wGRN
A platform using wheat integrative regulatory networks to guide functional gene discovery
wGRN is a free-accessible interactive platform for guiding functional gene discovery using integrative gene regulatory networks in wheat. The platform assembles transcription factor (TF)-target regulations from large-scale functional datasets and provides a series of versatile analysis tools for the community to mine functional genes and regulations for crop improvement. All analyses are based on the IWGSC v2.1 genome and an updated annotation. We will update the platform regularly.
News
  • Dec. 26, 2022   Cheers! The paper is published in Molecular Plant

  • Oct. 20, 2021   wGRN database is now open

Quick links

Search by gene


Regulator prediction


Pathway network


QTG miner


If use wGRN in pulication, please cite:
Yongming Chen, Yiwen Guo, Panfeng Guan, Yongfa Wang, Xiaobo Wang, Zihao Wang, Zhen Qin, Shengwei Ma, Mingming Xin, Zhaorong Hu, Yingyin Yao, Zhongfu Ni, Qixin Sun, Weilong Guo, and Huiru Peng. (2023) A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement. Molecular Plant, 16, 393-414. doi: 10.1016/j.molp.2022.12.019.

2. Gene ID

eg. TraesCS5A03G0919800 TraesCS5A02G383800

Analysis in progress...

Search

You can obtain the interested gene's annotations, expression, transcription factor (TF)-target interactions, and multi-omic dataset tracks. Interactions will be sorted according to the accuracy of predictions.

Regulator prediction

Using this tool, you can predict a series of regulators, or TFs, which function in regulating expression of interested genes. Interactions will be sorted according to the accuracy of predictions.

1. Input genes

Paste a gene list
Or upload file

2.

Analysis in progress...


Optional parameters

Enter background genes

1. Transcription factor/Gene ID

eg. TraesCS5A03G1116700

2. Functional prediction

Analysis in progress...

Function inference

Using this tool, you can obtain the function prediction of each TF based on Gene ontology (GO) biological processes, plant trait ontology (TO), and plant ontology (PO).

1. Select/Search ontology

only TF

Analysis in progress...

Pathway network

Using this tool, you can query networks of the interested GO biological process. The pathway network is based on function inference of each TFs and GO annotation.

1. Input gene

2. Cutoff of expression correlation
3. Include transcript not in the genome

Analysis in progress...

Coexpression

Using this tool, you can analyze coexpression patterns of genes of interest. Pearson correlation coefficient will be calculated

1. Input gene

eg. TraesCS5B03G1184600

Analysis in progress...

Homoeolog triad

Using this tool, you can view expression and regulation patterns of homoeolog triads.

1.1. Selected a genome assembly

The QTGs in the IWGSC RefSeq v1.1 will be converted to IWGSC RefSeq v2.1 gene models

1.2. Input QTL regions

2. QTL-related genes

3.

Analysis in progress...

QTG miner

Using this tool, you can prioritize high-confidence candidate genes for GWAS, map-based cloning, and BSA studies

Search gene by

Keyword
eg. TraesCS4B03G0748100,Heat stress,MYB
Location
eg. chr3A:1000000-2000000

Download

Analysis in progress...

Gene browser

Using this tool, you can search for gene information using keywords or locations.

1. Input gene

eg. TraesCS4B03G0748100,TraesCS3B03G1175400

2. Normalization

3. Include transcript not in the genome

Analysis in progress...

Expression

Using this tool, you can search for expression patterns of genes in diverse tissues and time-series transcriptomes.

2. Gene 1

eg. TraesCS2A03G1099400

3. Gene 2

eg. TraesCS2D03G0379400

Analysis in progress...

GRN comparison

Using this tool, you can compare functional relevance of interested genes based on two analysis methods, upstream regulator and downstream target

Search eQTL by

Gene ID
eg. TraesCS1A03G0572400
Location
eg. chr1A:12000000-13000000

Download

Analysis in progress...

eQTL

Using this tool, you can search for eQTL (expression quantitative trait loci) from 2-week-old seedlings and young spikes at the double-ridge stage.

Search miRNA-target interaction by miRNA or gene ID

eg. TraesCS5A03G1116700.1 miR172

Download

Analysis in progress...

miRNA-target interaction

Using this tool, you can search for miRNA-target interactions from the psRNATarget and psRobot prediction.

TF enrichment

Using this tool, you can perform TF enrichment ananlysis.

1. Input genes

Paste a gene list
Or upload file

2.

Analysis in progress...


Optional parameters

Enter background genes

1. Gene ID

3. expand GRN?

Analysis in progress...

GRN extraction

Using this tool, you can extract interactions linked to gene sets of interest.

Download wGRN_v1 annontation

We generated a new genome annotation, wGRN_v1, which is based on the IWGSC RefSeq v2.1 assembly. The wGRN_v1 annotation corrects gene models, and adds additional coding genes and lncRNAs, and assembled novel transcripts not in the genome.
If use the wGRN_v1 annotation in publication, please cite Chen et al., 2023.

