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学者姓名:杨铁林

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Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women SCIE PubMed
期刊论文 | 2019 , 19 | CANCER CELL INTERNATIONAL
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BackgroundEstrogen exposure is a widely known risk factor for BC. And the interaction of estrogen with estrogen receptor (ER) plays an important role in breast cancer development. This case-control study aims to assess the association of genetic polymorphisms in the estrogen receptor genes with breast cancer (BC) susceptibility in Chinese Han women.MethodsFour polymorphisms (rs2881766, rs9383951, rs9340799 in ESR1 and rs3020449 in ESR2) were genotyped in 459 patients and 549 healthy controls using the Sequenom MassARRAY method. Odds ratio (OR) and 95% confidence intervals (95% CI) were calculated to evaluate the associations. False-positive report probability (FPRP) was utilized to examine the noteworthiness of significant findings.ResultsWe observed that rs2881766 was associated with a decreased BC risk (GG vs. TT: OR=0.63, 95% CI=0.44-0.91; GG vs. TT/GT: OR=0.68, 95% CI=0.49-0.95), while rs3020449 was associated with an increased risk of BC (CT vs. TT: OR=1.58, 95% CI=1.21-2.06; CT/CC vs. TT: OR=1.54, 95% CI=1.20-1.98; TT/CC vs. CT: OR=1.48, 95% CI=1.15-1.90). The other two polymorphisms have no relation with BC susceptibility. In addition, rs2881766 was correlated with lymph node metastasis and ER expression, and rs3020449 was related to tumor size, histological grade and ER expression. The values of false-positive report probability indicated that the significant associations of BC risk with both rs2881766 and rs3020449 were noteworthy.ConclusionsOur study suggests that polymorphisms rs2881766 and rs3020449 in estrogen receptor genes were associated with BC susceptibility as well as clinical features in Chinese women. These findings need further validation in a large population.

Keyword :

Polymorphism Breast cancer Estrogen receptor genes Susceptibility

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GB/T 7714 Dai, Zhijun , Tian, Tian , Wang, Meng et al. Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women [J]. | CANCER CELL INTERNATIONAL , 2019 , 19 .
MLA Dai, Zhijun et al. "Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women" . | CANCER CELL INTERNATIONAL 19 (2019) .
APA Dai, Zhijun , Tian, Tian , Wang, Meng , Yang, Tielin , Li, Hongtao , Lin, Shuai et al. Genetic polymorphisms of estrogen receptor genes are associated with breast cancer susceptibility in Chinese women . | CANCER CELL INTERNATIONAL , 2019 , 19 .
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Integrating regulatory features data for prediction of functional disease-associated SNPs SCIE PubMed
期刊论文 | 2019 , 20 (1) , 26-32 | BRIEFINGS IN BIOINFORMATICS
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Genome-wide association studies (GWASs) are an effective strategy to identify susceptibility loci for human complex diseases. However, missing heritability is still a big problem. Most GWASs single-nucleotide polymorphisms (SNPs) are located in noncoding regions, which has been considered to be the unexplored territory of the genome. Recently, data from the Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenomics projects have shown that many GWASs SNPs in the noncoding regions fall within regulatory elements. In this study, we developed a pipeline named functional disease-associated SNPs prediction (FDSP), to identify novel susceptibility loci for complex diseases based on the interpretation of the functional features for known disease-associated variants with machine learning. We applied our pipeline to predict novel susceptibility SNPs for type 2 diabetes (T2D) and hypertension. The predicted SNPs could explain heritability beyond that explained by GWAS-associated SNPs. Functional annotation by expression quantitative trait loci analyses showed that the target genes of the predicted SNPs were significantly enriched in T2D or hypertension-related pathways in multiple tissues. Our results suggest that combining GWASs and regulatory features data could identify additional functional susceptibility SNPs for complex diseases. We hope FDSP could help to identify novel susceptibility loci for complex diseases and solve the missing heritability problem.

Keyword :

FDSP SNPs regulatory feature data machine learning complex diseases missing heritability

