
"id": 1499,
"name": "CTNNB1",
"pos": [
30,
12
]
} | {
"id": "C0744333",
"name": "Gastrointestinal polyps",
"pos": [
52,
23
]
} |
Genetic variation at CCL2 is associated with markers of disease aggressiveness. | NA | {
"id": 6347,
"name": "CCL2",
"pos": [
21,
4
]
} | {
"id": "C0001807",
"name": "Aggressive behavior",
"pos": [
64,
14
]
} |
Defects in mismatch repair (MMR) genes have been involved in several types of sporadic and hereditary cancers. | NA | {
"id": 4360,
"name": "MRC1",
"pos": [
28,
3
]
} | {
"id": "C1853237",
"name": "Isolated cases",
"pos": [
78,
8
]
} |
In addition, the MNT served as an indicator of chromosome breakage/aneuploidy. | NA | {
"id": 4335,
"name": "MNT",
"pos": [
17,
3
]
} | {
"id": "C0376628",
"name": "Chromosome Breakage",
"pos": [
47,
19
]
} |
We screened the exons, splice sites, and predicted promoters of 24 bilateral congenital idiopathic clubfoot patients and 24 matched controls in MYH 1, 2, 3, and 8 via sequence-based analysis, and screened an additional 76 patients in each discovered SNP. | NA | {
"id": 4595,
"name": "MUTYH",
"pos": [
144,
3
]
} | {
"id": "C0009081",
"name": "Congenital clubfoot",
"pos": [
99,
8
]
} |
We studied the immunoreactivity to six CgA epitopes and SV2 in ten typical (TC) and ten atypical (ACT) carcinoids, five large-cell NE carcinomas (LCNEC) and five small-cell carcinomas (SCLC), also comparing the results with clinicopathological characteristics of tumors. | NA | {
"id": 9900,
"name": "SV2A",
"pos": [
56,
3
]
} | {
"id": "C0007097",
"name": "Carcinoma",
"pos": [
173,
10
]
} |
At prolonged hypoxia, HIF-2alpha remained accumulated, whereas HIF-1alpha protein levels decreased, in agreement with the oxygen level and time-dependent induction of HIFs recently reported in neuroblastoma. | NA | {
"id": 3091,
"name": "HIF1A",
"pos": [
63,
10
]
} | {
"id": "C0242184",
"name": "Hypoxia",
"pos": [
13,
7
]
} |
Thus, HSI-I likely contributes to the pathogenesis of P. aeruginosa in CF patients. | biomarker | {
"id": 57016,
"name": "AKR1B10",
"pos": [
6,
3
]
} | {
"id": "C0010674",
"name": "Cystic Fibrosis",
"pos": [
71,
2
]
} |
E-cadherin-dependent adhesion of dendritic and Langerhans cells to keratinocytes is defective in cervical human papillomavirus-associated (pre)neoplastic lesions. | NA | {
"id": 999,
"name": "CDH1",
"pos": [
0,
10
]
} | {
"id": "C0001511",
"name": "Tissue Adhesions",
"pos": [
21,
8
]
} |
GLP-1/dexamethasone inhibits food reward without inducing mood and memory deficits in mice. | biomarker | {
"id": 100125288,
"name": "ZGLP1",
"pos": [
0,
5
]
} | {
"id": "C0233794",
"name": "Memory impairment",
"pos": [
67,
15
]
} |
Growing evidence supports that proinflammatory cytokines, such as interleukin-1 (IL-1) and tumor necrosis factor (TNF), released by activated spinal glial cells and within the dorsal root ganglia (DRG) are critical in enhancing pain in various animal models of neuropathic pain. | NA | {
"id": 4733,
"name": "DRG1",
"pos": [
197,
3
]
} | {
"id": "C0027796",
"name": "Neuralgia",
"pos": [
261,
16
]
} |
This growth enhancement was also seen in cells transfected with the BCL-2 gene with its own promoter juxtaposed to the immunoglobulin heavy chain gene enhancer, which represents the translocated form of the BCL-2 gene observed in follicular lymphomas with the t(14;18) translocation. | NA | {
"id": 3492,
"name": "IGH",
"pos": [
119,
31
]
} | {
"id": "C0040715",
"name": "Chromosomal translocation",
"pos": [
269,
13
]
} |
Effect of beta-adrenergic receptor antagonists on nicotine-induced tail-tremor in rats. | therapeutic | {
"id": 154,
"name": "ADRB2",
"pos": [
10,
24
]
} | {
"id": "C0751564",
"name": "Pill Rolling Tremor",
"pos": [
72,
6
]
} |
Fanconi Anemia (FA) is a rare genetic disease characterized by chromosome instability mostly resulting from an improper regulation of FANCD2 monoubiquitination. | NA | {
