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Ni Ong S, Chin Tan B, Hanada K, How Teo C. Unearth of small open reading frames (sORFs) in drought stress transcriptome of Oryza sativa subsp. indica. Gene 2023:147579. [PMID: 37336274 DOI: 10.1016/j.gene.2023.147579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Drought is a major abiotic stress that influences rice production. Although the transcriptomic data of rice against drought is widely available, the regulation of small open reading frames (sORFs) in response to drought stress in rice is yet to be investigated. Different levels of drought stress have different regulatory mechanisms in plants. In this study, drought stress was imposed on four-leaf stage rice, divided into two treatments, 40% and 30% soil moisture content (SMC). The RNAs of the samples were extracted, followed by the RNA sequencing analysis on their sORF expression changes under 40%_SMC and 30%_SMC, and lastly, the expression was validated through NanoString. A total of 122 and 143 sORFs were differentially expressed (DE) in 40%_SMC and 30%_SMC, respectively. In 40%_SMC, 69 sORFs out of 696 (9%) DEGs were found to be upregulated. On the other hand, 69 sORFs out of 449 DEGs (11%) were significantly downregulated. The trend seemed to be higher in 30%_SMC, where 112 (12%) sORFs were found to be upregulated from 928 significantly upregulated DEGs. However, only 8% (31 sORFs out of 385 DEGs) sORFs were downregulated in 30%_SMC. Among the identified sORFs, 110 sORFs with high similarity to rice proteome in the PsORF database were detected in 40%_SMC, while 126 were detected in 30%_SMC. The Gene Ontology (GO) enrichment analysis of DE sORFs revealed their involvement in defense-related biological processes, such as defense response, response to biotic stimulus, and cellular homeostasis, whereas enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways indicated that DE sORFs were associated with tryptophan and phenylalanine metabolisms. Several DE sORFs were identified, including the top five sORFs (OsisORF_3394, OsisORF_0050, OsisORF_3007, OsisORF_6407, and OsisORF_7805), which have yet to be characterised. Since these sORFs were responsive to drought stress, they might hold significant potential as targets for future climate-resilient rice development.
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Affiliation(s)
- Sheue Ni Ong
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka‑shi, Fukuoka 820‑8502, Japan
| | - Chee How Teo
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, Khurana P, Khurana JP. Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1207-1231. [PMID: 36404527 DOI: 10.1111/pce.14496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Susmita M Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Martin Kieffer
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Global Food and Environment Institute, University of Leeds, Leeds, UK
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Liaquat F, Munis MFH, Arif S, Manzoor MA, Haroon U, Shah IH, Ashraf M, Kim HS, Che S, Qunlu L. Reprisal of Schima superba to Mn stress and exploration of its defense mechanism through transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1022686. [PMID: 36311055 PMCID: PMC9615920 DOI: 10.3389/fpls.2022.1022686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
One of the most diverse protein families, ATP-binding cassette (ABC) transporters, play a role in disease resistance, heavy metal tolerance, and food absorption.Differentially expressed genes contribute in the investigation of plant defense mechanisms under varying stress conditions. To elucidate the molecular mechanisms involved in Mn metal stress, we performed a transcriptomic analysis to explore the differential gene expression in Schima superba with the comparison of control. A total of 79.84 G clean data was generated and 6558 DEGs were identified in response to Mn metal stress. Differentially expressed genes were found to be involved in defense, signaling pathways, oxidative burst, transcription factors and stress responses. Genes important in metal transport were more expressive in Mn stress than control plants. The investigation of cis-acting regions in the ABC family indicated that these genes might be targeted by a large variety of trans-acting elements to control a variety of stress circumstances. Moreover, genes involved in defense responses, the mitogen-activated protein kinase (MAPK) signaling and signal transduction in S. superba were highly induced in Mn stress. Twenty ABC transporters were variably expressed on 1st, 5th, and 10th day of Mn treatment, according to the qRT PCR data. Inclusively, our findings provide an indispensable foundation for an advanced understanding of the metal resistance mechanisms. Our study will enrich the sequence information of S. superba in a public database and would provide a new understanding of the molecular mechanisms of heavy metal tolerance and detoxification.
