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Protocols

ATRM specifications

Information


Unique identifier OMICS_24574
Name ATRM
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

Maintainer


  • person_outline Ge Gao

Publication for Arabidopsis Transcriptional Regulatory Map

ATRM citations

 (3)
call_split

The founder cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

2016
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 […]

library_books

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

2016
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 […]

library_books

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

2016
Front Plant Sci
PMCID: 4756167
PMID: 26925069
DOI: 10.3389/fpls.2016.00125

[…] an polarity, lateral organ growth and cell fate. The association of these TFs with organ polarity and boundary definition was further substantiated in the transcriptional networks generated using the ATRM data set (Jin et al., ), which suggests that these TFs may play a role in defining the separation layer within the multilayer LAZ. The most prominent TFs associated with each of the phases of abs […]

Citations

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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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