简介
rentrez包可以调用ncbi数据库中的API来进行对数据的查询和汇总。这里就介绍一下目前可以想到的用法。其核心用法是基于entrez_search通过关键词搜索指定数据库。最终得到指定关键词的在某一数据库中检索到的结果的唯一ID，利用entrez_summary对执行ID进行总结。利用extract_from_esummary提取总结的制定内容。另外还可以通过entrez_link得到唯一ID的相关信息。最后主要是通过entrez_fetch可以得到ID的详细信息。具体哪个数据库可以通过entrez_fetch得到什么信息可以参见(表格)[https://www.ncbi.nlm.nih.gov/books/NBK25499/table/chapter4.T._valid_values_of__retmode_and/]
基于pubmed数据库
通过检索pubmed数据库可以得到相关关键词的相关文献的PMID.通过PMID可以进行下面操作。关键词检索方式支持ncbi数据库中的Advanced检索。这里以RNF180为例。其中由于和网页一样。pubmed检索结果最多一页显示200个检索结果。所以，一般我们返回的也就是最多的200个结果。这个结果可以通过retmax参数来改变返回结果。PS:有时候检索结果太会会被拒绝，所以这个时候我们可以写个循环即可
##加载包
library(rentrez)
pmid <- entrez_search(db = "pubmed", term = "RNF180", retmat = 3000)
id <- pmid$ids ##得到检索结果的pmid
id
## [1] "29278698" "27223257" "27050149" "26805552" "25945129" "25769451"
## [7] "25202403" "24833402" "23926250" "23262338" "22563461" "21717426"
## [13] "18363970"
提取文章相关信息
通过entrez_summary我们可以得到PMID的相关信息。其中可以用到的比如pmid、doi、杂志名、发表时间、被引次数、文章名等
pub_sum <- entrez_summary(db = "pubmed", id = id)
extract_pub <- extract_from_esummary(pub_sum, c("uid","pubdate","pmcrefcount", "title", "fulljournalname", "lastauthor"))
res1 <- data.frame(t(extract_pub))
head(res1)
## uid pubdate pmcrefcount
## 29278698 29278698 2018 Mar
## 27223257 27223257 2016 Jul 12
## 27050149 27050149 2016 Apr 26 1
## 26805552 26805552 2016 Mar 1
## 25945129 25945129 2015 15
## 25769451 25769451 2015 4
## title
## 29278698 GWAS links variants in neuronal development and actin remodeling related loci with pseudoexfoliation syndrome without glaucoma.
## 27223257 Mediation of the malignant biological characteristics of gastric cancer cells by the methylated CpG islands in RNF180 DNA promoter.
## 27050149 Promoter methylation of RNF180 is associated with H.pylori infection and serves as a marker for gastric cancer and atrophic gastritis.
## 26805552 Clinical and experimental role of ring finger protein 180 on lymph node metastasis and survival in gastric cancer.
## 25945129 DNA methylation and gene expression profiles show novel regulatory pathways in hepatocellular carcinoma.
## 25769451 Evaluating the clinical feasibility: The direct bisulfite genomic sequencing for examination of methylated status of E3 ubiquitin ligase RNF180 DNA promoter to predict the survival of gastric cancer.
## fulljournalname lastauthor
## 29278698 Experimental eye research Hennig EE
## 27223257 Oncotarget Liang H
## 27050149 Oncotarget Yuan Y
## 26805552 The British journal of surgery Hao X
## 25945129 Clinical epigenetics Friso S
## 25769451 Cancer biomarkers : section A of Disease markers Liang H
提取文章摘要
通过entrez_fetch我们可以提取相关文章的摘要信息
pub_ab <- entrez_fetch(db = "pubmed", id = id, rettype = "xml")
res_ab <- parse_pubmed_xml(pub_ab)
res_ab_df <- data.frame(do.call("rbind", res_ab))
head(res_ab_df)
## title
## 1 GWAS links variants in neuronal development and actin remodeling related loci with pseudoexfoliation syndrome without glaucoma.
## 2 Mediation of the malignant biological characteristics of gastric cancer cells by the methylated CpG islands in RNF180 DNA promoter.
## 3 Promoter methylation of RNF180 is associated with H.pylori infection and serves as a marker for gastric cancer and atrophic gastritis.
## 4 Clinical and experimental role of ring finger protein 180 on lymph node metastasis and survival in gastric cancer.
## 5 DNA methylation and gene expression profiles show novel regulatory pathways in hepatocellular carcinoma.
## 6 Evaluating the clinical feasibility: The direct bisulfite genomic sequencing for examination of methylated status of E3 ubiquitin ligase RNF180 DNA promoter to predict the survival of gastric cancer.
