ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks Article Swipe
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· 2015
· Open Access
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· DOI: https://doi.org/10.1093/nar/gkv398
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.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkv398
- https://academic.oup.com/nar/article-pdf/43/W1/W264/17435872/gkv398.pdf
- OA Status
- gold
- Cited By
- 25
- References
- 38
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2092194125
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W2092194125Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkv398Digital Object Identifier
- Title
-
ChIP-Array 2: integrating multiple omics data to construct gene regulatory networksWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2015Year of publication
- Publication date
-
2015-04-27Full publication date if available
- Authors
-
Panwen Wang, Jing Qin, Yiming Qin, Yun Zhu, Lily Yan Wang, Mulin Jun Li, Michael Q. Zhang, Junwen WangList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkv398Publisher landing page
- PDF URL
-
https://academic.oup.com/nar/article-pdf/43/W1/W264/17435872/gkv398.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/nar/article-pdf/43/W1/W264/17435872/gkv398.pdfDirect OA link when available
- Concepts
-
Biology, Chromatin, Gene regulatory network, Computational biology, Histone, Epigenetics, ChIA-PET, Transcription factor, Chromatin immunoprecipitation, Epigenomics, Regulation of gene expression, Genetics, Gene, Transcriptome, Cis-regulatory module, Gene expression, Chromatin remodeling, Promoter, DNA methylation, EnhancerTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
25Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1, 2024: 2, 2023: 1, 2022: 1, 2021: 2Per-year citation counts (last 5 years)
- References (count)
-
38Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W2103494816, https://openalex.org/W2000672459, https://openalex.org/W1966505629, https://openalex.org/W2038235796, https://openalex.org/W2101481512, https://openalex.org/W2004966039, https://openalex.org/W2070196639, https://openalex.org/W2102499347, https://openalex.org/W1964963969, https://openalex.org/W2142923264, https://openalex.org/W2127458423, https://openalex.org/W2093009550, https://openalex.org/W2117968640, https://openalex.org/W2159547203, https://openalex.org/W2035421116, https://openalex.org/W2167155938, https://openalex.org/W2149769193, https://openalex.org/W2017524046, https://openalex.org/W2161951664, https://openalex.org/W2171808845, https://openalex.org/W2099199578, https://openalex.org/W2131610374, https://openalex.org/W4231356616, https://openalex.org/W2146512944, https://openalex.org/W2141458291, https://openalex.org/W2033201031, https://openalex.org/W2107249189, https://openalex.org/W2157009395, https://openalex.org/W2130410032, https://openalex.org/W2006599064, https://openalex.org/W2159733516, https://openalex.org/W2013722146, https://openalex.org/W2110015307, https://openalex.org/W2120064326, https://openalex.org/W4232123484, https://openalex.org/W1988294855, https://openalex.org/W2030362521, https://openalex.org/W2155826575 |
| referenced_works_count | 38 |
| abstract_inverted_index.a | 22, 116 |
| abstract_inverted_index.18 | 122 |
| abstract_inverted_index.2, | 50, 113 |
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| abstract_inverted_index.we | 44, 79, 114 |
| abstract_inverted_index.Our | 27 |
| abstract_inverted_index.The | 10, 131 |
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| abstract_inverted_index.(GRNs). | 42 |
| abstract_inverted_index.(mESC). | 130 |
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| abstract_inverted_index.ChIP-Array, | 30 |
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| abstract_inverted_index.Arabidopsis, | 94 |
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| countries_distinct_count | 3 |
| institutions_distinct_count | 8 |
| citation_normalized_percentile.value | 0.85472594 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |