Determination and inference of eukaryotic transcription factor sequence specificity (Q35249717)

7 August 2017

Determination and inference of eukaryotic transcription factor sequence specificity (English)

1 reference

7 August 2017

13

1 reference

7 August 2017

26

1 reference

Alejandro Montenegro-Montero

7 August 2017

Samuel A Lambert

8

0 references

Alejandro Montenegro-Montero

5

0 references

Mathew G Lewsey

Mathew Lewsey

16

0 references

Gad Shaulsky

Gad Shaulsky

22

0 references

Gunnar Rätsch

Gunnar Ratsch

25

0 references

Marian Walhout

23

Albertha J M Walhout

1 reference

7 August 2017

20

John S Reece-Hoyes

1 reference

7 August 2017

7

Hamed S Najafabadi

1 reference

7 August 2017

1

Matthew T Weirauch

1 reference

7 August 2017

2

Ally Yang

1 reference

7 August 2017

Mihai Albu

3

1 reference

7 August 2017

Atina Cote

4

1 reference

7 August 2017

Philipp Drewe

6

1 reference

7 August 2017

Ishminder Mann

9

1 reference

7 August 2017

Kate Cook

10

1 reference

7 August 2017

Hong Zheng

11

1 reference

7 August 2017

Alejandra Goity

12

1 reference

7 August 2017

Jean-Claude Lozano

14

1 reference

7 August 2017

Mary Galli

15

1 reference

7 August 2017

Eryong Huang

17

1 reference

7 August 2017

Tuhin Mukherjee

18

1 reference

7 August 2017

Xiaoting Chen

19

1 reference

7 August 2017

Sridhar Govindarajan

21

1 reference

7 August 2017

François-Yves Bouget

24

1 reference

7 August 2017

Joseph R Ecker

27

1 reference

7 August 2017

Timothy R Hughes

28

1 reference

7 August 2017

language of work or name

English

0 references

publication date

1 September 2014

1 reference

7 August 2017

1 reference

7 August 2017

158

1 reference

7 August 2017

1431-1443

1 reference

7 August 2017

6

1 reference

Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages

7 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A compendium of RNA-binding motifs for decoding gene regulation.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Evaluation of methods for modeling transcription factor sequence specificity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

DNA-binding specificities of human transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Systematic localization of common disease-associated variation in regulatory DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Increasing coverage of transcription factor position weight matrices through domain-level homology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Recognition models to predict DNA-binding specificities of homeodomain proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Quantitative analysis demonstrates most transcription factors require only simple models of specificity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Identification of Transcription Factor-DNA Interactions In Vivo

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Determining the specificity of protein-DNA interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

VND-INTERACTING2, a NAC domain transcription factor, negatively regulates xylem vessel formation in Arabidopsis.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A new generation of homology search tools based on probabilistic inference

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

The Pfam protein families database

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

ChIP-seq: advantages and challenges of a maturing technology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Distinguishing direct versus indirect transcription factor-DNA interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Diversity and complexity in DNA recognition by transcription factors

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Genomic location analysis by ChIP-Seq

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A transcription factor affinity-based code for mammalian transcription initiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Predicting the binding preference of transcription factors to individual DNA k-mers.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Transcription factors in fungi.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A high-resolution atlas of nucleosome occupancy in yeast

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Design of a combinatorial DNA microarray for protein-DNA interaction studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Clustering of DNA sequences in human promoters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Statistical analysis of over-represented words in human promoter sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Computational analysis of core promoters in the Drosophila genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A kingdom-level phylogeny of eukaryotes based on combined protein data

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Mutations in the zinc-finger region of the yeast regulatory protein ADR1 affect both DNA binding and transcriptional activation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Sequence logos: a new way to display consensus sequences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Toward rules relating zinc finger protein sequences and DNA binding site preferences

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Sequence-specific recognition of double helical nucleic acids by proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A unified model for yeast transcript definition

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

The Arabidopsis NAC transcription factor VNI2 integrates abscisic acid signals into leaf senescence via the COR/RD genes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Function and Evolution of C2H2 Zinc Finger Arrays

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

Altering the DNA-binding specificity of the yeast Matalpha 2 homeodomain protein

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4163041

A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25215497

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.CELL.2014.08.009

1 reference

7 August 2017

1 reference

7 August 2017

1 reference