Defining the condensate landscape of fusion oncoproteins DOI Creative Commons

Swarnendu Tripathi,

Hazheen K. Shirnekhi, Scott D. Gorman

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 28, 2023

Abstract Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality this phenomenon is unknown. We explored question testing 166 HeLa cells found that 58% formed condensates. The condensate-forming displayed physicochemical features distinct those condensate-negative segregated into feature-based groups aligned with their sub-cellular localization biological function. Using Machine Learning, we developed a predictor FO condensation behavior, discovered 67% ~3000 additional likely 35% predicted function altering gene expression. 47% were associated cell signaling functions, suggesting functional dichotomy between condensate-positive -negative FOs. Our Datasets reagents rich resources interrogate future.

Язык: Английский

KEGG mapping tools for uncovering hidden features in biological data DOI Open Access
Minoru Kanehisa, Yoko Sato,

Masayuki Kawashima

и другие.

Protein Science, Год журнала: 2021, Номер 31(1), С. 47 - 53

Опубликована: Авг. 23, 2021

Abstract In contrast to artificial intelligence and machine learning approaches, KEGG ( https://www.kegg.jp ) has relied on human develop “models” of biological systems, especially in the form pathway maps that are manually created by capturing knowledge from published literature. The models can then be used big data analysis, for example, uncovering systemic functions an organism hidden its genome sequence through simple procedure mapping. Here we present updated version Mapper, a suite mapping tools reported previously (Kanehisa Sato, Protein Sci 2020; 29:28–35), together with new versions map viewer BRITE hierarchy viewer. Significant enhancements have been made mapping, where result examined manipulation hierarchical trees, such as pruning zooming. tree feature also implemented taxonomy tool linking KO (KEGG Orthology) groups modules phenotypes.

Язык: Английский

Процитировано

520
FlyBase: a guided tour of highlighted features DOI Creative Commons
L. Sian Gramates,

Julie Agapite,

Helen Attrill

и другие.

Genetics, Год журнала: 2022, Номер 220(4)

Опубликована: Март 10, 2022

FlyBase provides a centralized resource for the genetic and genomic data of Drosophila melanogaster. As enters our fourth decade service to research community, we reflect on unique aspects look forward continued collaboration with larger model organism communities. In this study, emphasize dedicated reports tools have constructed meet specialized needs fly researchers but also facilitate use by other We highlight ways that support including an external resources page, help resources, multiple avenues which can interact FlyBase.

Язык: Английский

Процитировано

463
GENCODE: reference annotation for the human and mouse genomes in 2023 DOI Creative Commons
Adam Frankish, Sílvia Carbonell Sala, Mark Diekhans

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D942 - D949

Опубликована: Ноя. 24, 2022

GENCODE produces high quality gene and transcript annotation for the human mouse genomes. All is supported by experimental data serves as a reference genome biology clinical genomics. The consortium generates targeted data, develops bioinformatic tools carries out analyses that, along with externally produced methods, support identification of structures determination their function. Here, we present an update on genes, including developments in tools, major collaborations which underpin this progress. For example, report creation set non-canonical ORFs identified transcripts, LRGASP collaboration to assess use long transcriptomic build models, progress RefSeq UniProt increase convergence protein-coding propagation across pan-genome development new regulatory features GENCODE. Our accessible via Ensembl, UCSC Genome Browser https://www.gencodegenes.org.

Язык: Английский

Процитировано

359
Genenames.org: the HGNC resources in 2023 DOI Creative Commons
Ruth L. Seal, Bryony Braschi, Kristian Gray

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D1003 - D1009

Опубликована: Окт. 16, 2022

Abstract The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, 19 200 of which are assigned protein-coding genes, 14 pseudogenes nearly 9000 non-coding RNA public website, www.genenames.org, displays all nomenclature within Symbol Reports that contain data curated by advisors links related genomic, clinical, proteomic information. Here, we describe updates our resource, including improvements search facility new download features.

Язык: Английский

Процитировано

307
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments DOI Creative Commons
Fayrouz Hammal, Pierre de Langen, Aurélie Bergon

и другие.

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D316 - D325

Опубликована: Окт. 13, 2021

Abstract ReMap (https://remap.univ-amu.fr) aims to provide manually curated, high-quality catalogs of regulatory regions resulting from a large-scale integrative analysis DNA-binding experiments in Human, Mouse, Fly and Arabidopsis thaliana for hundreds transcription factors regulators. In this 2022 update, we have uniformly processed >11 000 sequencing datasets public sources across four species. The updated Human atlas includes 8103 covering total 1210 transcriptional regulators (TRs) with catalog 182 million (M) peaks, while the reaches 4.8M 423 TRs 694 datasets. Also, release is enriched by two new Mus musculus Drosophila melanogaster. First, Mouse consists 123M peaks 648 as result integration validation 5503 ChIP-seq Second, melanogaster contains 16.6M 550 1205 are browsable through track hubs at UCSC, Ensembl NCBI genome browsers. Finally, comes Cis Regulatory Module identification method, improved quality controls, faster search results, better user experience an interactive tour video tutorials on browsing filtering catalogs.

Язык: Английский

Процитировано

293
The UCSC Genome Browser database: 2024 update DOI Creative Commons
Brian J. Raney,

Galt P Barber,

Anna Benet‐Pagès

и другие.

