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Protocols

LegumeIP specifications

Information


Unique identifier OMICS_04491
Name LegumeIP
Restrictions to use None
Version 2.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Cicer arietinum
    • Glycine max
    • Medicago truncatula
    • Populus trichocarpa

Maintainer


  • person_outline Patrick Zhao

Publications for LegumeIP

LegumeIP citations

 (6)
library_books

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST SSR markers

2017
BMC Genomics
PMCID: 5445377
PMID: 28545396
DOI: 10.1186/s12864-017-3780-9

[…] s of NCBI, Swiss-Prot and Uniref90 using BLASTX with an E-value cut-off of 1e-05. BLASTX searches were also performed on the assembled transcripts using the legume database (http://plantgrn.noble.org/LegumeIP) and only the top hits were considered. The Annocript v1.1.2 pipeline [] was employed to obtain Gene Ontology (GO) terms for describing biological process, cellular components, and molecular […]

call_split

Development of Molecular Markers for Iron Metabolism Related Genes in Lentil and Their Expression Analysis under Excess Iron Stress

2017
Front Plant Sci
PMCID: 5390492
PMID: 28450880
DOI: 10.3389/fpls.2017.00579
call_split See protocol

[…] transcription factor or FER-like transcription factor gene sequence () was synthesized. Primers were also designed for the iron-related transporter gene based on the IRT1 mRNA coding sequence (CDS) (LegumeIP database reference no. IMGA[Medtr8g105030.1] of M. truncatula for the amplification of lentil IRT-1 in the qPCR experiment. The amplicon of the ferritin gene as well as the BHLH transcription […]

library_books

A Snapshot of Functional Genetic Studies in Medicago truncatula

2016
Front Plant Sci
PMCID: 4977297
PMID: 27555857
DOI: 10.3389/fpls.2016.01175

[…] also available for Medicago, some have been developed specifically for Medicago (and legumes) such as the Medicago Gbrowser (http://gb.sc.noble.org/cgi-bin/gb2/gbrowse), LegumeGRN (Wang M. et al., ), legumeIP (Li et al., ), and Legoo (http://www.legoo.org); and others have been adapted from Arabidopsis to Medicago such as PathExpress (Goffard and Weiller, ) and AgriGO (Du et al., ). Another key st […]

library_books

Transcriptome Response Mediated by Cold Stress in Lotus japonicus

2016
Front Plant Sci
PMCID: 4811897
PMID: 27066029
DOI: 10.3389/fpls.2016.00374

[…] ology (GO) enrichment analysis was carried out to reveal the biological processes differentially expressed under the stress conditions, using Fisher's exact test against the L. japonicus entry in the legumeIP database (Al-Shahrour et al., ; Li et al., ). Blast2GO software (https://www.blast2go.com/) was used and applied only for those transcripts that showed significant differential expression, de […]

library_books

Genome wide investigation and expression analysis of AP2 ERF gene family in salt tolerant common bean

2015
PMCID: 4849109
PMID: 27152109
DOI: 10.17179/excli2015-600

[…] A total of 180 common bean AP2-ERF genes were analyzed in LegumeIP in order to obtain promoter sequences of identified genes. The 2000 bp fragment upstream of the transcriptional start site of PvAP2-ERFs was determined […]

call_split

An improved protocol to study the plant cell wall proteome

2015
Front Plant Sci
PMCID: 4392696
PMID: 25914713
DOI: 10.3389/fpls.2015.00237
call_split See protocol

[…] 19/PXD001927. Finally, all identifications obtained based on the NCBI database were matched on the Medicago truncatula reference genome using an online platform available at http://plantgrn.noble.org/LegumeIP/v2/blasttranscript.jsp. Sequences were imported as FASTA sequences and blasted to the Mt4.0v1_GenesCDSSeq_20130731_1800 database. Searches were performed with an E-value cut-off of 1e-04 and […]

Citations

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LegumeIP institution(s)
Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, USA
LegumeIP funding source(s)
National Science Foundation [Grant DBI: 0960897, 1458597]; Samuel Roberts Noble Foundation

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