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Database Commons - LegumeIP

LegumeIP

Citations: 27

z-index 4.37

Short name LegumeIP
Full name An Integrative Platform to Study Gene Function and Genome Evolution in Legumes
Description LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes,to understand mechanisms that are fundamental to the legume species, especially the process of nitrogen-fixing endosymbiosis, which will be of great value to healthy, low input sustainable agriculture by decreasing the use of fertilizers, and ultimately to develope molecular based breeding tools to improve yield and quality of crop legumes.
URL http://plantgrn.noble.org/LegumeIP/
Year founded 2011
Last update & version 2015-11-17    v2.0
Availability Free to all users
University/Institution hosted The Samuel Roberts Noble Foundation
Address Plant Biology Division,The Samuel Roberts Noble Foundation,2510 Sam Noble Parkway,Ardmore,OK 73401,USA
City Ardmore
Province/State OK
Country/Region United States
Contact name Patrick Xuechun Zhao
Contact email pzhao@noble.org
Data type(s)
Major organism(s)
Keyword(s)
  • gene function
  • genome evolution
Publication(s)
  • LegumeIP 2.0-a platform for the study of gene function and genome evolution in legumes. [PMID: 26578557]

    Jun Li, Xinbin Dai, Zhaohong Zhuang, Patrick X Zhao
    Nucleic acids research 2016:44(D1)
    Citation (to be updated)

    Abstract: The LegumeIP 2.0 database hosts large-scale genomics and transcriptomics data and provides integrative bioinformatics tools for the study of gene function and evolution in legumes. Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein families and phylogenetic trees for six legume species: Medicago truncatula, Glycine max (soybean), Lotus japonicus, Phaseolus vulgaris (common bean), Cicer arietinum (chickpea) and Cajanus cajan (pigeon pea) and two outgroup reference species: Arabidopsis thaliana and Poplar trichocarpa. Moreover, the LegumeIP 2.0 features the following new data resources and bioinformatics tools: (i) an integrative gene expression atlas for four model legumes that include 550 array hybridizations from M. truncatula, 962 gene expression profiles of G. max, 276 array hybridizations from L. japonicas and 56 RNA-Seq-based gene expression profiles for C. arietinum. These datasets were manually curated and hierarchically organized based on Experimental Ontology and Plant Ontology so that users can browse, search, and retrieve data for their selected experiments. (ii) New functions/analytical tools to query, mine and visualize large-scale gene sequences, annotations and transcriptome profiles. Users may select a subset of expression experiments and visualize and compare expression profiles for multiple genes. The LegumeIP 2.0 database is freely available to the public at http://plantgrn.noble.org/LegumeIP/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. [PMID: 22110036]

    Jun Li, Xinbin Dai, Tingsong Liu, Patrick Xuechun Zhao
    Nucleic acids research 2012:40(Database issue)
    27 Citations (Google Scholar as of 2016-01-28)

    Abstract: Legumes play a vital role in maintaining the nitrogen cycle of the biosphere. They conduct symbiotic nitrogen fixation through endosymbiotic relationships with bacteria in root nodules. However, this and other characteristics of legumes, including mycorrhization, compound leaf development and profuse secondary metabolism, are absent in the typical model plant Arabidopsis thaliana. We present LegumeIP (http://plantgrn.noble.org/LegumeIP/), an integrative database for comparative genomics and transcriptomics of model legumes, for studying gene function and genome evolution in legumes. LegumeIP compiles gene and gene family information, syntenic and phylogenetic context and tissue-specific transcriptomic profiles. The database holds the genomic sequences of three model legumes, Medicago truncatula, Glycine max and Lotus japonicus plus two reference plant species, A. thaliana and Populus trichocarpa, with annotations based on UniProt, InterProScan, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes databases. LegumeIP also contains large-scale microarray and RNA-Seq-based gene expression data. Our new database is capable of systematic synteny analysis across M. truncatula, G. max, L. japonicas and A. thaliana, as well as construction and phylogenetic analysis of gene families across the five hosted species. Finally, LegumeIP provides comprehensive search and visualization tools that enable flexible queries based on gene annotation, gene family, synteny and relative gene expression.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
200 OK2018-11-13
200 OK2018-11-09
200 OK2018-11-06
200 OK2018-11-02
200 OK2018-10-30
200 OK2018-10-26
200 OK2018-10-23
200 OK2018-10-19
200 OK2018-10-16
200 OK2018-10-12
200 OK2018-10-09
200 OK2018-10-05
200 OK2018-10-02
200 OK2018-09-28
200 OK2018-09-25
200 OK2018-09-21
200 OK2018-09-18
200 OK2018-09-14
200 OK2018-09-11
200 OK2018-09-07
200 OK2018-09-04
200 OK2018-08-31
200 OK2018-08-28
200 OK2018-08-24
200 OK2018-08-21
200 OK2018-08-17
200 OK2018-08-14
200 OK2018-08-10
200 OK2018-08-07
200 OK2018-08-03
200 OK2018-07-31
200 OK2018-07-27
200 OK2018-07-24
200 OK2018-07-20
200 OK2018-07-17
200 OK2018-07-13
200 OK2018-07-10
200 OK2018-07-06
200 OK2018-07-03
200 OK2018-06-29
200 OK2018-06-26
200 OK2018-06-22
200 OK2018-06-19
200 OK2018-06-15
200 OK2018-06-12
200 OK2018-06-08
200 OK2018-06-05
200 OK2018-06-01
200 OK2018-05-29
200 OK2018-05-25
200 OK2018-05-22
200 OK2018-05-18
200 OK2018-05-15
200 OK2018-05-11
200 OK2018-05-08
200 OK2018-05-04
200 OK2018-05-01
200 OK2018-04-27
200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
200 OK2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
200 OK2018-01-16
200 OK2018-01-12
200 OK2018-01-09
200 OK2018-01-05
200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
200 OK2017-12-01
200 OK2017-11-28
200 OK2017-11-24
200 OK2017-11-21
200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
502 Failed2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
404 Failed2017-03-28
404 Failed2017-03-24
404 Failed2017-03-21
404 Failed2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
-1 Failed2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
-1 Failed2016-11-01
-1 Failed2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
-1 Failed2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

DNA Expression RNA Standard, Ontology and Nomenclature
Legumes
gene function genome evolution

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Chunlei Yu [2016-03-31]
    • Lin Liu [2016-01-05]
    • Chunlei Yu [2015-11-20]
    • Chunlei Yu [2015-06-29]
Stats