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Genomics, Proteomics & Bioinformatics

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https://www.readbyqxmd.com/read/30472416/ancestrypainter-a-graphic-program-for-displaying-ancestry-composition-of-populations-and-individuals
#1
Qidi Feng, Dongsheng Lu, Shuhua Xu
Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program, AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save space...
November 22, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30268932/the-genome-of-opium-poppy-reveals-evolutionary-history-of-morphinan-pathway
#2
Yiheng Hu, Ran Zhao, Peng Xu, Yuannian Jiao
No abstract text is available yet for this article.
September 28, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30268934/gaad-a-gene-and-autoimmiune-disease-association-database
#3
Guanting Lu, Xiaowen Hao, Wei-Hua Chen, Shijie Mu
Autoimmune diseases (ADs) arise from an abnormal immune response of the body against substances and tissues normally present in the body. More than a hundred of ADs have been described in the literature so far. Although their etiology remains largely unclear, various types of ADs tend to share more associated genes with other types of ADs than with non-AD types. Here we present GAAD, a gene and AD association database. In GAAD, we collected 44,762 associations between 49 ADs and 4249 genes from public databases and MEDLINE documents...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30268933/bioinformatics-commons-the-cornerstone-of-life-and-health-sciences
#4
EDITORIAL
Zhang Zhang, Yu Xue, Fangqing Zhao
No abstract text is available yet for this article.
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30268931/deepnitro-prediction-of-protein-nitration-and-nitrosylation-sites-by-deep-learning
#5
Yubin Xie, Xiaotong Luo, Yupeng Li, Li Chen, Wenbin Ma, Junjiu Huang, Jun Cui, Yong Zhao, Yu Xue, Zhixiang Zuo, Jian Ren
Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases. Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30266410/hccdb-a-database-of-hepatocellular-carcinoma-expression-atlas
#6
Qiuyu Lian, Shicheng Wang, Guchao Zhang, Dongfang Wang, Guijuan Luo, Jing Tang, Lei Chen, Jin Gu
Hepatocellular carcinoma (HCC) is highly heterogeneous in nature and has been one of the most common cancer types worldwide. To ensure repeatability of identified gene expression patterns and comprehensively annotate the transcriptomes of HCC, we carefully curated 15 public HCC expression datasets that cover around 4000 clinical samples and developed the database HCCDB to serve as a one-stop online resource for exploring HCC gene expression with user-friendly interfaces. The global differential gene expression landscape of HCC was established by analyzing the consistently differentially expressed genes across multiple datasets...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30266409/plad-a-transcriptomics-database-for-plant-defense-responses-to-pathogens-providing-new-insights-into-plant-immune-system
#7
Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He, Ziding Zhang
High-throughput transcriptomics technologies have been widely used to study plant transcriptional reprogramming during the process of plant defense responses, and a large quantity of gene expression data have been accumulated in public repositories. However, utilization of these data is often hampered by the lack of standard metadata annotation. In this study, we curated 2444 public pathogenesis-related gene expression samples from the model plant Arabidopsis and three major crops (maize, rice, and wheat). We organized the data into a user-friendly database termed as PlaD...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30244175/ptmd-a-database-of-human-disease-associated-post-translational-modifications
#8
Haodong Xu, Yongbo Wang, Shaofeng Lin, Wankun Deng, Di Peng, Qinghua Cui, Yu Xue
Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30223042/tsnadb-a-database-for-tumor-specific-neoantigens-from-immunogenomics-data-analysis
#9
Jingcheng Wu, Wenyi Zhao, Binbin Zhou, Zhixi Su, Xun Gu, Zhan Zhou, Shuqing Chen
Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA)...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30208340/ccgd-escc-a-comprehensive-database-for-genetic-variants-associated-with-esophageal-squamous-cell-carcinoma-in-chinese-population
#10
Linna Peng, Sijin Cheng, Yuan Lin, Qionghua Cui, Yingying Luo, Jiahui Chu, Mingming Shao, Wenyi Fan, Yamei Chen, Ai Lin, Yiyi Xi, Yanxia Sun, Lei Zhang, Chao Zhang, Wen Tan, Ge Gao, Chen Wu, Dongxin Lin
Esophageal squamous-cell carcinoma (ESCC) is one of the most lethal malignancies in the world and occurs at particularly higher frequency in China. While several genome-wide association studies (GWAS) of germline variants and whole-genome or whole-exome sequencing studies of somatic mutations in ESCC have been published, there is no comprehensive database publically available for this cancer. Here, we developed the Chinese Cancer Genomic Database-Esophageal Squamous Cell Carcinoma (CCGD-ESCC) database, which contains the associations of 69,593 single nucleotide polymorphisms (SNPs) with ESCC risk in 2022 cases and 2039 controls, survival time of 1006 ESCC patients (survival GWAS) and gene expression (expression quantitative trait loci, eQTL) in 94 ESCC patients...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30196115/heterometh-a-database-of-cell-to-cell-heterogeneity-in-dna-methylation
#11
Qing Huan, Yuliang Zhang, Shaohuan Wu, Wenfeng Qian
DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing (BS-seq) data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30172046/circpedia-v2-an-updated-database-for-comprehensive-circular-rna-annotation-and-expression-comparison
#12
Rui Dong, Xu-Kai Ma, Guo-Wei Li, Li Yang
Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic...
