Welcome to WheatCENet!

WheatCENet (Comparing Co-expression Networks of allohexaploid Wheat and its progenitors) database integrated 425 transcriptomic datasets (112 for Triticum aestivum (AABBDD), 153 for Triticum dicoccoides (AABB), 76 for Triticum urartu (AA), 42 for Aegilops tauschii (DD) from public databases to construct four global (T. aestivum, T. dicoccoides, T. urartu, and Ae. tauschii) and two T. aestivum conditional (tissue-specific and stress-treatment) co-expression network based on the PCC and MR algorithms.
We also collected comprehensive functional annotations (for example, Gene family, Ontology, miRNA, Metabolic pathway and so on) to predict gene functions. Besides, we provided analysis tools like GSEA, GO, module and motif analysis to analyze the possible function of gene sets and some basic tools like ID conversion, BLAST, sequence/FPKM extract. We hope that our database might help plant research communities to identify wheat functional genes or modules that regulate important agronomic traits.


How to cite:

Li, et al. "WheatCENet: A Database for Comparative Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors." Genomics, Proteomics & Bioinformatics (doi: 10.1016/j.gpb.2022.04.007). [Link]


Functional data

ClassificationCategory (Source/Method)AABBDDAABBAADD
OntologyGene Ontology (IWGSC/Blast2GO/MBKBASE)
Trait Ontology (IWGSC/ortholog relationship)
Plant Ontology (IWGSC)---
Pfam domainFunction domain (PfamScan)
Gene familyUbiquitin (UUCD)
Transcription factor/regulator (iTAK)
Protein kinase (iTAK)
Cytochrome P450 (BLAST+Pfam)
carbohydrate-active enzyme (ortholog)
Metabolic pathwayplantReactome (gramene)
PlantCyc (PlantCyc/ortholog)
KEGG (KEGG/KAAS/MBKBASE)
miRNAmiRNA target (miRbase/IWGSC/literature)-
PPIprotein-protein interaction (Inparanoid)

Tools

ClassificationCategoryMain application
Basic toolsQuick SearchGene search (detail information about gene), ortholog search (rice and arabidopsis) and Function search (Pfam, Gene Ontology, Functional module) .
Co-expression NetworkNetwork search (four global or two conditional); Network comparison (compare networks between two species or global and conditional); Ortholog network Comparison among three species.
BLAST analysisGene, CDS, protein sequence can be used.
ID conversionID conversion of different genome versions.
FPKM extractGene expression profile can be extracted or visualized by this tools.
Sequence extractRetrieve sequence by genomic interval or gene id.
UCSC genome browserEpigenomics data of T. aestivum and RNA-seq data of T. dicoccoides can be visualized.
Analysis toolsGene Sets AnalysisThese gene sets are divided into 5 categories, including GO gene sets (G1), Gene Family based gene sets (G2), Pathway gene sets (G3), Target gene sets (G4), other ontology gene sets (G5) based on PlantGSEA/PlantGSAD.
GO analysisGene ontology analysis can be used to predict the function of gene sets.
Motif analysismotif analysis can be used to predict the binding site of sequence or gene.
Module analysismodule analysis can be used to predict the function of gene sets based on co-expression network.

News

  • September 24, 2022 to October 30, 2022, the network may not be stable! During this time, the alternative link for WheatCENet (http://bioinformatics.cpolar.cn/WheatCENet/) can use.
  • 2022-3-26: Due to some reason, our Sever will be not reachable from 8:00a.m to 8:00p.m form April.3rd to April.5th (UTC+08:00). The mirror site of WheatCENet (http://139.186.22.30/WheatCENet) can be accessed normally! We are sincerely sorry for the inconvenience caused by us.
  • 2022-2-9: We setup a mirror site of WheatCENet (http://139.186.22.30/WheatCENet) to keep the access stability.
  • 2021-9-10: Transcription factors (TFs) targets (from Yijing Zhang group!) of Triticum urartu were integrated to GSEA analysis tools.
  • 2021-5-16: FPKM and Sequence extraction tools is available!
  • 2021-1-20: ID conversion tools is available!

  

  • 2020-9-20: The Module SEA tools is available!
  • 2020-7-20: Function search is available!
  • 2020-7-15: ortholog search is available!
  • 2020-6-2: Analysis tools is available!
  • 2020-4-1: The network comparison is available!
  • 2020-2-10: The function annotation is available!
  • 2019-11-20: The network is available!
  • 2019-9-30: The correlation was computed.
  • 2019-8-01: Collecting the transcriptomics data.


Links


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