Abstract
etiolated seedlings to identify protein kinases and phosphatases relevant to skotomorphogenic development, a phase during which seedlings rely on tightly regulated signaling networks to ensure survival in darkness. This meta-analysis provided a comprehensive view of gene and protein expression, revealing discrepancies between transcript and protein abundance, suggesting post-transcriptional and post-translational regulation. By integrating multiple datasets, OmicIntegrator reduces experimental bias and enables the detection of phosphorylation events that may be missed in single-condition studies. Distinct phosphorylation patterns were detected across different protein kinase families. Motif enrichment analysis showed a strong overrepresentation of RxxS motifs among phosphosites in protein phosphatases and microtubule-associated proteins, consistent with potential regulation by calcium-dependent protein kinases (CPKs). Across omics layers, CPK3 and CPK9 repeatedly emerged as prominent candidates, highlighting them as priorities for future functional studies in skotomorphogenesis. Overall, our results demonstrate the power of OmicIntegrator as a flexible framework to contextualize signaling landscapes and identify robust patterns and candidate genes and for generating testable hypotheses from integrated multi-omics data in plant developmental biology.
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Claims 6
Claim · model-written summary
Transcript and protein abundance differed.
- Outcome
- discrepancies between transcript and protein abundancee0
Not reportedTaxon
Verbatim
e0“discrepancies between transcript and protein abundance”
Claim · model-written summary
Distinct phosphorylation patterns were found across kinase families.
Not reportedTaxon
Verbatim
e0“Distinct phosphorylation patterns were detected across different protein kinase families”
Claim · model-written summary
RxxS motifs were strongly overrepresented among phosphosites in phosphatases and microtubule-associated proteins.
- Gene
- protein phosphatases and microtubule-associated proteinse0
- Outcome
- RxxS motifs among phosphositese0
- Direction
- overrepresentatione0
Not reportedTaxon
Verbatim
e0“strong overrepresentation of RxxS motifs among phosphosites in protein phosphatases and microtubule-associated proteins”
Claim · model-written summary
CPK3 emerged repeatedly as a candidate in skotomorphogenesis.
Not reportedTaxon
Verbatim
e0“CPK3 and CPK9 repeatedly emerged as prominent candidates”
Claim · model-written summary
CPK9 emerged repeatedly as a candidate in skotomorphogenesis.
Not reportedTaxon
Verbatim
e0“CPK3 and CPK9 repeatedly emerged as prominent candidates”
Claim · model-written summary
OmicIntegrator integrates datasets to detect phosphorylation events missed by single-condition studies.
Not reportedTaxon
Verbatim
e0“OmicIntegrator reduces experimental bias and enables the detection of phosphorylation events that may be missed in single-condition studies”