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Affiliation(s)
- Fiza Liaquat
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Department of Agriculture, Forestry, and Bioresources, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Samiah Arif
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Urooj Haroon
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Muhammad Ashraf
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hyun Seok Kim
- Department of Agriculture, Forestry, and Bioresources, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural and Forest Meteorology, Seoul National University, Seoul, South Korea
- National Center for AgroMeteorology, Seoul, South Korea
| | - Shengquan Che
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Liu Qunlu
- Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai, China
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Abdul Aziz M, Sabeem M, Mullath SK, Brini F, Masmoudi K. Plant Group II LEA Proteins: Intrinsically Disordered Structure for Multiple Functions in Response to Environmental Stresses. Biomolecules 2021; 11:1662. [PMID: 34827660 PMCID: PMC8615533 DOI: 10.3390/biom11111662] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
In response to various environmental stresses, plants have evolved a wide range of defense mechanisms, resulting in the overexpression of a series of stress-responsive genes. Among them, there is certain set of genes that encode for intrinsically disordered proteins (IDPs) that repair and protect the plants from damage caused by environmental stresses. Group II LEA (late embryogenesis abundant) proteins compose the most abundant and characterized group of IDPs; they accumulate in the late stages of seed development and are expressed in response to dehydration, salinity, low temperature, or abscisic acid (ABA) treatment. The physiological and biochemical characterization of group II LEA proteins has been carried out in a number of investigations because of their vital roles in protecting the integrity of biomolecules by preventing the crystallization of cellular components prior to multiple stresses. This review describes the distribution, structural architecture, and genomic diversification of group II LEA proteins, with some recent investigations on their regulation and molecular expression under various abiotic stresses. Novel aspects of group II LEA proteins in Phoenix dactylifera and in orthodox seeds are also presented. Genome-wide association studies (GWAS) indicated a ubiquitous distribution and expression of group II LEA genes in different plant cells. In vitro experimental evidence from biochemical assays has suggested that group II LEA proteins perform heterogenous functions in response to extreme stresses. Various investigations have indicated the participation of group II LEA proteins in the plant stress tolerance mechanism, spotlighting the molecular aspects of group II LEA genes and their potential role in biotechnological strategies to increase plants' survival in adverse environments.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
| | - Miloofer Sabeem
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
| | - Sangeeta Kutty Mullath
- Department of Vegetable Science, College of Agriculture, Kerala Agricultural University, Thrissur 680656, India;
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax (CBS), University of Sfax, B.P 1177, Sfax 3018, Tunisia;
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (M.A.A.); (M.S.)
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Bhaskar A, Paul LK, Sharma E, Jha S, Jain M, Khurana JP. OsRR6, a type-A response regulator in rice, mediates cytokinin, light and stress responses when over-expressed in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:98-112. [PMID: 33581623 DOI: 10.1016/j.plaphy.2021.01.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/28/2021] [Indexed: 05/27/2023]
Abstract
Plants have evolved a complex network of components that sense and respond to diverse signals. In the present study, we have characterized OsRR6, a type-A response regulator, which is part of the two-component sensor-regulator machinery in rice. The expression of OsRR6 is induced by exogenous cytokinin and various abiotic stress treatments, including drought, cold and salinity stress. Organ-specific expression analysis revealed that its expression is high in anther and low in shoot apical meristem. The Arabidopsis plants constitutively expressing OsRR6 (OsRR6OX) exhibited reduced cytokinin sensitivity, adventitious root formation and enhanced anthocyanin accumulation in seeds. OsRR6OX plants were more tolerant to drought and salinity conditions when compared to wild-type. The hypocotyl growth in OsRR6OX seedlings was significantly inhibited under red, far-red and blue-light conditions and also a decline in transcript levels of OsRR6 was observed in rice under the above monochromatic as well as white light treatments. Transcriptome profiling revealed that the genes associated with defense responses and anthocyanin metabolism are up-regulated in OsRR6OX seedlings. Comparative transcriptome analysis showed that the genes associated with phenylpropanoid and triterpenoid biosynthesis are enriched among differentially expressed genes in OsRR6OX seedlings of Arabidopsis, which is in conformity with reanalysis of the transcriptome data performed in rice transgenics for OsRR6. Further, genes like DREB1A/CBF3, COR15A, KIN1, ERD10 and RD29A are significantly upregulated in OsRR6OX seedlings when subjected to ABA and abiotic stress treatments. Thus, a negative regulator of cytokinin signaling, OsRR6, plays a positive role in imparting abiotic stress tolerance.
