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Regulator prediction
Pathway network
QTG miner
1.1. Selected a genome assembly
The QTGs in the IWGSC RefSeq v1.1 will be converted to IWGSC RefSeq v2.1 gene models
3.
Analysis in progress...
QTG miner
Using this tool, you can prioritize high-confidence candidate genes for GWAS, map-based cloning, and BSA studies
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Gene browser
Using this tool, you can search for gene information using keywords or locations.
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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
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miRNA-target interaction
Using this tool, you can search for miRNA-target interactions from the psRNATarget and psRobot prediction.
Download wGRN_v1 annontation
If use the wGRN_v1 annotation in publication, please cite Chen et al., 2023.
Download gff3 file
MD5: 3c36c9d6708e33003dcc22c54bbd78d2
Download protein sequencesMD5: 230ada0e84fe5c9792b6985f791c831d
Download transcript sequencesMD5: 51154278d1e55eb6be0fd4b7933b413e
Download assembly of unmapped transcript sequencesMD5: cd9afd1ccde8355c86aad7ee3224cb05
Download transcription factors (TFs)
Download TF listMD5: 49edcc7d9d4928b733d43cd4fce0abc5
Search gene
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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:
- Triticeae-GeneTribe (TGT) - A homology database for Triticeae tribe
- Wheat SnpHub Portal - Genomic variation datasets of wheat and its progenitors
- WheatOmics - A platform combining multiple omics data to accelerate functional genomics studies in wheat
- Wheat-expVIP - Wheat Expression Browser
- CSCS - Chinese Spring Chromatin State Database