AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors.
TLDR
The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.Abstract:
The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to provide the most comprehensive and accurate information for animal transcription factors (TFs) and cofactors. The AnimalTFDB has been maintained and updated for seven years and we will continue to improve it. Recently, we updated the AnimalTFDB to version 3.0 (http://bioinfo.life.hust.edu.cn/AnimalTFDB/) with more data and functions to improve it. AnimalTFDB contains 125,135 TF genes and 80,060 transcription cofactor genes from 97 animal genomes. Besides the expansion in data quantity, some new features and functions have been added. These new features are: (i) more accurate TF family assignment rules; (ii) classification of transcription cofactors; (iii) TF binding sites information; (iv) the GWAS phenotype related information of human TFs; (v) TF expressions in 22 animal species; (vi) a TF binding site prediction tool to identify potential binding TFs for nucleotide sequences; (vii) a separate human TF database web interface (HumanTFDB) was designed for better utilizing the human TFs. The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.read more
Citations
More filters
Journal ArticleDOI
A molecular cell atlas of the human lung from single-cell RNA sequencing.
Kyle J. Travaglini,Ahmad N. Nabhan,Ahmad N. Nabhan,Lolita Penland,Rahul Sinha,Astrid Gillich,Rene Sit,Stephen Chang,Stephanie D. Conley,Yasuo Mori,Yasuo Mori,Jun Seita,Gerald J. Berry,Joseph B. Shrager,Ross J. Metzger,Christin S. Kuo,Norma Neff,Irving L. Weissman,Stephen R. Quake,Mark A. Krasnow +19 more
TL;DR: Droplet- and plate-based single cell RNA sequencing applied to ~75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, have allowed them to define the gene expression profiles and anatomical locations of 58 cell populations in the human lung.
Journal ArticleDOI
Decoding human fetal liver haematopoiesis
Dorin-Mirel Popescu,Rachel A. Botting,Emily Stephenson,Kile Green,Simone Webb,Laura Jardine,Emily Calderbank,Krzysztof Polanski,Issac Goh,Mirjana Efremova,Meghan Acres,Daniel Maunder,Peter Vegh,Yorick Gitton,Jong-Eun Park,Roser Vento-Tormo,Zhichao Miao,Zhichao Miao,David Dixon,Rachel Rowell,David McDonald,James Fletcher,Elizabeth Poyner,Gary Reynolds,Michael W. Mather,Corina Moldovan,Lira Mamanova,Frankie Greig,Matthew D. Young,Kerstin B. Meyer,Steven Lisgo,Jaume Bacardit,Andrew Fuller,Ben Millar,Barbara A. Innes,Susan Lindsay,Michael J. T. Stubbington,Monika S. Kowalczyk,Bo Li,Orr Ashenberg,Marcin Tabaka,Danielle Dionne,Timothy L. Tickle,Timothy L. Tickle,Michal Slyper,Orit Rozenblatt-Rosen,Andrew Filby,Peter D. Carey,Alexandra-Chloé Villani,Alexandra-Chloé Villani,Anindita Roy,Aviv Regev,Aviv Regev,Alain Chédotal,Irene Roberts,Berthold Göttgens,Sam Behjati,Sam Behjati,Elisa Laurenti,Sarah A. Teichmann,Sarah A. Teichmann,Muzlifah Haniffa,Muzlifah Haniffa +62 more
TL;DR: A shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs is demonstrated, which is validated to produce an integrated map of fetal liver haematopoiesis.
Journal ArticleDOI
A cell atlas of human thymic development defines T cell repertoire formation.
Jong-Eun Park,Rachel A. Botting,Cecilia Domínguez Conde,Dorin-Mirel Popescu,Marieke Lavaert,Daniel J Kunz,Daniel J Kunz,Daniel J Kunz,Issac Goh,Emily Stephenson,Roberta Ragazzini,Roberta Ragazzini,Elizabeth Tuck,Anna Wilbrey-Clark,Kenny Roberts,Veronika R. Kedlian,John R. Ferdinand,Xiaoling He,Simone Webb,Daniel Maunder,Niels Vandamme,Krishnaa T. Mahbubani,Krzysztof Polanski,Lira Mamanova,Liam Bolt,David Crossland,David Crossland,Fabrizio De Rita,Andrew Fuller,Andrew Filby,Gary Reynolds,David Dixon,Kourosh Saeb-Parsy,Steven Lisgo,Deborah J. Henderson,Roser Vento-Tormo,Omer Ali Bayraktar,Roger A. Barker,Kerstin B. Meyer,Yvan Saeys,Paola Bonfanti,Paola Bonfanti,Sam Behjati,Sam Behjati,Menna R. Clatworthy,Menna R. Clatworthy,Menna R. Clatworthy,Tom Taghon,Muzlifah Haniffa,Muzlifah Haniffa,Sarah A. Teichmann,Sarah A. Teichmann +51 more
TL;DR: The authors' single-cell transcriptome profile of the thymus across the human lifetime and across species provides a high-resolution census of T cell development within the native tissue microenvironment, and identifies novel subpopulations of human thymic fibroblasts and epithelial cells and located them in situ.
