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funMotifs: Tissue-specific transcription factor motifs

https://doi.org/10.1101/683722
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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A Novel, Evolutionarily Conserved Gene Family with Putative Sequence-Specific Single-Stranded DNA-Binding Activity
inferredcites →https://doi.org/10.1016/0959-437x(94)90098-1openalex-snapshot
Myc—Max—Mad: a transcription factor network controlling cell cycle progression, differentiation and death
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2016.04.027openalex-snapshot
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
inferredcites →https://doi.org/10.1016/j.cell.2016.07.049openalex-snapshot
Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2016.10.042openalex-snapshot
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease
inferredcites →https://doi.org/10.1016/j.molcel.2015.05.004openalex-snapshot
High-Throughput Sequencing Technologies
inferredcites →https://doi.org/10.1016/s0092-8674(02)01284-9openalex-snapshot
X-Ray Structures of Myc-Max and Mad-Max Recognizing DNA
inferredcites →https://doi.org/10.1038/emm.2015.33openalex-snapshot
CTCF as a multifunctional protein in genome regulation and gene expression
inferredcites →https://doi.org/10.1038/gene.2010.20openalex-snapshot
Opposing effects of the HLA-DRB1*0301-DQB1*0201 haplotype on the risk for multiple sclerosis in diverse Arab populations in Israel
inferredcites →https://doi.org/10.1038/nature11232openalex-snapshot
The accessible chromatin landscape of the human genome
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12787openalex-snapshot
An atlas of active enhancers across human cell types and tissues
inferredcites →https://doi.org/10.1038/nature13182openalex-snapshot
A promoter-level mammalian expression atlas
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature15393openalex-snapshot
A global reference for human genetic variation
inferredcites →https://doi.org/10.1038/nature17661openalex-snapshot
Nucleotide excision repair is impaired by binding of transcription factors to DNA
inferredcites →https://doi.org/10.1038/nature24277openalex-snapshot
Genetic effects on gene expression across human tissues
inferredcites →https://doi.org/10.1038/nature24284openalex-snapshot
Association analysis identifies 65 new breast cancer risk loci
inferredcites →https://doi.org/10.1038/nbt.3678openalex-snapshot
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions
inferredcites →https://doi.org/10.1038/ng.2892openalex-snapshot
A general framework for estimating the relative pathogenicity of human genetic variants
inferredcites →https://doi.org/10.1038/ng.2982openalex-snapshot
An atlas of genetic influences on human blood metabolites
inferredcites →https://doi.org/10.1038/srep39709openalex-snapshot
The pan-cancer pathological regulatory landscape
inferredcites →https://doi.org/10.1073/pnas.1318948111openalex-snapshot
Defining functional DNA elements in the human genome
inferredcites →https://doi.org/10.1093/bioinformatics/btr064openalex-snapshot
FIMO: scanning for occurrences of a given motif
inferredcites →https://doi.org/10.1093/bioinformatics/btr539openalex-snapshot
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
inferredcites →https://doi.org/10.1093/bioinformatics/btv643openalex-snapshot
De novo identification of replication-timing domains in the human genome by deep learning
inferredcites →https://doi.org/10.1093/database/baw105openalex-snapshot
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gkv1176openalex-snapshot
JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles
inferredcites →https://doi.org/10.1093/nar/gkv1340openalex-snapshot
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease
inferredcites →https://doi.org/10.1093/nar/gkw1133openalex-snapshot
The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)
inferredcites →https://doi.org/10.1093/nar/gkx1081openalex-snapshot
The Encyclopedia of DNA elements (ENCODE): data portal update
inferredcites →https://doi.org/10.1101/237313openalex-snapshot
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
inferredcites →https://doi.org/10.1101/gr.121541.111openalex-snapshot
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
inferredcites →https://doi.org/10.1101/gr.137323.112openalex-snapshot
Annotation of functional variation in personal genomes using RegulomeDB
inferredcites →https://doi.org/10.1126/science.1141319openalex-snapshot
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.2667136openalex-snapshot
Transcriptional Regulation in Mammalian Cells by Sequence-Specific DNA Binding Proteins
inferredcites →https://doi.org/10.1177/1947601910378691openalex-snapshot
MYC and Breast Cancer
inferredcites →https://doi.org/10.1186/s13059-014-0560-6openalex-snapshot
Gateways to the FANTOM5 promoter level mammalian expression atlas
inferredcites →https://doi.org/10.1214/11-aoas466openalex-snapshot
Measuring reproducibility of high-throughput experiments
inferredcites →https://doi.org/10.12688/f1000research.10742.1openalex-snapshot
haploR: an R package for querying web-based annotation tools
inferredcites →https://doi.org/10.1371/journal.pgen.1002178openalex-snapshot
Identification of Novel Genetic Markers Associated with Clinical Phenotypes of Systemic Sclerosis through a Genome-Wide Association Strategy
inferredcites →https://doi.org/10.1371/journal.pgen.1006761openalex-snapshot
Identification of breast cancer associated variants that modulate transcription factor binding

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41467-024-47391-5openalex-snapshot
Emergence of enhancers at late DNA replicating regions
inferred← citeshttps://doi.org/10.1093/nar/gkz966openalex-snapshot
Ensembl 2020
inferred← citeshttps://doi.org/10.1101/2022.12.22.521323openalex-snapshot
Emergence of new enhancers at late DNA replicating regions
inferred← citeshttps://doi.org/10.1242/dev.200133openalex-snapshot
Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration
inferred← citeshttps://doi.org/10.1371/journal.pgen.1010614openalex-snapshot
Differential modularity of the mammalian Engrailed 1 enhancer network directs sweat gland development
inferred← citeshttps://doi.org/10.26508/lsa.201900523openalex-snapshot
Functional annotation of noncoding mutations in cancer
inferred← citeshttps://doi.org/10.3390/life16010015openalex-snapshot
Positive Selection in Aggression-Linked Genes and Their Protein Interaction Networks
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