"id": 2177,
"name": "FANCD2",
"pos": [
134,
6
]
} | {
"id": "C1257806",
"name": "Chromosomal Instability",
"pos": [
63,
22
]
} |
This led to the suggestion that IAPP might be a circulating hormone regulating peripheral insulin sensitivity. | NA | {
"id": 3375,
"name": "IAPP",
"pos": [
32,
4
]
} | {
"id": "C0920563",
"name": "Insulin Sensitivity",
"pos": [
90,
19
]
} |
Moreover, BRUCE-depleted cells display reduced homologous recombination repair, and BRUCE-mutant mice exhibit repair defects and genomic instability. | NA | {
"id": 57448,
"name": "BIRC6",
"pos": [
84,
5
]
} | {
"id": "C0919532",
"name": "Genomic Instability",
"pos": [
129,
19
]
} |
These studies identified novel gene targets, such as CD40, DCNP1 and PTGS2, for asthma and allergen sensitization whereas many others replicated the genetic associations on known candidate genes for asthma and atopic dermatitis. | biomarker | {
"id": 958,
"name": "CD40",
"pos": [
53,
4
]
} | {
"id": "C0011615",
"name": "Dermatitis, Atopic",
"pos": [
210,
17
]
} |
Interestingly, the expression of NME1 in either villi or decidua is higher significantly in miscarriage than that of the normal early pregnancy. | NA | {
"id": 4830,
"name": "NME1",
"pos": [
33,
4
]
} | {
"id": "C0000786",
"name": "Spontaneous abortion",
"pos": [
92,
11
]
} |
Using a mouse model in which high-fat diet enhances HCC induction by the hepatic carcinogen DEN, we examined whether mTORC1 inhibition attenuates liver inflammation and tumorigenesis. | NA | {
"id": 84668,
"name": "FAM126A",
"pos": [
52,
3
]
} | {
"id": "C0007621",
"name": "Neoplastic Cell Transformation",
"pos": [
169,
13
]
} |
The lethal group of short-rib polydactyly (SRP) includes type I (Saldino-Noonan; MIM 263530), type II (Majewski; MIM 263520), type III (Verma-Naumoff; MIM 263510) and type IV (Beemer-Langer; MIM 269860). | NA | {
"id": 9788,
"name": "MTSS1",
"pos": [
191,
3
]
} | {
"id": "C0152427",
"name": "Polydactyly",
"pos": [
30,
11
]
} |
The VEGF/ VPF concentration in the cyst fluid obtained from patients who required repeated aspiration or underwent surgical resection because of recurrent accumulation (84.8 +/- 58.3 ng/mL, mean +/- SD, n = 18) was significantly higher than that in the cysts that regressed or disappeared after a single aspiration (4.3 +/- 4.4 ng/mL, n = 12, P < 0.001). | NA | {
"id": 7422,
"name": "VEGFA",
"pos": [
10,
3
]
} | {
"id": "C2712334",
"name": "Actual Aspiration",
"pos": [
304,
10
]
} |
These findings indicate that mutant PIK3CA is likely to function as an oncogene among ATC and less frequently well-differentiated thyroid carcinomas. | genomic_alterations | {
"id": 5290,
"name": "PIK3CA",
"pos": [
36,
6
]
} | {
"id": "C0238461",
"name": "Anaplastic thyroid carcinoma",
"pos": [
86,
3
]
} |
We resequenced the coding region, flanking intronic, and proximal promoter regions of the lamin a/c gene in 43 women with PCOS with evidence of upper-body obesity (waist circumference >88 cm) and identified 56 variants, two of which were nonsynonymous substitutions (lmna11 exon1 E98D; lmna24 exon 7 R455C). | NA | {
"id": 4000,
"name": "LMNA",
"pos": [
90,
14
]
} | {
"id": "C0455829",
"name": "Waist Circumference",
"pos": [
164,
19
]
} |
Alterations in TP53 have been described in many cancer types including hematological neoplasms. | genomic_alterations | {
"id": 7157,
"name": "TP53",
"pos": [
15,
4
]
} | {
"id": "C1306459",
"name": "Primary malignant neoplasm",
"pos": [
48,
6
]
} |