Journal ArticleDOI
Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity.
Chrysothemis C. Brown,Chrysothemis C. Brown,Herman Gudjonson,Yuri Pritykin,Deeksha Deep,Vincent-Philippe Lavallée,Alejandra Mendoza,Rachel M. Fromme,Linas Mazutis,Charlotte E. Ariyan,Christina S. Leslie,Dana Pe'er,Alexander Y. Rudensky +12 more
TL;DR: Two principal cDC2 lineages are identified defined by distinct developmental pathways and transcriptional regulators, including T-bet and RORγt, two key transcription factors known to define innate and adaptive lymphocyte subsets in human cancer.
Journal ArticleDOI
An integrative multi-omics analysis to identify candidate DNA methylation biomarkers related to prostate cancer risk.
Lang Wu,Yaohua Yang,Xingyi Guo,Xiao-Ou Shu,Qiuyin Cai,Xiang Shu,Bingshan Li,Bingshan Li,Ran Tao,Chong Wu,Jason B. Nikas,Yanfa Sun,Yanfa Sun,Jingjing Zhu,Monique J. Roobol,Graham G. Giles,Graham G. Giles,Hermann Brenner,Esther M. John,Judith A. Clements,Judith A. Clements,Eli Marie Grindedal,Jong Y. Park,Janet L. Stanford,Janet L. Stanford,Zsofia Kote-Jarai,Christopher A. Haiman,Rosalind A. Eeles,Wei Zheng,Jirong Long +29 more
TL;DR: DNA methylation biomarkers associated with PrCa are identified and the findings suggest that specific CpG sites may influence PrCa via regulating expression of candidate PrCa target genes.
References
More filters
Journal ArticleDOI
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang,Tao Liu,Clifford A. Meyer,Jérôme Eeckhoute,David S. Johnson,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,Richard M. Myers,Myles Brown,Wei Li,X. Shirley Liu +11 more
TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Journal ArticleDOI
dbSNP: the NCBI database of genetic variation
Stephen T. Sherry,Minghong Ward,Michael Kholodov,Jonathan Baker,Lon Phan,Elizabeth M. Smigielski,Karl Sirotkin +6 more
TL;DR: The dbSNP database is a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, and is integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data.
Journal ArticleDOI
The Pfam protein families database: towards a more sustainable future
Robert D. Finn,Penelope Coggill,Ruth Y. Eberhardt,Ruth Y. Eberhardt,Sean R. Eddy,Sean R. Eddy,Jaina Mistry,Alex L. Mitchell,Simon C. Potter,Marco Punta,Marco Punta,Matloob Qureshi,Amaia Sangrador-Vegas,Gustavo A. Salazar,John Tate,John Tate,Alex Bateman +16 more
TL;DR: Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set, and the facility to view the relationship between families within a clan has been improved by the introduction of a new tool.
Journal ArticleDOI
FIMO: scanning for occurrences of a given motif.
TL;DR: Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices, and provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats.
Journal ArticleDOI
Systematic localization of common disease-associated variation in regulatory DNA.
Matthew T. Maurano,Richard Humbert,Eric Rynes,Robert E. Thurman,Eric Haugen,Hao Wang,Alex Reynolds,Richard Sandstrom,Hongzhu Qu,Hongzhu Qu,Jennifer A. Brody,Anthony Shafer,Fidencio Neri,Kristen Lee,Tanya Kutyavin,Sandra Stehling-Sun,Audra K. Johnson,Theresa K. Canfield,Erika Giste,Morgan Diegel,Daniel Bates,R. Scott Hansen,Shane Neph,Peter J. Sabo,Shelly Heimfeld,Antony Raubitschek,Steven F. Ziegler,Chris Cotsapas,Nona Sotoodehnia,Ian A. Glass,Shamil R. Sunyaev,Rajinder Kaul,John A. Stamatoyannopoulos +32 more
TL;DR: P pervasive involvement of regulatory DNA variation in common human disease and provide pathogenic insights into diverse disorders are suggested.