Download gff3 file

MD5: 3c36c9d6708e33003dcc22c54bbd78d2

Download protein sequences

MD5: 230ada0e84fe5c9792b6985f791c831d

Download transcript sequences

MD5: 51154278d1e55eb6be0fd4b7933b413e

Download assembly of unmapped transcript sequences

MD5: cd9afd1ccde8355c86aad7ee3224cb05

Download transcription factors (TFs)

Download TF list

MD5: 49edcc7d9d4928b733d43cd4fce0abc5

Search gene

eg. TraesCS1A01G070400

Download

Analysis in progress...

ID conversion

Using this tool, you can submit one or more gene IDs to obtain its matching IDs in different annotation versions of Chinese Spring.

Contact us:

Technical contact: Chen, Yongming (E-mail: chen_yongming@126.com)

Corresponding contact: Guo, Weilong (E-mail: guoweilong@cau.edu.cn); Peng, Huiru (E-mail: penghuiru1452@163.com)

References:

  • Chen Y, Song W, Xie X, et al. A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era[J]. Molecular Plant, 2020, 13(12): 1694-1708.
  • Appels R, Eversole K, Stein N, et al. Shifting the limits in wheat research and breeding using a fully annotated reference genome[J]. Science, 2018, 361(6403).
  • Zhu T, Wang L, Rimbert H, et al. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly[J]. The Plant Journal, 2021, 107(1): 303-314.
  • Ramírez-González R H, Borrill P, Lang D, et al. The transcriptional landscape of polyploid wheat[J]. Science, 2018, 361(6403).
  • Wickham H. ggplot2: elegant graphics for data analysis[M]. springer, 2016.
  • Yu G, Wang L G, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters[J].Omics: a journal of integrative biology, 2012, 16(5): 284-287.
  • Almende B V, Thieurmel B, Robert T. visNetwork: Network Visualization using ‘vis. js’ Library. R package version 2.0. 8[J]. 2019.
  • Carbon S, Ireland A, Mungall C J, et al. AmiGO: online access to ontology and annotation data[J]. Bioinformatics, 2009, 25(2): 288-289.
  • Bastian M, Heymann S, Jacomy M. Gephi: an open source software for exploring and manipulating networks[C]//Third international AAAI conference on weblogs and social media. 2009.
  • Jin J, Tian F, Yang D C, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants[J]. Nucleic acids research, 2016: gkw982.
  • Wang M, Li Z, Zhang Y, et al. An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses[J]. The Plant Cell, 2021, 33(4): 865-881.
  • Bolser D M, Staines D M, Perry E, et al. Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data[M]//Plant genomics databases. Humana Press, New York, NY, 2017: 1-31.
  • Skinner M E, Uzilov A V, Stein L D, et al. JBrowse: a next-generation genome browser[J]. Genome research, 2009, 19(9): 1630-1638.
  • Xiang D, Quilichini T D, Liu Z, et al. The transcriptional landscape of polyploid wheats and their diploid ancestors during embryogenesis and grain development[J]. The Plant Cell, 2019, 31(12): 2888-2911.
  • De Clercq I, Van de Velde J, Luo X, et al. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators[J]. Nature Plants, 2021, 7(4): 500-513.
  • Zheng Y, Jiao C, Sun H, et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases[J]. Molecular plant, 2016, 9(12): 1667-1670.
  • He F, Wang W, Rutter W B, et al. Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat[J]. Nature communications, 2022, 13(1): 1-15.
  • Chen C, Li J, Feng J, et al. sRNAanno—a database repository of uniformly annotated small RNAs in plants[J]. Horticulture Research, 2021, 8.
  • Dai X, Zhuang Z, Zhao P X. psRNATarget: a plant small RNA target analysis server (2017 release)[J]. Nucleic acids research, 2018, 46(W1): W49-W54.
  • Wu H J, Ma Y K, Chen T, et al. PsRobot: a web-based plant small RNA meta-analysis toolbox[J]. Nucleic acids research, 2012, 40(W1): W22-W28.
  • Borrill P, Harrington S A, Simmonds J, et al. Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling[J]. Plant Physiology, 2019, 180(3): 1740-1755.
  • Bailey T L, Boden M, Buske F A, et al. MEME SUITE: tools for motif discovery and searching[J]. Nucleic acids research, 2009, 37(suppl_2): W202-W208.
  • Wang Y, Yu H, Tian C, et al. Transcriptome association identifies regulators of wheat spike architecture[J]. Plant Physiology, 2017, 175(2): 746-757.
  • Jia L, Yao W, Jiang Y, et al. Development of interactive biological web applications with R/Shiny[J]. Briefings in Bioinformatics, 2022, 23(1): bbab415.

External links:

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Technical contact: Chen, Yongming (E-mail: chen_yongming@126.com)
Corresponding contact: Guo, Weilong (E-mail: guoweilong@cau.edu.cn); Peng, Huiru (E-mail: penghuiru1452@163.com)