## authors
## 1 Zagajewska, Katarzyna, Pi膮tkowska, Magdalena, Goryca, Krzysztof, Ba艂abas, Aneta, Kluska, Anna, Paziewska, Agnieszka, Po艣piech, Ewelina, Grabska-Liberek, Iwona, Hennig, Ewa E
## 2 Deng, Jingyu, Guo, Jiangtao, Guo, Xiaofan, Hou, Yachao, Xie, Xingming, Sun, Changyu, Zhang, Rupeng, Yu, Xiaohua, Liang, Han
## 3 Han, Fang, Sun, Li-Ping, Liu, Shuang, Xu, Qian, Liang, Qiao-Yi, Zhang, Zhe, Cao, Hai-Chao, Yu, Jun, Fan, Dai-Ming, Nie, Yong-Zhan, Wu, Kai-Chun, Yuan, Yuan
## 4 Deng, J, Liang, H, Zhang, R, Hou, Y, Liu, Y, Ying, G, Pan, Y, Hao, X
## 5 Udali, Silvia, Guarini, Patrizia, Ruzzenente, Andrea, Ferrarini, Alberto, Guglielmi, Alfredo, Lotto, Valentina, Tononi, Paola, Pattini, Patrizia, Moruzzi, Sara, Campagnaro, Tommaso, Conci, Simone, Olivieri, Oliviero, Corrocher, Roberto, Delledonne, Massimo, Choi, Sang-Woon, Friso, Simonetta
## 6 Xie, Xing-Ming, Deng, Jing-Yu, Hou, Ya-Chao, Cui, Jing-Li, Wu, Wei-Peng, Ying, Guo-Guang, Dong, Qiu-Ping, Hao, Xi-Shan, Liang, Han
## year journal volume issue
## 1 2018 Experimental eye research 168 NULL
## 2 2016 Oncotarget 7 28
## 3 2016 Oncotarget 7 17
## 4 2016 The British journal of surgery 103 4
## 5 2015 Clinical epigenetics 7 NULL
## 6 2015 Cancer biomarkers : section A of Disease markers 15 3
## pages
## 1 138-148
## 2 43461-43474
## 3 24800-9
## 4 407-16
## 5 43
## 6 259-65
## key_words
## 1 Actins, Aged, Aged, 80 and over, Alleles, Case-Control Studies, Exfoliation Syndrome, Female, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Logistic Models, Male, Microarray Analysis, Middle Aged, Neurons, Polymorphism, Single Nucleotide
## 2 Animals, Apoptosis, Carcinogenesis, Cell Cycle, Cell Line, Tumor, Cell Proliferation, Cell Survival, CpG Islands, DNA Methylation, Disease Progression, Gene Expression Regulation, Neoplastic, Humans, Male, Mice, Mice, Nude, Neoplasm Invasiveness, Promoter Regions, Genetic, Stomach, Stomach Neoplasms, Transfection, Ubiquitin-Protein Ligases, Xenograft Model Antitumor Assays
## 3 Biomarkers, Tumor, CpG Islands, DNA Methylation, Disease Progression, Female, Gastritis, Atrophic, Helicobacter Infections, Humans, Male, Middle Aged, Prognosis, Promoter Regions, Genetic, Stomach Neoplasms, Ubiquitin-Protein Ligases
## 4 Animals, Blotting, Western, Cell Line, Tumor, China, Follow-Up Studies, Gene Expression Regulation, Neoplastic, Humans, Immunohistochemistry, Lymph Nodes, Lymphatic Metastasis, Mice, Mice, Nude, Neoplasms, Experimental, RNA, Neoplasm, Retrospective Studies, Reverse Transcriptase Polymerase Chain Reaction, Signal Transduction, Stomach Neoplasms, Survival Rate, Ubiquitin-Protein Ligases
## 5 NULL
## 6 Adult, Aged, Aged, 80 and over, DNA Methylation, Humans, Male, Middle Aged, Promoter Regions, Genetic, Sequence Analysis, DNA, Stomach Neoplasms, Sulfites, Survival Rate, Ubiquitin-Protein Ligases, Young Adult
## doi
## 1 10.1016/j.exer.2017.12.006
## 2 10.18632/oncotarget.9494
## 3 10.18632/oncotarget.8523
## 4 10.1002/bjs.10066
## 5 10.1186/s13148-015-0077-1
## 6 10.3233/CBM-150466
## pmid
## 1 29278698
## 2 27223257, 10411935, 19638575, 23300023, 21717426, 24980149, 16094395, 11498573, 18337604, 20974534, 21163902, 18363970, 16005018, 19325623, 25769451, 26254344, 24833402, 22075980, 18687884, 11891299, 2981636, 25016183, 16909914, 20686660, 2423876
## 3 27050149, 17848950, 18288406, 15736067, 21717426, 18528333, 12042769, 22017425, 25202403, 16491070, 25823664, 26086571, 16428266, 8827022, 25939322, 20824703, 25605238, 12154405, 23455381, 18363970, 25769451, 25232493, 24833402, 21386836, 18687884, 24686037, 23165367, 23058321, 14645235, 20959400, 19570204, 19307977, 16707623
## 4 26805552
## 5 25945129, 18632756, 19787223, 21692051, 17320506, 18612301, 23300023, 19639168, 21717426, 12520017, 11498573, 10539767, 22407776, 18337604, 24313162, 17585020, 18616668, 19957376, 20305825, 14643421, 17646865, 17438096, 22732356, 10087932, 18541040, 18813805, 19733471, 20205967, 20032811, 22315437, 20821239, 19588096, 21324880, 12161434, 18845355, 16007088, 21913943, 22234943, 11113131, 10361102, 22306342, 16054987, 12163697, 23527199, 15082451, 24730561, 17590990, 16909914, 11929966, 22689435, 18336669, 12925520
## 6 25769451
## abstract
## 1 Pseudoexfoliation syndrome (PEXS) is an age-related elastosis, strongly associated with the development of secondary glaucoma. It is clearly suggested that PEXS has a genetic component, but this has not been extensively studied. Here, a genome-wide association study (GWAS) using a DNA-pooling approach was conducted to explore the potential association of genetic variants with PEXS in a Polish population, including 103 PEXS patients without glaucoma and 106 perfectly (age- and gender-) matched controls. Individual sample TaqMan genotyping was used to validate GWAS-selected single-nucleotide polymorphism (SNP) associations. Multivariate binary logistic regression analysis was applied to develop a prediction model for PEXS. In total, 15 SNPs representing independent PEXS susceptibility loci were selected for further validation in individual samples. For 14 of these variants, significant differences in the allele and genotype frequencies between cases and controls were identified, of which 12 remained significant after Benjamini-Hochberg adjustment. The minor allele of five SNPs was associated with an increased risk of PEXS development, while for nine SNPs, it showed a protective effect. Beyond the known LOXL1 variant rs2165241, nine other SNPs were located within gene regions, including in OR11L1, CD80, TNIK, CADM2, SORBS2, RNF180, FGF14, FMN1, and RBFOX1 genes. None of these associations with PEXS has previously been reported. Selected SNPs were found to explain nearly 69% of the total risk of PEXS development. The overall risk prediction accuracy for PEXS, expressed by the area under the ROC聽curve (AUC) value, increased by 0.218, from 0.672 for LOXL1 rs2165241 alone to 0.89 when seven additional SNPs were included in the proposed 8-SNP prediction model. In conclusion, several new聽susceptibility loci for PEXS without glaucoma suggested that neuronal development and actin remodeling are potentially involved in either PEXS onset or inhibition or delay of its conversion to glaucoma.
## 2 We previously demonstrated that the methylation of ring finger protein 180 (RNF180) DNA promoter was specific to gastric cancer tissues. We reported that four hypermethylated CpG islands, namely, CpG-116, CpG-80, CpG+97, and CpG+102, in RNF180 promoter were significantly associated with the postoperative overall survival of gastric cancer patients. Correlation analysis revealed that the methylated status of CpG islands was significantly associated with the lymph node metastasis of gastric cancer. We formulated four types of MGC-803 cells with the specific demethylation of one of the four CpG islands through vector transfection method. Conventional detections for the biological characteristics of cancer cells showed that 1) the methylation of CpG+102 island in RNF180 DNA promoter could remarkably influence the comprehensively malignant biological characteristics of gastric cancer cells, including their proliferation, invasion, cell cycle, anti-apoptosis, and tumorigenicity. 2) The CpG+97 island, in addition to the CpG+102 island, should be considered as the other key methylated locus in RNF180 DNA promoter to mediate the malignant biological characteristics of gastric cancer cells. The methylated status of the key CpG islands of RNF180 DNA promoter may be used to predict the variations of the malignant biological characteristics of gastric cancer cells. The proposed method is a promising molecular therapy for gastric cancer.