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GB/T 7714 Dong, Shan-Shan , Guo, Yan , Yao, Shi et al. Integrating regulatory features data for prediction of functional disease-associated SNPs [J]. | BRIEFINGS IN BIOINFORMATICS , 2019 , 20 (1) : 26-32 .
MLA Dong, Shan-Shan et al. "Integrating regulatory features data for prediction of functional disease-associated SNPs" . | BRIEFINGS IN BIOINFORMATICS 20 . 1 (2019) : 26-32 .
APA Dong, Shan-Shan , Guo, Yan , Yao, Shi , Chen, Yi-Xiao , He, Mo-Nan , Zhang, Yu-Jie et al. Integrating regulatory features data for prediction of functional disease-associated SNPs . | BRIEFINGS IN BIOINFORMATICS , 2019 , 20 (1) , 26-32 .
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Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. PubMed SCIE
期刊论文 | 2019 , 9 (1) , 56 | Translational psychiatry
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Nearly 95% of susceptibility SNPs identified by genome-wide association studies (GWASs) are located in non-coding regions, which causes a lot of difficulty in deciphering their biological functions on disease pathogenesis. Here, we aimed to conduct a comprehensive functional annotation for all the schizophrenia susceptibility loci obtained from GWASs. Considering varieties of epigenomic regulatory elements, we annotated all 22,688 acquired susceptibility SNPs according to their genomic positions to obtain functional SNPs. The comprehensive annotation indicated that these functional SNPs are broadly involved in diverse biological processes. Histone modification enrichment showed that H3K27ac, H3K36me3, H3K4me1, and H3K4me3 were related to the development of schizophrenia. Transcription factors (TFs) prediction, methylation quantitative trait loci (meQTL) analyses, expression quantitative trait loci (eQTL) analyses, and proteomic quantitative trait loci analyses (pQTL) identified 447 target protein-coding genes. Subsequently, differential expression analyses between schizophrenia cases and controls, nervous system phenotypes from mouse models, and protein-protein interaction with known schizophrenia-related pathways and genes were carried out with our target genes. We finaly prioritized 10 target genes for schizophrenia (CACNA1C, CLU, CSNK2B, GABBR1, GRIN2A, MAPK3, NOTCH4, SRR, TNF, and SYNGAP1). Our results may serve as an encyclopedia of schizophrenia susceptibility SNPs and offer holistic guides for post-GWAS functional experiments.

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GB/T 7714 Niu Hui-Min , Yang Ping , Chen Huan-Huan et al. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. [J]. | Translational psychiatry , 2019 , 9 (1) : 56 .
MLA Niu Hui-Min et al. "Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia." . | Translational psychiatry 9 . 1 (2019) : 56 .
APA Niu Hui-Min , Yang Ping , Chen Huan-Huan , Hao Ruo-Han , Dong Shan-Shan , Yao Shi et al. Comprehensive functional annotation of susceptibility SNPs prioritized 10 genes for schizophrenia. . | Translational psychiatry , 2019 , 9 (1) , 56 .
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DETECTING EPISTASIS WITHIN CHROMATIN REGULATORY CIRCUITRY REVEALS FRRS1L AS A NOVEL SUSCEPTIBILITY GENE FOR OSTEOPOROSIS CPCI-S SCIE
会议论文 | 2018 , 29 , S389-S390 | WCO-IOF-ESCEO World Congress on Osteoporosis, Osteoarthritis and Musculoskeletal Diseases
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GB/T 7714 Yang, B. , Yao, S. , Dong, S. -S. et al. DETECTING EPISTASIS WITHIN CHROMATIN REGULATORY CIRCUITRY REVEALS FRRS1L AS A NOVEL SUSCEPTIBILITY GENE FOR OSTEOPOROSIS [C] . 2018 : S389-S390 .
MLA Yang, B. et al. "DETECTING EPISTASIS WITHIN CHROMATIN REGULATORY CIRCUITRY REVEALS FRRS1L AS A NOVEL SUSCEPTIBILITY GENE FOR OSTEOPOROSIS" . (2018) : S389-S390 .
APA Yang, B. , Yao, S. , Dong, S. -S. , Guo, Y. , Yang, T. -L. . DETECTING EPISTASIS WITHIN CHROMATIN REGULATORY CIRCUITRY REVEALS FRRS1L AS A NOVEL SUSCEPTIBILITY GENE FOR OSTEOPOROSIS . (2018) : S389-S390 .
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MODULATION OF LONG NONCODING RNAS BY RISK SNPS UNDERLYING GENETIC PREDISPOSITIONS TO OSTEOARTHRITIS CPCI-S SCIE
会议论文 | 2018 , 29 , S368-S368 | WCO-IOF-ESCEO World Congress on Osteoporosis, Osteoarthritis and Musculoskeletal Diseases
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GB/T 7714 Yang, B. , Yao, S. , Zhang, Y. -J. et al. MODULATION OF LONG NONCODING RNAS BY RISK SNPS UNDERLYING GENETIC PREDISPOSITIONS TO OSTEOARTHRITIS [C] . 2018 : S368-S368 .
MLA Yang, B. et al. "MODULATION OF LONG NONCODING RNAS BY RISK SNPS UNDERLYING GENETIC PREDISPOSITIONS TO OSTEOARTHRITIS" . (2018) : S368-S368 .
APA Yang, B. , Yao, S. , Zhang, Y. -J. , Dong, S. -S. , Guo, Y. , Yang, T. -L. . MODULATION OF LONG NONCODING RNAS BY RISK SNPS UNDERLYING GENETIC PREDISPOSITIONS TO OSTEOARTHRITIS . (2018) : S368-S368 .
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Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy SCIE PubMed Scopus
期刊论文 | 2018 , 17 (1) , 1775-1781 | MOLECULAR MEDICINE REPORTS
WoS CC Cited Count: 5 SCOPUS Cited Count: 3
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Cardiac fibrosis is one of the pathological characteristics of diabetic cardiomyopathy (DbCM). Matrine treatment has proven to be effective in cases of organ fibrosis and cardiovascular diseases. In the present study, the anti-fibrosis-associated cardioprotective effects of matrine on DbCM were investigated. Rats with experimental DbCM were administered matrine orally. Cardiac functions were evaluated using invasive hemodynamic examinations. Cardiac compliance was assessed in isolated hearts. Using Sirius Red and fluorescence staining, the collagen in diabetic hearts was visualized. MTT assay was used to select non-cytotoxic concentrations of matrine, which were subsequently used to treat isolated cardiac fibroblasts incubated under various conditions. Western blotting was performed to assess activation of the transforming growth factor-1 (TGF-1)/Smad signaling pathway. Rats with DbCM exhibited impaired heart compliance and left ventricular (LV) functions. Excessive collagen deposition in cardiac tissue was also observed. Furthermore, TGF-1/R-Smad (Smad2/3) signaling was revealed to be markedly activated; however, the expression of inhibitory Smad (I-Smad, also termed Smad7) was reduced in DbCM. Matrine administration led to a marked recovery in LV function and heart compliance by exerting inhibitory effects on TGF-1/R-Smad signaling pathway-induced fibrosis without affecting I-Smad. Incubation with a high concentration of glucose triggered the TGF-1/R-Smad (Smad2/3) signaling pathway and suppressed I-Smad signaling transduction in cultured cardiac fibroblasts, which led to an increase in the synthesis of collagen. After cardiac fibroblasts had been treated with matrine at non-cytotoxic concentrations without affecting I-Smad, matrine blocked TGF-1/R-Smad signaling transduction to repress collagen production and deposition. In conclusion, the results of the present study demonstrated that TGF-1/Smad signaling-associated cardiac fibrosis is involved in the impairment of heart compliance and LV dysfunction in DbCM. By exerting therapeutic effects against cardiac fibrosis via its influence on TGF-1/Smad signaling, matrine exhibited cardioprotective effects in DbCM.