Samples of odontogenic cyst-lining keratinocytes and oral keratinocytes collected at surgery, and of cultured oral keratinocytes, were analyzed (1) by immunohistochemical staining of granulocyte macrophage colony stimulating factor (GM-CSF), human beta defensin-2 (HBD-2) and chemokine receptor 6 (CCR6) expressing cell (Langerhans cell, helper T cell and suppressor T cell) antibodies, (2) by reverse transcription-polymerase chain reaction (RT-PCR) to determine the expression of GM-CSF and HBD-2 mRNA and (3) by gas chromatography to evaluate the composition of fatty acids (16:0, 18:2, 20:4) in the cell membranes of the keratinocytes. | NA | {
"id": 1673,
"name": "DEFB4A",
"pos": [
493,
5
]
} | {
"id": "C0028879",
"name": "Odontogenic Cysts",
"pos": [
11,
16
]
} |
Moreover, the CCR4 ligand CCL22 is secreted by glioblastomas and may explain the specific Treg accumulation seen in these tumors. | biomarker | {
"id": 1233,
"name": "CCR4",
"pos": [
14,
4
]
} | {
"id": "C0027651",
"name": "Neoplasms",
"pos": [
122,
6
]
} |
In Sweden, a small portion of the inherited susceptibility is explained by the presence of germline mutations in the tumor suppressor gene CDKN2A. | genomic_alterations | {
"id": 1029,
"name": "CDKN2A",
"pos": [
139,
6
]
} | {
"id": "C0027651",
"name": "Neoplasms",
"pos": [
117,
5
]
} |
Knockdown of PTPN11, which encodes SHP-2, reduced the invasion, migration, adhesion, spreading, and survival of RA FLS. | NA | {
"id": 5781,
"name": "PTPN11",
"pos": [
35,
5
]
} | {
"id": "C0001511",
"name": "Tissue Adhesions",
"pos": [
75,
8
]
} |
Telomere length was evaluated by terminal repeat fragment method (TRF) in 50 patients with myelodysplastic syndromes (MDS) and acute myelogenous leukemia (AML) arising from MDS and in 21 patients with untreated primary AML to ascertain, whether telomere erosion was associated with progression of MDS towards overt leukemia. | NA | {
"id": 3567,
"name": "IL5",
"pos": [
66,
3
]
} | {
"id": "C3463824",
"name": "MYELODYSPLASTIC SYNDROME",
"pos": [
91,
25
]
} |
We have identified haploinsufficiency of the COL5A1 gene that encodes the proalpha1(V) chain of type V collagen in the classical form of the Ehlers-Danlos syndrome (EDS), a heritable connective-tissue disorder that severely alters the collagen-fibrillar structure of the dermis, joints, eyes, and blood vessels. | genomic_alterations | {
"id": 1289,
"name": "COL5A1",
"pos": [
45,
6
]
} | {
"id": "C0410787",
"name": "Hereditary Connective Tissue Disorder",
"pos": [
173,
36
]
} |
SNCA, UCH-L1, and LRRK2 mutations cause autosomal dominant PD and the remaining gene mutations autosomal recessive PD. | genomic_alterations | {
"id": 120892,
"name": "LRRK2",
"pos": [
18,
5
]
} | {
"id": "C0030567",
"name": "Parkinson Disease",
"pos": [
115,
2
]
} |
Our study suggests that HIF-1α promotes cap-dependent translation of selective mRNAs through up-regulating eIF4E1, which contributes to tumorsphere growth of breast cancer cells at hypoxia. | NA | {
"id": 3091,
"name": "HIF1A",
"pos": [
24,
6
]
} | {
"id": "C0242184",
"name": "Hypoxia",
"pos": [
181,
7
]
} |
A phase III, randomized, placebo-controlled trial has now demonstrated that octreotide long-acting repeatable (LAR) 30 mg can significantly prolong time to tumor progression among patients with metastatic midgut NETs regardless of functional status, chromogranin A level or age. | NA | {
"id": 5792,
"name": "PTPRF",
"pos": [
111,
3
]
} | {
"id": "C0178874",
"name": "Tumor Progression",
"pos": [
156,
17
]
} |
The epigenetic regulation of the REG1A promoter region may offer a potential therapeutic approach to improve chemotherapy for metastatic melanoma patients. | NA | {
"id": 5967,
"name": "REG1A",
"pos": [
33,
5
]
} | {
"id": "C0278883",
"name": "Metastatic melanoma",
"pos": [
126,
19
]
} |
We evaluated expression of Sox10 and DOG1 in normal cutaneous adnexa and in 194 primary skin adnexal tumors, and compared their performance in discriminating primary skin adnexal tumors from cutaneous metastatic adenocarcinomas with that of p40 and p63. | biomarker | {
"id": 10244,
"name": "RABEPK",
