ArticleBMC genomics2013
Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease.BMC plant biology · 2015Pooled it
- The Ectopic Expression of thePlants (Basel, Switzerland) · 2024Article
- Identifying the earliest citrus responses toFrontiers in plant science · 2024Article
- Genome-wide TCP transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in Pinus tabuliformis.BMC plant biology · 2022Article
- Molecular signatures between citrus and Candidatus Liberibacter asiaticus.PLoS pathogens · 2021Review
- Article
- Overexpression of Salicylic Acid Carboxyl Methyltransferase (International journal of molecular sciences · 2021Article
- Transcriptomic Response of Huanglongbing-InfectedFrontiers in plant science · 2021Article
- Potential Mechanisms ofInternational journal of molecular sciences · 2020Article
- Characterization of Metabolites and Transcripts Involved in Flower Pigmentation inFrontiers in plant science · 2020Article
- In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style.Scientific reports · 2019Article
- Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss's Wilt of Maize.G3 (Bethesda, Md.) · 2019Article
- Unified feature association networks through integration of transcriptomic and proteomic data.PLoS computational biology · 2019Article
- The Ferredoxin-Like Protein FerR Regulates PrbP Activity inApplied and environmental microbiology · 2019Article
- Integrating Coexpression Networks with GWAS to Prioritize Causal Genes in Maize.The Plant cell · 2018Article
- Global gene expression in two potato cultivars in response to 'Candidatus Liberibacter solanacearum' infection.BMC genomics · 2017Article
- Transcriptional analysis of sweet orange trees co-infected with 'Candidatus Liberibacter asiaticus' and mild or severe strains of Citrus tristeza virus.BMC genomics · 2017Article
- Gene coexpression network analysis of fruit transcriptomes uncovers a possible mechanistically distinct class of sugar/acid ratio-associated genes in sweet orange.BMC plant biology · 2017Article
- Biochemical and Comparative Transcriptomic Analyses Identify Candidate Genes Related to Variegation Formation in Paeonia rockii.Molecules (Basel, Switzerland) · 2017Article
- PAMPs, PRRs, effectors and R-genes associated with citrus-pathogen interactions.Annals of botany · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHuanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with Ca. Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood.
resultsAs a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response.
conclusionThrough integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the Ca. Liberibacter spp. infection causing HLB.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.