AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations

WK Shen, SY Chen, ZQ Gan, YZ Zhang… - Nucleic acids …, 2023 - academic.oup.com
Transcription factors (TFs) are proteins that interact with specific DNA sequences to regulate
gene expression and play crucial roles in all kinds of biological processes. To keep up with …

AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors

H Hu, YR Miao, LH Jia, QY Yu, Q Zhang… - Nucleic acids …, 2019 - academic.oup.com
Abstract The Animal Transcription Factor DataBase (AnimalTFDB) is a resource aimed to
provide the most comprehensive and accurate information for animal transcription factors …

[HTML][HTML] Matrix stiffness controls lymphatic vessel formation through regulation of a GATA2-dependent transcriptional program

M Frye, A Taddei, C Dierkes, I Martinez-Corral… - Nature …, 2018 - nature.com
Tissue and vessel wall stiffening alters endothelial cell properties and contributes to
vascular dysfunction. However, whether extracellular matrix (ECM) stiffness impacts …

KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors

C Feng, C Song, Y Liu, F Qian, Y Gao… - Nucleic acids …, 2020 - academic.oup.com
Transcription factors (TFs) and their target genes have important functions in human
diseases and biological processes. Gene expression profile analysis before and after …

A human-specific progenitor sub-domain extends neurogenesis and increases motor neuron production

S Jang, E Gumnit, H Wichterle - Nature Neuroscience, 2024 - nature.com
Neurogenesis lasts~ 10 times longer in developing humans compared to mice, resulting in
a> 1,000-fold increase in the number of neurons in the CNS. To identify molecular and …

T cell cytolytic capacity is independent of initial stimulation strength

AC Richard, ATL Lun, WWY Lau, B Göttgens… - Nature …, 2018 - nature.com
How cells respond to myriad stimuli with finite signaling machinery is central to immunology.
In naive T cells, the inherent effect of ligand strength on activation pathways and endpoints …

KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-) factors in multiple species

C Feng, C Song, S Song, G Zhang, M Yin… - Nucleic Acids …, 2024 - academic.oup.com
Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform
essential functions in diseases and biological processes. KnockTF 2.0 (http://www …

Deep learning in LncRNAome: contribution, challenges, and perspectives

T Alam, HRH Al-Absi, S Schmeier - Non-coding RNA, 2020 - mdpi.com
Long non-coding RNAs (lncRNA), the pervasively transcribed part of the mammalian
genome, have played a significant role in changing our protein-centric view of genomes …

TF-Marker: a comprehensive manually curated database for transcription factors and related markers in specific cell and tissue types in human

M Xu, X Bai, B Ai, G Zhang, C Song, J Zhao… - Nucleic acids …, 2022 - academic.oup.com
Transcription factors (TFs) play key roles in biological processes and are usually used as
cell markers. The emerging importance of TFs and related markers in identifying specific cell …

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

D Huang, HM Petrykowska, BF Miller, L Elnitski… - Genome …, 2019 - genome.cshlp.org
Compared to enhancers, silencers are notably difficult to identify and validate
experimentally. In search for human silencers, we utilized H3K27me3-DNase I …