"pos": [
241,
3
]
} | {
"id": "C0001418",
"name": "Adenocarcinoma",
"pos": [
212,
15
]
} |
In both lines, a limited but consistent percentage of cells expresses gpIIbIIIa (CD41a), gpIIIa (CD61) and CD36, with no expression of gplb (CD42b), glycophorin A, hemoglobin and CD34. | NA | {
"id": 948,
"name": "CD36",
"pos": [
107,
4
]
} | {
"id": "C2239101",
"name": "Hemoglobin, CTCAE",
"pos": [
164,
10
]
} |
The t(17;19) translocation in acute lymphoblastic leukemias results in creation of E2A-hepatic leukemia factor (HLF) chimeric proteins that contain the DNA-binding and protein dimerization domains of the basic leucine zipper (bZIP) protein HLF fused to a portion of E2A proteins with transcriptional activation properties. | NA | {
"id": 3131,
"name": "HLF",
"pos": [
240,
3
]
} | {
"id": "C0040715",
"name": "Chromosomal translocation",
"pos": [
13,
13
]
} |
This suggests that DR5 is modulated by the ATF4-ATF3-CHOP axis in NSCLC after Sirt1/2 inhibition or salermide treatment. | biomarker | {
"id": 467,
"name": "ATF3",
"pos": [
48,
4
]
} | {
"id": "C0007131",
"name": "Non-Small Cell Lung Carcinoma",
"pos": [
66,
5
]
} |
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Dataset Card for TBGA
Dataset Summary
TBGA is a comprehensive dataset created for the purpose of Gene-Disease Association (GDA) extraction, generated from over 700,000 publications. It features more than 200,000 instances and 100,000 unique gene-disease pairs. Each instance in the dataset includes the specific sentence from which the GDA was extracted, the extracted GDA itself, and detailed information about the gene-disease pair involved. This dataset was semi-automatically annotated by Marchesin and Silvello using data sourced from the DisGeNET database, which houses one of the most extensive collections of genes and variants associated with human diseases. The dataset follows the OpenNRE format and contains the following relations:
{"NA": 0, "therapeutic": 1, "biomarker": 2, "genomic_alterations": 3}
Languages
The language in the dataset is English.
Dataset Structure
Dataset Instances
An example of 'train' looks as follows:
{
"text": "A monocyte chemoattractant protein-1 gene polymorphism is associated with occult ischemia in a high-risk asymptomatic population.",
"relation": "NA",
"h": {
"id": 6347,
"name": "CCL2",
"pos": [2, 34]
},
"t": {
"id": "C0231221",
"name": "Asymptomatic",
"pos": [105, 12]
}
}
Data Fields
text: the text of this example, astringfeature.h: the gene entityid: NCBI Entrez ID associated with the gene entity, astringfeature.pos: list consisting of starting position and length of the gene mention withintext, a list ofint32features.name: NCBI official gene symbol associated with the gene entity (not the text of the mention), astringfeature.
t: the disease entityid: UMLS Concept Unique Identifier (CUI) associated with the disease entity, astringfeature.pos: list consisting of starting position and length of the disease mention withintext, a list ofint32features.name: UMLS preferred term associated with the disease entity (not the text of the mention), astringfeature.
relation: a class label associated with the given GDA.
Citation
BibTeX:
@article{marchesin-silvello-2022,
title = "TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction",
author = "S. Marchesin and G. Silvello",
journal = "BMC Bioinformatics",
year = "2022",
url = "https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04646-6",
doi = "10.1186/s12859-022-04646-6",
volume = "23",
number = "1",
pages = "111"
}
APA:
- Marchesin, S., & Silvello, G. (2022). TBGA: A large-scale Gene-Disease Association dataset for Biomedical Relation Extraction. BMC Bioinformatics, 23(1), 111. https://doi.org/10.1186/s12859-022-04646-6
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