KEA3: improved kinase enrichment analysis via data integration DOI Creative Commons
Maxim V. Kuleshov, Zhuorui Xie,

Alexandra B. London

и другие.

Nucleic Acids Research, Год журнала: 2021, Номер 49(W1), С. W304 - W316

Опубликована: Апрель 23, 2021

Phosphoproteomics and proteomics experiments capture a global snapshot of the cellular signaling network, but these methods do not directly measure kinase state. Kinase Enrichment Analysis 3 (KEA3) is webserver application that infers overrepresentation upstream kinases whose putative substrates are in user-inputted list proteins. KEA3 can be applied to analyze data from phosphoproteomics studies predict responsible for observed differential phosphorylations. The background database contains measured predicted kinase-substrate interactions (KSI), kinase-protein (KPI), supported by co-expression co-occurrence data. To benchmark performance KEA3, we examined whether perturbed single-kinase perturbation followed gene expression experiments, collected kinase-targeting small molecules. We show integrating KSIs KPIs across sources produce composite ranking improves recovery expected kinase. available at https://maayanlab.cloud/kea3.

Язык: Английский

COSMIC: the Catalogue Of Somatic Mutations In Cancer DOI Creative Commons
John Tate,

Sally Bamford,

Harry Jubb

и другие.

Nucleic Acids Research, Год журнала: 2018, Номер 47(D1), С. D941 - D947

Опубликована: Окт. 11, 2018

COSMIC, the Catalogue Of Somatic Mutations In Cancer (https://cancer.sanger.ac.uk) is most detailed and comprehensive resource for exploring effect of somatic mutations in human cancer. The latest release, COSMIC v86 (August 2018), includes almost 6 million coding across 1.4 tumour samples, curated from over 26 000 publications. addition to mutations, covers all genetic mechanisms by which promote cancer, including non-coding gene fusions, copy-number variants drug-resistance mutations. primarily hand-curated, ensuring quality, accuracy descriptive data capture. Building on our manual curation processes, we are introducing new initiatives that allow us prioritize key genes diseases, react more quickly comprehensively findings literature. Alongside improvements public website data-download systems, functionality COSMIC-3D allows exploration within three-dimensional protein structures, their structural functional impacts, implications druggability. parallel with COSMIC's deep broad variant coverage, Gene Census (CGC) describes a catalogue driving every form Currently describing 719 genes, CGC has recently introduced descriptions how each drives disease, summarized into 10 cancer Hallmarks.

Язык: Английский

Процитировано

4124
ChEA3: transcription factor enrichment analysis by orthogonal omics integration DOI Creative Commons

Alexandra Keenan,

Denis Torre, Alexander Lachmann

и другие.

Nucleic Acids Research, Год журнала: 2019, Номер 47(W1), С. W212 - W224

Опубликована: Май 9, 2019

Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step understanding regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) a factor enrichment analysis tool that ranks TFs associated with user-submitted sets. The ChEA3 background database contains collection of set libraries generated from multiple sources including TF-gene co-expression RNA-seq studies, TF-target associations ChIP-seq experiments, and co-occurrence computed crowd-submitted lists. results these distinct are integrated to generate composite rank improves prediction correct upstream TF compared produced by individual libraries. We compare existing tools show performs better. By integrating libraries, we illuminate general properties such as whether behaves activator or repressor. web-server available https://amp.pharm.mssm.edu/ChEA3.

Язык: Английский

Процитировано

788
The UCSC Genome Browser database: 2021 update DOI Creative Commons
Jairo Navarro Gonzalez,

Ann S. Zweig,

Matthew L Speir

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D1046 - D1057

Опубликована: Ноя. 19, 2020

Abstract For more than two decades, the UCSC Genome Browser database (https://genome.ucsc.edu) has provided high-quality genomics data visualization and genome annotations to research community. As field of grows become available, new modes display are required accommodate technologies. New features released this past year include a Hi-C heatmap display, phased family trio for VCF files, various track improvements. Striving keep up-to-date, updates gene GENCODE Genes, NCBI RefSeq Ensembl Genes. tracks added human mouse genomes ENCODE registry candidate cis-regulatory elements, promoters from Eukaryotic Promoter Database, Select Matched Annotation EMBL-EBI (MANE). Within weeks learning about outbreak coronavirus, browser, with detailed annotation tracks, SARS-CoV-2 RNA reference assembly.

