Manual Documents

The functional analysis platform for plant EAR motif-containing proteins was designed to provide users a useful and unique tools in studying genes that encoding EAR motif-containing proteins in plants. In plantEAR, we identified 20,542 EAR motif-containing proteins from 71 plants based on a Hidden Markov Model and orthologous gene search, and then we constructed a functional analysis platform for plant EAR motif-containing proteins by integrating a variety of functional annotations and processed data. Several tools were provided as functional support for EAR motif-containing proteins, such as browse, search, co-expression and protein-protein interaction (PPI) network analysis as well as cis-element analysis and gene set enrichment analysis (GSEA).


Home Page

Users can view basic introduction, contents and construction methods of plantEAR in the main page. User also can obtain basic function of this platform by Navigation Bar.


Browse Page

Through the browse interface, EAR motif-containing proteins can be browsed by species and gene family as following.

Browse by species as follows by click a species. User can view the EAR motif-containing proteins that bind directly to DNA or bind indirectly to DNA and other EAR motif-containing proteins that bind to DNA have not yet been identified.

Through the browse interface, EAR motif-containing protein can also be browsed by Gene Family. Browse by gene family as follows by click a gene family. User can view number of EAR motif-containing proteins and links to their details.

Users can find extensive information concerning a gene. There are many parts in this page: Basic Information, Gene Structure, Protein Sequence Feature Details, GO annotations, putative orthologs, blast search to NCBI and Uniprot.As to Arabidopsis thaliana, expression profiles and literature information are also provided. Most of they are easy to understand. The protein and transcript sequences of the gene are esay to download. Two model images of each gene were produced seperatedly, demonstrating the gene's structure and the protein's pfam domain and position of EAR motifs. For genes have more than one gene model, user can swith gene model in the basic information table. In putative orthologs part, families of its orthologous protein can also be obtained.


Search Page

Users could select at least one plant species in the corresponding form. Keyword search, Search by hormone ,Search by stress and search by epigenetic modification are offered in this page.

The description of EAR motif-containing proteins that related to phytohormone and stress can be search by evidence of publication, GO and microarray expression profile. If the species is not Arabidopsis, the EAR motif-containing proteins homologous to Arabidopsis can be searched. As shown in the following figure, an associated expression profile or a link to the reference literature could be viewed.


Tools Page

In this page, users can browse three tools of plantEAR including blast search, motif analysis and GSEA analysis.

BLAST search against transcript sequence or consensus peptide sequence of genes that encoding EAR motif-containing protein as following.

The Plant GeneSet Enrichment Analysis Toolkit (PlantGSEA) is an online websever for gene set enrichment analysis of plant organisms developed by our Lab in China Agricultural University. We developed this to meet the increasing demands of unearthing the biological meaning from large amounts of data. The PlantGSEA was designed to serve researchers from plant community as well as performance-efficient frame.

This page was designed for scanning motifs in the gene's promoter sequence. All motifs appearing in the sequence are listed and counted using the in-house script if users input a promoter sequence in fasta format. For a list of genes, users can not only get all the motifs presented in the genes' promoter sequence, but can also perform motif significance analysis.


Network Page

Users could submit a gene ID. Then corresponding interaction pairs will be visualized and showed. Protein-proteins in Arabidopsis obtained from BioGRID, PAIR, BAR and CCSB databases. Arabidopsis thaliana, Sorghum bicolor, Gossypium arboreum and Gossypium hisutum have integrated co-expression Network and predicted protein-protein Network. If species is not one of them, then network of its orthologous gene to Arabidopsis thaliana were chose to present.


Download Page

From the download interface, the transcripts sequences, CDS sequences, piptied sequences of genes that encoding the EAR motif-containing protein can be downloaded according to the species of the plant. And pattern of EAR motif, classification of gene family, annotations of EAR motif-containing protein also can be download.

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