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Citations per year

Number of citations per year for the bioinformatics software tool ATRM

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This map represents all the scientific publications referring to ATRM per scientific context
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ATRM specifications


Unique identifier OMICS_24574
Alternative name Arabidopsis Transcriptional Regulatory Map
Software type Application/Script
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Ge Gao

Publication for Arabidopsis Transcriptional Regulatory Map

ATRM citations


The founder cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

BMC Genomics
PMCID: 5093967
PMID: 27809788
DOI: 10.1186/s12864-016-3189-x
call_split See protocol

[…] Benjamini and Hochberg correction at a significance level set to a value of 0.05 in our analyses. To construct the transcriptional network within the DRNL-marked founder-cell population, we used the Arabidopsis Transcriptional Regulatory Map (ATRM) dataset [], supplemented with some additional gene–gene interactions from the literature. Transcription factors from the transcriptome dataset that we […]


Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

Sci Rep
PMCID: 5056366
PMID: 27721457
DOI: 10.1038/srep35064

[…] e known regulatory network data available in public databases.After removing redundant interactions, we collected 50,824 TF-target binary interactions between 529 TFs and 22,793 target genes from the Arabidopsis Transcriptional Regulatory Map (ATRM), AGRIS and AthaMap (). In total, 13,879 interactions between 333 TFs and 5,371 targets were retained for further analysis by filtering out stably expr […]


Transcriptome Analysis of Soybean Leaf Abscission Identifies Transcriptional Regulators of Organ Polarity and Cell Fate

Front Plant Sci
PMCID: 4756167
PMID: 26925069
DOI: 10.3389/fpls.2016.00125

[…] use members in this family were prominent in TF Cluster 1. Three members of the YABBY gene family (AFO, INO, and YAB5) were also prominent in the transcriptional regulatory network generated with the ATRM data (Jin et al., ; Figure ). In Arabidopsis, YABs regulate growth of the integuments and lateral organs, which includes leaves, sepals, petals, and carpels (Eshed et al., , , ; Kerstetter et al. […]

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ATRM institution(s)
State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Center for Bioinformatics, Peking University, Beijing, China; Monsanto Biotechnology R&D Center, Beijing, China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
ATRM funding source(s)
Supported by the National Natural Science Foundation of China (31470330), China 863 Programs (2006AA02Z334), the State Key Laboratory of Protein and Plant Gene Research, the National Program for Support of Top-notch Young Professionals and a China Postdoctoral Science Foundation Grant (2014M560017).

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