Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites.
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites.
复制标题
因子：转录因子基序和候选调控基序位点的更新目录。
DOI：
10.1093/nar/gkab1039
复制
发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Weng Z
中科院分区：
文献类型：
--
作者：
Pratt HE;Andrews GR;Phalke N;Purcaro MJ;van der Velde A;Moore JE;Weng Z
人类基因组含有约2000种转录调控蛋白，其中包括约1600种DNA结合转录因子（TF），它们识别特征序列基序，对基因表达产生调控作用。这些因子的结合特异性已经在体外（使用诸如HT-SELEX的技术）和体内（使用包括ChIP-seq的技术）进行了分析。我们之前开发了Factorbook，这是一个以TF为中心的注释，图案和综合分析数据库，基于ENCODE项目第二阶段的ChIP-seq数据。在这里，我们提出了Factorbook的更新，它显着扩展了细胞类型和TF覆盖范围的广度。该更新包括一个扩展的基序目录，该基序目录来自数千个ENCODE II期和III期ChIP-seq实验和HT-SELEX实验;该基序目录与候选顺式调控元件的ENCODE注册表整合，以注释全基因组候选TF结合位点的全面集合。该数据库还提供了新的工具，用于在机器学习框架内应用基序模型，并使用这些模型进行综合分析，包括变异和疾病的注释和性状遗传力。Factorbook可在www.example.com上公开获取;随着ENCODE第四阶段数据的发布，我们将继续扩大资源。
The human genome contains ∼2000 transcriptional regulatory proteins, including ∼1600 DNA-binding transcription factors (TFs) recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX, and in vivo, using techniques including ChIP-seq. We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. Factorbook is publicly available at www.factorbook.org; we will continue to expand the resource as ENCODE Phase IV data are released.
登录
查看更多内容
影响因子：
64.5
作者：
Slattery M;Riley T;Liu P;Abe N;Gomez-Alcala P;Dror I;Zhou T;Rohs R;Honig B;Bussemaker HJ;Mann RS
通讯作者：
Mann RS
影响因子：
7
作者：
Wang J;Zhuang J;Iyer S;Lin X;Whitfield TW;Greven MC;Pierce BG;Dong X;Kundaje A;Cheng Y;Rando OJ;Birney E;Myers RM;Noble WS;Snyder M;Weng Z
通讯作者：
Weng Z
影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
影响因子：
30.8
作者：
Finucane HK;Bulik-Sullivan B;Gusev A;Trynka G;Reshef Y;Loh PR;Anttila V;Xu H;Zang C;Farh K;Ripke S;Day FR;ReproGen Consortium;Schizophrenia Working Group of the Psychiatric Genomics Consortium;RACI Consortium;Purcell S;Stahl E;Lindstrom S;Perry JR;Okada Y;Raychaudhuri S;Daly MJ;Patterson N;Neale BM;Price AL
通讯作者：
Price AL
影响因子：
14.9
作者：
Khan A;Fornes O;Stigliani A;Gheorghe M;Castro-Mondragon JA;van der Lee R;Bessy A;Chèneby J;Kulkarni SR;Tan G;Baranasic D;Arenillas DJ;Sandelin A;Vandepoele K;Lenhard B;Ballester B;Wasserman WW;Parcy F;Mathelier A
通讯作者：
Mathelier A