## 3 Promoter methylation (PM) of RING-finger protein (RNF) 180 affects gastric cancer (GC) prognosis, but its association with risk of GC or atrophic gastritis (AG) is unclear. We investigated relationships between RNF180 PM and GC or AG, and the effects of Helicobactor pylori (H.pylori) infection on RNF180 PM. This study included 513 subjects (159 with GC, 186 with AG, and 168 healthy controls [CON]) for RNF180 PM analysis, and another 55 GC patients for RNF180 gene expression analysis. Methylation was quantified using average methylation rates (AMR), methylated CpG site counts (MSC) and hypermethylated CpG site counts (HSC). RNF180 promoter AMR and MSC increased with disease severity. Optimal cut-offs were GC + AG: AMR > 0.153, MSC > 4 or HSC > 1; GC: AMR > 0.316, MSC > 15 and HSC > 6\. Hypermethylation at 5 CpG sites differed significantly between GC/AG and CON groups, and was more common in GC patients than AG and CON groups for 2 other CpG sites. The expression of RNF180 mRNA levels in tumor were significantly lower than those in non-tumor, with the same as in hypermethylation than hypomethylation group. H.pylori infection increased methylation in normal tissue or mild gastritis, and increased hypermethylation risk at 3 CpG sites in AG. In conclusion, higher AMR, MSC and HSC levels could identify AG + GC or GC. Some RNF180 promoter CpG sites could identify precancerous or early-stage GC. H.pylori affects RNF180 PM in normal tissue or mild gastritis, and increases hypermethylation in 3 CpG sites in AG.
## 4 The hypermethylation of ring finger protein (RNF) 180 DNA promoter is significantly associated with lymph node metastasis of gastric cancer. The present study explored the potential mechanism of RNF180-regulated lymph node metastasis of gastric cancer., Associations between clinicopathological and survival data and RNF180 expression in gastric cancer tissues were analysed. The effects of RNF180 re-expression on gastric cancer cells were determined by means of proliferation, invasion, growth and lymphangiogenesis assays. A genome microarray was used to find potential target genes associated with lymphatic metastasis of gastric cancer cells regulated by RNF180., RNF180 was silenced or downregulated in 99 (73路9 per cent) of 134 gastric cancer tissues compared with 41路8 per cent of paired non-tumour tissues from patients. As an independent prognostic indicator of gastric cancer, RNF180 expression in gastric cancer tissues was negatively related to the number of metastatic lymph nodes. RNF180 was also downregulated in all seven gastric cancer cell lines examined. The re-expression of RNF180 in gastric cancer cells inhibited colony formation, proliferation, migration and invasion in vitro; re-expression of RNF180 also suppressed tumour growth and lymphangiogenesis in mice. Furthermore, re-expression of RNF180 downregulated the expression of hepatocyte growth factor, matrix metalloproteinase (MMP) 2, MMP-14, vascular endothelial growth factor C/D and chemokine receptor 7 in gastric cancer cells; it also downregulated the expression of podoplanin in tumour tissue of nude mice., RNF180 appears to act as a suppressor gene that inhibits lymph node metastasis in gastric cancer., Biological mechanisms that lead to lymph node metastasis in gastric cancer have not been clarified. Ring finger protein (RNF) 180 has been shown to participate in the processes of lymph node metastasis in several human malignancies. In this study, silencing or downregulation of RNF180 expression was significantly associated with lymph node metastasis of gastric cancer. In vitro, RNF180 expression suppressed the common biological characteristics of gastric cancer cells (HGC-27), including proliferation, invasion, lymphangio genesis and chemotaxis. RNF180 expression also inhibited tumour growth and tumour lymphangiogenesis in vivo. These results show that RNF180 is capable of inhibiting lymph node metastasis of gastric cancer by suppressing the intracellular activation of malignant molecular signals. Therefore, RNF180 could be considered as a promising biomarker for evaluation of the tumour aggressiveness and may be a target for future therapeutic intervention.