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matrine transforming growth factor-1 diabetic cardiomyopathy Smads fibrosis cardiac fibroblasts

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GB/T 7714 Zhang, Yong , Cui, Lei , Guan, Gongchang et al. Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy [J]. | MOLECULAR MEDICINE REPORTS , 2018 , 17 (1) : 1775-1781 .
MLA Zhang, Yong et al. "Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy" . | MOLECULAR MEDICINE REPORTS 17 . 1 (2018) : 1775-1781 .
APA Zhang, Yong , Cui, Lei , Guan, Gongchang , Wang, Junkui , Qiu, Chuan , Yang, Tielin et al. Matrine suppresses cardiac fibrosis by inhibiting the TGF-/Smad pathway in experimental diabetic cardiomyopathy . | MOLECULAR MEDICINE REPORTS , 2018 , 17 (1) , 1775-1781 .
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ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma SCIE PubMed Scopus
期刊论文 | 2018 , 9 | NATURE COMMUNICATIONS
WoS CC Cited Count: 6 SCOPUS Cited Count: 6
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In human mutant BRAF melanoma cells, the stemness transcription factor FOXD3 is rapidly induced by inhibition of ERK1/2 signaling and mediates adaptive resistance to RAF inhibitors. However, the mechanism underlying ERK signaling control of FOXD3 expression remains unknown. Here we show that SOX10 is both necessary and sufficient for RAF inhibitor-induced expression of FOXD3 in mutant BRAF melanoma cells. SOX10 activates the transcription of FOXD3 by binding to a regulatory element in FOXD3 promoter. Phosphorylation of SOX10 by ERK inhibits its transcription activity toward multiple target genes by interfering with the sumoylation of SOX10 at K55, which is essential for its transcription activity. Finally, depletion of SOX10 sensitizes mutant BRAF melanoma cells to RAF inhibitors in vitro and in vivo. Thus, our work discovers a novel phosphorylation-dependent regulatory mechanism of SOX10 transcription activity and completes an ERK1/2/SOX10/FOXD3/ERBB3 axis that mediates adaptive resistance to RAF inhibitors in mutant BRAF melanoma cells.

