Evidence map›Paper›PMID 25480687›Full record

ArticleDatabase : the journal of biological databases and curation2014

AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants.

Yi Wang, Roger Thilmony, Yunjun Zhao, Guoping Chen, Yong Q Gu

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

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.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Yi WangUSDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA USDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA Yong.Gu@ars.usda.gov.
Roger ThilmonyUSDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA.
Yunjun ZhaoUSDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA.
Guoping ChenUSDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA.
Yong Q GuUSDA-ARS, Western Regional Research Center, Genomics and Gene Discovery Research Unit, Albany, CA 94710, USA, Department of Plant Sciences, University of California, Davis, CA 95616, USA, Bioengineering College, Campus A, Chongqing University, Chongqing 400030, China, USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA 94710, USA and Energy Biosciences Institute, University of California, Berkeley, CA 94720, USA Yi.Wang@ars.usda.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Systems biology analysis of protein modules is important for understanding the functional relationships between proteins in the interactome. Here, we present a comprehensive database named AIM for Arabidopsis (Arabidopsis thaliana) interactome modules. The database contains almost 250,000 modules that were generated using multiple analysis methods and integration of microarray expression data. All the modules in AIM are well annotated using multiple gene function knowledge databases. AIM provides a user-friendly interface for different types of searches and offers a powerful graphical viewer for displaying module networks linked to the enrichment annotation terms. Both interactive Venn diagram and power graph viewer are integrated into the database for easy comparison of modules. In addition, predicted interologs from other plant species (homologous proteins from different species that share a conserved interaction module) are available for each Arabidopsis module. AIM is a powerful systems biology platform for obtaining valuable insights into the function of proteins in Arabidopsis and other plants using the modules of the Arabidopsis interactome. Database URL:http://probes.pw.usda.gov/AIM

Indexed as

Databases, ProteinProtein Interaction MapsAbscisic AcidArabidopsisArabidopsis ProteinsInternetPlantsUp-RegulationUser-Computer InterfaceAbscisic AcidArabidopsis Proteins

Identifiers

PMID25480687
PMCPMC4256526

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.