## 5 Alcohol is a well-known risk factor for hepatocellular carcinoma (HCC), but the mechanisms underlying the alcohol-related hepatocarcinogenesis are still poorly understood. Alcohol alters the provision of methyl groups within the hepatic one-carbon metabolism, possibly inducing aberrant DNA methylation. Whether specific pathways are epigenetically regulated in alcohol-associated HCC is, however, unknown. The aim of the present study was to investigate the genome-wide promoter DNA methylation and gene expression profiles in non-viral, alcohol-associated HCC. From eight HCC patients undergoing curative surgery, array-based DNA methylation and gene expression data of all annotated genes were analyzed by comparing HCC tissue and homologous cancer-free liver tissue., After merging the DNA methylation with gene expression data, we identified 159 hypermethylated-repressed, 30 hypomethylated-induced, 49 hypermethylated-induced, and 56 hypomethylated-repressed genes. Notably, promoter DNA methylation emerged as a novel regulatory mechanism for the transcriptional repression of genes controlling the retinol metabolism (ADH1A, ADH1B, ADH6, CYP3A43, CYP4A22, RDH16), iron homeostasis (HAMP), one-carbon metabolism (SHMT1), and genes with a putative, newly identified function as tumor suppressors (FAM107A, IGFALS, MT1G, MT1H, RNF180)., A genome-wide DNA methylation approach merged with array-based gene expression profiles allowed identifying a number of novel, epigenetically regulated candidate tumor-suppressor genes in alcohol-associated hepatocarcinogenesis. Retinol metabolism genes and SHMT1 are also epigenetically regulated through promoter DNA methylation in alcohol-associated HCC. Due to the reversibility of epigenetic mechanisms by environmental/nutritional factors, these findings may open up to novel interventional strategies for hepatocarcinogenesis prevention in HCC related to alcohol, a modifiable dietary component.
## 6 E3 ubiquitin ligase Ring finger protein 180 (RNF180) has been identified as a novel tumor suppressor in gastric cancer and the methylated CpG site count of RNF180 DNA promoter can predict the prognosis for gastric cancer patients., In the previous study, we demonstrated that methylated CpG site count of RNF180 DNA promoter was significantly associated with the survival of patients with gastric cancer using the bisulfite genomic sequencing (BGS) in the gastric cancer tissue with five clones per sample. It was so complicate for each patient underwent the BGS detection with clones. It is important to explore a simple, rapid and accurate method to detect methylated CpG site count to predicting the prognosis for gastric cancer patients., At present study, we detected hypermethylated and hypomethylated CpG site count of RNF180 DNA promoter in samples of 480 gastric cancer patients by direct bisulfite sequencing., We found that patients who possessed seven or less hypermethylated CpG sites of RNF180 DNA promoter had much better survival (p= 0.008), which was similar to our previous research results by using the BGS with clones. With the multivariate survival analysis, we found that T stage, N stage and hypermethylated CpG site count of RNF180 DNA promoter were the independent predictors of prognosis for gastric cancer patients., hypermethylated CpG site count of RNF180 DNA promoter for evaluating the prognosis of gastric cancer was reasonable by using the direct bisulfite sequencing.
提取和文章相关的其他数据库的信息
通过entrez_link可以查找某一类型相似的其他文章。通过db参数可以指定检索的数据库。
##检索pubmed数据库中和改文章相关的文章
pub_link <- entrez_link(dbfrom = "pubmed", db = "pubmed", id = id, cmd = "neighbor")
##得到引用这篇文章的文章ID(这样得到的是引用一类文章的其他文章。如果要用单独的文章的话。lapply一下即可)
citeid <- pub_link$links$pubmed_pubmed_citedin
##可以通过改变cmd为 acheck 了解上一个检索结果当中每个结果的含义
##检索gene数据库中和改文章相关的基因
gene_link <- entrez_link(dbfrom = "pubmed", db = "gene", id = id, cmd = "neighbor")
geneid <- gene_link[["links"]][["pubmed_gene"]]
###这种结果得到的基因不是很准确最好还是总摘要中提取
基于mesh数据库
利用主题词数据库。我们可以提取检索的某一关键词的所有相关主题词。这样可以检索的更全面一些。适用于meta检索的时候使用使用
###得到特殊ID
mesh_id <- entrez_search("mesh", "gastric cancer")
##提取mesh数据库的总结信息
mehs_summary <- entrez_summary("mesh", mesh_id$ids)
##提取检索结果的相同关键词
extract_mesh <- extract_from_esummary(mehs_summary, c("ds_scopenote", "ds_meshterms"))
res_mesh <- data.frame(t(extract_mesh))
基于gene数据库
利用主题词所有可以所有某一基因及其相关基因的信息。同时也可以检索某一疾病的相关基因
##默认是显示20个基因。可以通过retmax参数修改
gene_id <- entrez_search("gene", "(gastric cancer) AND \"Homo sapiens\"[porgn:__txid9606] ")
gene_sum <- entrez_summary("gene", gene_id$ids)
###提取检索结果的基因的相关信息
extrac_gene <- extract_from_esummary(gene_sum, c("uid", "name", "description", "chromosome", "maplocation", "otheraliases"))
res_gene <- data.frame(t(extrac_gene))
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