ArticleNucleic acids research2015
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 25 citations in OpenAlex.
- A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks.Briefings in bioinformatics · 2024Article
- Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data.NPJ systems biology and applications · 2023Review
- Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation.Journal of the Royal Society, Interface · 2020Article
- Integration of single-cell multi-omics for gene regulatory network inference.Computational and structural biotechnology journal · 2020Review
- Post genome-wide association analysis: dissecting computational pathway/network-based approaches.Briefings in bioinformatics · 2019Review
- From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo.Developmental cell · 2018Article
- An integrative method to decode regulatory logics in gene transcription.Nature communications · 2017Article
- Transcription factor-DNA binding: beyond binding site motifs.Current opinion in genetics & development · 2017Review
- Bacterial regulon modeling and prediction based on systematic cis regulatory motif analyses.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) play an important role in gene regulation. The interconnections among TFs, chromatin interactions, epigenetic marks and cis-regulatory elements form a complex gene transcription apparatus. Our previous work, ChIP-Array, combined TF binding and transcriptome data to construct gene regulatory networks (GRNs). Here we present an enhanced version, ChIP-Array 2, to integrate additional types of omics data including long-range chromatin interaction, open chromatin region and histone modification data to dissect more comprehensive GRNs involving diverse regulatory components. Moreover, we substantially extended our motif database for human, mouse, rat, fruit fly, worm, yeast and Arabidopsis, and curated large amount of omics data for users to select as input or backend support. With ChIP-Array 2, we compiled a library containing regulatory networks of 18 TFs/chromatin modifiers in mouse embryonic stem cell (mESC). The web server and the mESC library are publicly free and accessible athttp://jjwanglab.org/chip-array.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.