August 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30037509/corrigendum-to-goldclip-gel-omitted-ligation-dependent-clip-genomics-proteomics-bioinformatics-16-2-2018-136-143
#13
Jiaqi Gu, Ming Wang, Yang Yang, Ding Qiu, Yiqun Zhang, Jinbiao Ma, Yu Zhou, Gregory J Hannon, Yang Yu
No abstract text is available yet for this article.
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30010036/5-hydroxymethylome-in-circulating-cell-free-dna-as-a-potential-biomarker-for-non-small-cell-lung-cancer
#14
Ji Zhang, Xiao Han, Chunchun Gao, Yurong Xing, Zheng Qi, Ruijuan Liu, Yueqin Wang, Xiaojian Zhang, Yun-Gui Yang, Xiangnan Li, Baofa Sun, Xin Tian
Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30010035/a-systems-biology-approach-for-studying-heterotopic-ossification-proteomic-analysis-of-clinical-serum-and-tissue-samples
#15
LETTER
Erin L Crowgey, Jennifer T Wyffels, Patrick M Osborn, Thomas T Wood, Laura E Edsberg
Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO+ ) and without (HO- ) heterotopic ossification...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/30005964/identification-and-analysis-of-human-sex-biased-micrornas
#16
Chunmei Cui, Weili Yang, Jiangcheng Shi, Yong Zhou, Jichun Yang, Qinghua Cui, Yuan Zhou
Sex differences are widely observed under various circumstances ranging from physiological processes to therapeutic responses, and a myriad of sex-biased genes have been identified. In recent years, transcriptomic datasets of microRNAs (miRNAs), an important class of non-coding RNAs, become increasingly accessible. However, comprehensive analysis of sex difference in miRNA expression has not been performed. Here, we identified the differentially-expressed miRNAs between males and females by examining the transcriptomic datasets available in public databases and conducted a systemic analysis of their biological characteristics...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29981854/genome-wide-microrna-expression-profiles-in-copd-early-predictors-for-cancer-development
#17
Andreas Keller, Tobias Fehlmann, Nicole Ludwig, Mustafa Kahraman, Thomas Laufer, Christina Backes, Claus Vogelmeier, Caroline Diener, Frank Biertz, Christian Herr, Rudolf A Jörres, Hans-Peter Lenhof, Eckart Meese, Robert Bals
Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908294/tet2-regulates-osteoclast-differentiation-by-interacting-with-runx1-and-maintaining-genomic-5-hydroxymethylcytosine-5hmc
#18
Yajing Chu, Zhigang Zhao, David Wayne Sant, Ganqian Zhu, Sarah M Greenblatt, Lin Liu, Jinhuan Wang, Zeng Cao, Jeanette Cheng Tho, Shi Chen, Xiaochen Liu, Peng Zhang, Jaroslaw P Maciejewski, Stephen Nimer, Gaofeng Wang, Weiping Yuan, Feng-Chun Yang, Mingjiang Xu
As a dioxygenase, Ten-Eleven Translocation 2 (TET2) catalyzes subsequent steps of 5-methylcytosine (5mC) oxidation. TET2 plays a critical role in the self-renewal, proliferation, and differentiation of hematopoietic stem cells, but its impact on mature hematopoietic cells is not well-characterized. Here we show that Tet2 plays an essential role in osteoclastogenesis. Deletion of Tet2 impairs the differentiation of osteoclast precursor cells (macrophages) and their maturation into bone-resorbing osteoclasts in vitro...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908293/reversible-rna-modification-n-1-methyladenosine-m-1-a-in-mrna-and-trna
#19
REVIEW
Chi Zhang, Guifang Jia
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6 -methyladenosine (m6 A), N1 -methyladenosine (m1 A) has been found as a reversible modification in tRNA and mRNA. m1 A occurs at positions 9, 14, and 58 of tRNA, with m1 A58 being critical for tRNA stability. Other than the hundreds of m1 A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1 A also identifies >20 m1 A sites in mitochondrial genes...
June 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29753129/applications-of-rna-indexes-for-precision-oncology-in-breast-cancer
#20
REVIEW
Liming Ma, Zirui Liang, Hui Zhou, Lianghu Qu
Precision oncology aims to offer the most appropriate treatments to cancer patients mainly based on their individual genetic information. Genomics has provided numerous valuable data on driver mutations and risk loci; however, it remains a formidable challenge to transform these data into therapeutic agents. Transcriptomics describes the multifarious expression patterns of both mRNAs and non-coding RNAs (ncRNAs), which facilitates the deciphering of genomic codes. In this review, we take breast cancer as an example to demonstrate the applications of these rich RNA resources in precision medicine exploration...
April 2018: Genomics, Proteomics & Bioinformatics
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