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GB/T 7714 Han, Shujun , Ren, Yibo , He, Wangxiao et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma [J]. | NATURE COMMUNICATIONS , 2018 , 9 .
MLA Han, Shujun et al. "ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma" . | NATURE COMMUNICATIONS 9 (2018) .
APA Han, Shujun , Ren, Yibo , He, Wangxiao , Liu, Huadong , Zhi, Zhe , Zhu, Xinliang et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma . | NATURE COMMUNICATIONS , 2018 , 9 .
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ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma (vol 9, 28, 2018) SCIE PubMed Scopus
期刊论文 | 2018 , 9 | NATURE COMMUNICATIONS
WoS CC Cited Count: 1
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GB/T 7714 Han, Shujun , Ren, Yibo , He, Wangxiao et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma (vol 9, 28, 2018) [J]. | NATURE COMMUNICATIONS , 2018 , 9 .
MLA Han, Shujun et al. "ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma (vol 9, 28, 2018)" . | NATURE COMMUNICATIONS 9 (2018) .
APA Han, Shujun , Ren, Yibo , He, Wangxiao , Liu, Huadong , Zhi, Zhe , Zhu, Xinliang et al. ERK-mediated phosphorylation regulates SOX10 sumoylation and targets expression in mutant BRAF melanoma (vol 9, 28, 2018) . | NATURE COMMUNICATIONS , 2018 , 9 .
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An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation SCIE PubMed Scopus
期刊论文 | 2018 , 102 (5) , 776-793 | AMERICAN JOURNAL OF HUMAN GENETICS
WoS CC Cited Count: 1
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Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/ Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (similar to 360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.

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GB/T 7714 Chen, Xiao-Feng , Zhu, Dong-Li , Yang, Man et al. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation [J]. | AMERICAN JOURNAL OF HUMAN GENETICS , 2018 , 102 (5) : 776-793 .
MLA Chen, Xiao-Feng et al. "An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation" . | AMERICAN JOURNAL OF HUMAN GENETICS 102 . 5 (2018) : 776-793 .
APA Chen, Xiao-Feng , Zhu, Dong-Li , Yang, Man , Hu, Wei-Xin , Duan, Yuan-Yuan , Lu, Bing-Jie et al. An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation . | AMERICAN JOURNAL OF HUMAN GENETICS , 2018 , 102 (5) , 776-793 .
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Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women SCIE PubMed Scopus
期刊论文 | 2018 , 10 , 867-872 | CANCER MANAGEMENT AND RESEARCH
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Background: Forkhead box P3 (FOXP3) is a key gene in the immune system which also plays a role in tumor development. This study aims to explore the association of two FOXP3 polymorphisms (rs3761548 and rs3761549) with susceptibility to breast cancer (BC). Method: A case-control study was conducted, involving 560 patients and 583 healthy individuals from the Chinese Han population. The genotypes of FOXP3 polymorphisms were detected using the Sequenom MassARRAY method. The association between FOXP3 polymorphisms and BC risk was evaluated using a chi(2) test with an odds ratio (OR) and 95% confidence intervals (95% CIs) under six genetic models. False-positive report probability was utilized to examine whether the significant findings were noteworthy. Results: We observed that rs3761548 was associated with a higher BC risk in heterozygous, dominant, overdominant, and allele genetic models (CA vs CC: OR = 1.32, P= 0.031; CA/AA vs CC: OR = 1.32, P= 0.023; CA vs CC/AA: OR = 1.29, P= 0.042; A vs C: OR = 1.26, P= 0.029), whereas no significant association was found between rs3761549 and BC risk. In addition, CA, CA/AA genotype, and A allele of rs3761548 were related to larger tumor size, and the A allele was also correlated with a positive status of Her-2 in BC patients. Conclusion: Our study suggests that FOXP3 polymorphism rs3761548 is associated with BC susceptibility in the Chinese and may be involved in tumor progression. Future studies are needed to confirm the results in a larger population with more races.

Keyword :

polymorphism forkhead box P3 breast cancer risk

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GB/T 7714 Tian, Tian , Wang, Meng , Zheng, Yi et al. Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women [J]. | CANCER MANAGEMENT AND RESEARCH , 2018 , 10 : 867-872 .
MLA Tian, Tian et al. "Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women" . | CANCER MANAGEMENT AND RESEARCH 10 (2018) : 867-872 .
APA Tian, Tian , Wang, Meng , Zheng, Yi , Yang, Tielin , Zhu, Wenge , Li, Hongtao et al. Association of two FOXP3 polymorphisms with breast cancer susceptibility in Chinese Han women . | CANCER MANAGEMENT AND RESEARCH , 2018 , 10 , 867-872 .
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