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Affiliation(s)
- Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Laju K Paul
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Sampoornananda Jha
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Mukesh Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India; School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Sharma E, Borah P, Kaur A, Bhatnagar A, Mohapatra T, Kapoor S, Khurana JP. A comprehensive transcriptome analysis of contrasting rice cultivars highlights the role of auxin and ABA responsive genes in heat stress response. Genomics 2021; 113:1247-1261. [PMID: 33705886 DOI: 10.1016/j.ygeno.2021.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/10/2021] [Accepted: 03/04/2021] [Indexed: 11/16/2022]
Abstract
Sensing a change in ambient temperature is key to survival among all living organisms. Temperature fluctuations due to climate change are a matter of grave concern since it adversely affects growth and eventually the yield of crop plants, including two of the major cereals, i.e., rice and wheat. Thus, to understand the response of rice seedlings to elevated temperatures, we performed microarray-based transcriptome analysis of two contrasting rice cultivars, Annapurna (heat tolerant) and IR64 (heat susceptible), by subjecting their seedlings to 37 °C and 42 °C, sequentially. The transcriptome analyses revealed a set of uniquely regulated genes and related pathways in red rice cultivar Annapurna, particularly associated with auxin and ABA as a part of heat stress response in rice. The changes in expression of few auxin and ABA associated genes, such as OsIAA13, OsIAA20, ILL8, OsbZIP12, OsPP2C51, OsDi19-1 and OsHOX24, among others, were validated under high-temperature conditions using RT-qPCR. In particular, the expression of auxin-inducible SAUR genes was enhanced considerably at both elevated temperatures. Further, using genes that expressed inversely under heat vs. cold temperature conditions, we built a regulatory network between transcription factors (TF) such as HSFs, NAC, WRKYs, bHLHs or bZIPs and their target gene pairs and determined regulatory coordination in their expression under varying temperature conditions. Our work thus provides useful insights into temperature-responsive genes, particularly under elevated temperature conditions, and could serve as a resource of candidate genes associated with thermotolerance or downstream components of temperature sensors in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India
| | - Pratikshya Borah
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India
| | - Amarjot Kaur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India
| | - Trilochan Mohapatra
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110001, India
| | - Sanjay Kapoor
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India; Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi 110021, India; Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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Maitra Majee S, Sharma E, Singh B, Khurana JP. Drought-induced protein (Di19-3) plays a role in auxin signaling by interacting with IAA14 in Arabidopsis. PLANT DIRECT 2020; 4:e00234. [PMID: 32582877 PMCID: PMC7306619 DOI: 10.1002/pld3.234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 05/08/2023]
Abstract
The members of early auxin response gene family, Aux/IAA, encode negative regulators of auxin signaling but play a central role in auxin-mediated plant development. Here we report the interaction of an Aux/IAA protein, AtIAA14, with Drought-induced-19 (Di19-3) protein and its possible role in auxin signaling. The Atdi19-3 mutant seedlings develop short hypocotyl, both in light and dark, and are compromised in temperature-induced hypocotyl elongation. The mutant plants accumulate more IAA and also show altered expression of NIT2, ILL5, and YUCCA genes involved in auxin biosynthesis and homeostasis, along with many auxin responsive genes like AUX1 and MYB77. Atdi19-3 seedlings show enhanced root growth inhibition when grown in the medium supplemented with auxin. Nevertheless, number of lateral roots is low in Atdi19-3 seedlings grown on the basal medium. We have shown that AtIAA14 physically interacts with AtDi19-3 in yeast two-hybrid (Y2H), bimolecular fluorescence complementation, and in vitro pull-down assays. However, the auxin-induced degradation of AtIAA14 in the Atdi19-3 seedlings was delayed. By expressing pIAA14::mIAA14-GFP in Atdi19-3 mutant background, it became apparent that both Di19-3 and AtIAA14 work in the same pathway and influence lateral root development in Arabidopsis. Gain-of-function slr-1/iaa14 (slr) mutant, like Atdi19-3, showed tolerance to abiotic stress in seed germination and cotyledon greening assays. The Atdi19-3 seedlings showed enhanced sensitivity to ethylene in triple response assay and AgNO3, an ethylene inhibitor, caused profuse lateral root formation in the mutant seedlings. These observations suggest that AtDi19-3 interacting with AtIAA14, in all probability, serves as a positive regulator of auxin signaling and also plays a role in some ethylene-mediated responses in Arabidopsis. SIGNIFICANCE STATEMENT This study has demonstrated interaction of auxin responsive Aux/IAA with Drought-induced 19 (Di19) protein and its possible implication in abiotic stress response.
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Affiliation(s)
- Susmita Maitra Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Brinderjit Singh
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
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Wiebe DS, Omelyanchuk NA, Mukhin AM, Grosse I, Lashin SA, Zemlyanskaya EV, Mironova VV. Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. Genes (Basel) 2020; 11:genes11040434. [PMID: 32316383 PMCID: PMC7230499 DOI: 10.3390/genes11040434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.
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Affiliation(s)
- Daniil S. Wiebe
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Nadezhda A. Omelyanchuk
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Aleksei M. Mukhin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Sergey A. Lashin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria V. Mironova
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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