Nucleic Acids Research, Год журнала: 2023, Номер 52(D1), С. D1082 - D1088

Опубликована: Ноя. 11, 2023

The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation on thousands of genome assemblies, ranging from human SARS-CoV2. This year, we have introduced new the Human Pangenome Reference Consortium viral genomes including We added 1,200 our GenArk system, increasing overall diversity representation. support for nine user-contributed track hubs public hub system. Additionally, released 29 tracks 11 mouse genome. Collectively, these features expand both breadth depth knowledge share publicly with

Язык: Английский

Процитировано

256
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations DOI Creative Commons
Nan Zhou, Xiaoqing Yuan, Qingsong Du

и другие.

Nucleic Acids Research, Год журнала: 2022, Номер 51(D1), С. D571 - D582

Опубликована: Окт. 28, 2022

Abstract Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation lipid peroxidation. It closely linked to the pathophysiological processes in many diseases. Since our publication first ferroptosis database 2020 (FerrDb V1), new findings have been published. To keep up with rapid progress research and provide timely high-quality data, here we present successor, FerrDb V2. contains 1001 regulators 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, which 264 drivers, 238 suppressors, 9 markers, 110 unclassified genes; 380 substance 201 inducers 179 inhibitors. Compared V1, articles increase >300%, 175%, 50.5%. Circular RNA pseudogene novel V2, percentage non-coding increases 7.3% 13.6%. External gene-related data were integrated, enabling thought-provoking gene-oriented analysis In conclusion, V2 will help acquire deeper insights into ferroptosis. freely accessible at http://www.zhounan.org/ferrdb/.

Язык: Английский

Процитировано

233
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility DOI Creative Commons
Juanjuan Kang, Qiang Tang, Jun He

и другие.

Nucleic Acids Research, Год журнала: 2021, Номер 50(D1), С. D326 - D332

Опубликована: Окт. 9, 2021

Abstract Establishing an RNA-associated interaction repository facilitates the system-level understanding of RNA functions. However, as these interactions are distributed throughout various resources, essential prerequisite for effectively applying data requires that they deposited together and annotated with confidence scores. Hence, we have updated database RNAInter (RNA Interactome Database) to version 4.0, which is freely accessible at http://www.rnainter.org or http://www.rna-society.org/rnainter/. Compared previous versions, current not only contains enlarged set, but also scoring system. The merits this 4.0 can be summarized in following points: (i) a redefined system achieved by integrating trust experimental evidence, scientific community types tissues/cells, (ii) redesigned fully functional enables more rapid retrieval browsing via upgraded user-friendly interface (iii) update entries >47 million manually mining literature six resources evidence from computational sources. Overall, will provide comprehensive readily interactome platform investigate regulatory landscape cellular RNAs.

Язык: Английский

Процитировано

165
IMPPAT 2.0: An Enhanced and Expanded Phytochemical Atlas of Indian Medicinal Plants DOI Creative Commons
R.P. Vivek-Ananth, Karthikeyan Mohanraj, Ajaya Kumar Sahoo

и другие.

ACS Omega, Год журнала: 2023, Номер 8(9), С. 8827 - 8845

Опубликована: Фев. 23, 2023

Compilation, curation, digitization, and exploration of the phytochemical space Indian medicinal plants can expedite ongoing efforts toward natural product traditional knowledge based drug discovery. To this end, we present IMPPAT 2.0, an enhanced expanded database compiling manually curated information on 4010 plants, 17,967 phytochemicals, 1095 therapeutic uses. Notably, 2.0 compiles associations at level plant parts provides a FAIR-compliant nonredundant in silico stereo-aware library phytochemicals from plants. The has been annotated with several useful properties to enable easier chemical space. We have also filtered subset 1335 drug-like which majority no similarity existing approved drugs. Using cheminformatics, characterized molecular complexity scaffold structural diversity performed comparative analysis other libraries. Altogether, is extensive atlas that accessible https://cb.imsc.res.in/imppat/.

Язык: Английский

Процитировано

122
Expanding PROTACtable genome universe of E3 ligases DOI Creative Commons
Yuan Liu, Jingwen Yang, Tianlu Wang

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 16, 2023

Abstract Proteolysis-targeting chimera (PROTAC) and other targeted protein degradation (TPD) molecules that induce by the ubiquitin-proteasome system (UPS) offer new opportunities to engage targets remain challenging be inhibited conventional small molecules. One fundamental element in process is E3 ligase. However, less than 2% amongst hundreds of ligases human genome have been engaged current studies TPD field, calling for recruiting additional ones further enhance therapeutic potential TPD. To accelerate development PROTACs utilizing under-explored ligases, we systematically characterize from seven different aspects, including chemical ligandability, expression patterns, protein-protein interactions (PPI), structure availability, functional essentiality, cellular location, PPI interface analyzing 30 large-scale data sets. Our analysis uncovers several as promising extant PROTACs. In total, combining confidence score, pattern, PPI, identified 76 PROTAC-interacting candidates. We develop a user-friendly flexible web portal ( https://hanlaboratory.com/E3Atlas/ ) aimed at assisting researchers rapidly identify with activities against specifically desired targets, facilitating these therapies cancer beyond.

Язык: Английский

Процитировано

71