Язык: Английский

Процитировано

446
miRNA-based biomarkers, therapies, and resistance in Cancer DOI Creative Commons
Boxue He, Zhenyu Zhao, Qidong Cai

и другие.

International Journal of Biological Sciences, Год журнала: 2020, Номер 16(14), С. 2628 - 2647

Опубликована: Янв. 1, 2020

MicroRNAs (miRNAs), small non-coding RNAs (ncRNAs) of about 22 nucleotides in size, play important roles gene regulation, and their dysregulation is implicated human diseases including cancer.A variety miRNAs could take the cancer progression, participate process tumor immune, function with miRNA sponges.During last two decades, connection between various cancers has been widely researched.Based on evidence miRNA, numerous potential biomarkers for diagnosis prognosis have put forward, providing a new perspective screening.Besides, there are several miRNA-based therapies among different being conducted, advanced treatments such as combination synergistic strategies use complementary provide significant clinical benefits to patients potentially.Furthermore, it demonstrated that many engaged resistance complex underlying regulatory mechanisms, whose comprehensive cognition can help clinicians improve patient prognosis.With belief studies would great implications, we attempt summarize current situation development prospects this review.

Язык: Английский

Процитировано

438
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework DOI Creative Commons
Sarah E. Brnich, Ahmad Abou Tayoun, Fergus J. Couch

и другие.

Genome Medicine, Год журнала: 2019, Номер 12(1)

Опубликована: Дек. 31, 2019

Abstract Background The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) clinical variant interpretation guidelines established criteria different types evidence. This includes the strong evidence codes PS3 BS3 “well-established” functional assays demonstrating a has abnormal or normal gene/protein function, respectively. However, they did not provide detailed guidance on how should be evaluated, differences in application PS3/BS3 are contributor to discordance between laboratories. recommendation seeks more structured approach assessment use various levels strength based assay validation. Methods Clinical Genome Resource (ClinGen) Sequence Variant Interpretation (SVI) Working Group used curated from ClinGen Curation Expert Panel-developed rule specifications expert opinions refine over multiple in-person virtual meetings. We estimated odds pathogenicity using numbers controls determine minimum required reach moderate level Feedback Steering Committee outside experts were incorporated into recommendations at stages development. Results SVI developed evaluators regarding validity data four-step provisional framework appropriate that can applied interpretation. These steps as follows: (1) define disease mechanism, (2) evaluate applicability general classes field, (3) specific instances assays, (4) apply individual found 11 total pathogenic benign moderate-level absence rigorous statistical analysis. Conclusions evaluation described here help clarify process assays. Further, we hope these will develop productive partnerships with basic scientists who have useful interrogating function variety genes.

Язык: Английский

Процитировано

434
FlyBase: updates to theDrosophila melanogasterknowledge base DOI Creative Commons
Aoife Larkin, Steven J Marygold, Giulia Antonazzo

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D899 - D907

Опубликована: Окт. 22, 2020

FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports overview displays ('ribbons') expression data. We also variety recent important updates, incorporation developmental proteome, upgrades GAL4 search tab, additional Experimental Tool migration JBrowse genome browsing improvements batch queries/downloads Fast-Track Your Paper tool.

