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1.
Nucleic Acids Res ; 51(W1): W520-W527, 2023 07 05.
Artículo en Inglés | MEDLINE | ID: mdl-37194711

RESUMEN

Super-enhancers (SEs) play an essential regulatory role in various biological processes and diseases through their specific interaction with transcription factors (TFs). Here, we present the release of SEanalysis 2.0 (http://licpathway.net/SEanalysis), an updated version of the SEanalysis web server for the comprehensive analyses of transcriptional regulatory networks formed by SEs, pathways, TFs, and genes. The current version added mouse SEs and further expanded the scale of human SEs, documenting 1 167 518 human SEs from 1739 samples and 550 226 mouse SEs from 931 samples. The SE-related samples in SEanalysis 2.0 were more than five times that in version 1.0, which significantly improved the ability of original SE-related network analyses ('pathway downstream analysis', 'upstream regulatory analysis' and 'genomic region annotation') for understanding context-specific gene regulation. Furthermore, we designed two novel analysis models, 'TF regulatory analysis' and 'Sample comparative analysis' for supporting more comprehensive analyses of SE regulatory networks driven by TFs. Further, the risk SNPs were annotated to the SE regions to provide potential SE-related disease/trait information. Hence, we believe that SEanalysis 2.0 has significantly expanded the data and analytical capabilities of SEs, which helps researchers in an in-depth understanding of the regulatory mechanisms of SEs.


Asunto(s)
Elementos de Facilitación Genéticos , Redes Reguladoras de Genes , Programas Informáticos , Factores de Transcripción , Animales , Humanos , Ratones , Regulación de la Expresión Génica , Genómica , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
2.
Nucleic Acids Res ; 49(D1): D1431-D1444, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33095866

RESUMEN

With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variations based on scores using nine annotation categories, and supports pathway downstream analysis. Importantly, VARAdb integrates a large amount of genetic and epigenomic data into five annotation sections, which include 'Variation information', 'Regulatory information', 'Related genes', 'Chromatin accessibility' and 'Chromatin interaction'. The detailed annotation information consists of motif changes, risk SNPs, LD SNPs, eQTLs, clinical variant-drug-gene pairs, sequence conservation, somatic mutations, enhancers, super enhancers, promoters, transcription factors, chromatin states, histone modifications, chromatin accessibility regions and chromatin interactions. This database is a user-friendly interface to query, browse and visualize variations and related annotation information. VARAdb is a useful resource for selecting potential functional variations and interpreting their effects on human diseases and biological processes.


Asunto(s)
Enfermedad de Alzheimer/genética , Bases de Datos Genéticas , Diabetes Mellitus Tipo 2/genética , Variación Genética , Genoma Humano , Sitios de Carácter Cuantitativo , Enfermedad de Alzheimer/metabolismo , Enfermedad de Alzheimer/patología , Cromatina , Ensamble y Desensamble de Cromatina , Diabetes Mellitus Tipo 2/metabolismo , Diabetes Mellitus Tipo 2/patología , Elementos de Facilitación Genéticos , Humanos , Internet , Anotación de Secuencia Molecular , Polimorfismo de Nucleótido Simple , Regiones Promotoras Genéticas , Programas Informáticos
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