Язык: Английский

Процитировано

420
Genenames.org: the HGNC and VGNC resources in 2021 DOI Creative Commons
Susan Tweedie, Bryony Braschi, Kristian Gray

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D939 - D946

Опубликована: Окт. 10, 2020

Abstract The HUGO Gene Nomenclature Committee (HGNC) based at EMBL’s European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene in our current database of which 19 000 for protein-coding While we still update placeholder problematic symbols, working towards stabilizing where possible; 2000 disease associated genes now marked as stable symbol reports. All data is available the HGNC website https://www.genenames.org. Vertebrate (VGNC) was established assign standardized nomenclature line with vertebrate species lacking their own committee. In addition previous VGNC core chimpanzee, cow, horse dog, name cat, macaque pig. groups have been added currently include two complex families: olfactory receptors (ORs) cytochrome P450s (CYPs). collaboration specialists also named CYPs beyond set. https://vertebrate.genenames.org/. This article provides an overview online resources, focusing on updates last years.

Язык: Английский

Процитировано

314
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data DOI Creative Commons

Igor Rodchenkov,

Özgün Babur, Augustin Luna

и другие.

Nucleic Acids Research, Год журнала: 2019, Номер unknown

Опубликована: Окт. 10, 2019

Abstract Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly biomolecular complexes, transport and catalysis events physical interactions involving proteins, DNA, RNA, small molecules (e.g. metabolites drug compounds). Data collected from multiple providers in standard formats, the Biological Exchange (BioPAX) language Proteomics Standards Initiative Molecular Interactions format, then integrated. provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering bulk sets pathway data tables gene sets), (iii) reusable software libraries for working several programming languages (Java, R, Python Javascript) (iv) web service programmatically querying entire dataset. Visualization supported using Systems Graphical Notation (SBGN). currently contains 22 databases 4794 detailed human processes (i.e. pathways) ∼2.3 million interactions. To enhance usability large end-users, we develop maintain interactive applications training materials that enable exploration advanced analysis.

Язык: Английский

Процитировано

277
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases DOI Creative Commons
Blake Sweeney, Anton I. Petrov, Carlos Eduardo Ribas

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D212 - D220

Опубликована: Окт. 5, 2020

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides single access point to 44 resources and >18 million ncRNA from wide range organisms types. now also includes secondary (2D) structure information for >13 sequences, making the world's largest 2D database. The diagrams are displayed using R2DT, new visualization method uses consistent, reproducible recognizable layouts related RNAs. sequence similarity search has been updated with faster interface featuring facets filtering results by type, organism, source or any keyword. This tool available as reusable web component, integrated into several member databases, including Rfam, miRBase snoDB. To allow more fine-grained assignment types subtypes, all have annotated Sequence Ontology terms. continues grow provide central data resource community. freely at https://rnacentral.org.

Язык: Английский

Процитировано

262
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data DOI Creative Commons
Yue Gao,

Shipeng Shang,

Shuang Guo

и другие.

Nucleic Acids Research, Год журнала: 2020, Номер 49(D1), С. D1251 - D1258

Опубликована: Ноя. 9, 2020

An updated Lnc2Cancer 3.0 (http://www.bio-bigdata.net/lnc2cancer or http://bio-bigdata.hrbmu.edu.cn/lnc2cancer) database, which includes comprehensive data on experimentally supported long non-coding RNAs (lncRNAs) and circular (circRNAs) associated with human cancers. In addition, web tools for analyzing lncRNA expression by high-throughput RNA sequencing (RNA-seq) single-cell RNA-seq (scRNA-seq) are described. was several new features, including (i) Increased cancer-associated entries over the previous version. The current release 9254 lncRNA-cancer associations, 2659 lncRNAs 216 cancer subtypes. (ii) Newly adding 1049 circRNA-cancer 743 circRNAs 70 (iii) Experimentally regulatory mechanisms of cancer-related circRNAs, involving microRNAs, transcription factors (TF), genetic variants, methylation enhancers were included. (iv) Appending biological functions cell growth, apoptosis, autophagy, epithelial mesenchymal transformation (EMT), immunity coding ability. (v) clinical relevance in metastasis, recurrence, circulation, drug resistance, prognosis Additionally, two flexible online tools, scRNA-seq developed to enable fast customizable analysis visualization is a valuable resource elucidating associations between lncRNA, circRNA cancer.

Язык: Английский

Процитировано

232