Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Overview of Microsoft Excel as a Data Analysis Tool01:13

Overview of Microsoft Excel as a Data Analysis Tool

1.5K
Microsoft Excel is a cornerstone tool for data analysis and statistical operations, offering a wide array of functionalities to manage, analyze, and visualize data efficiently. Recognized for its versatility, Excel facilitates the performance of basic to complex statistical operations, serving as an indispensable asset for analysts, researchers, and students alike. Excel's significance in data analysis emanates from its spreadsheet environment, where data can be organized in rows and...
1.5K
Directing Effect of Substituents: meta-Directing Groups01:09

Directing Effect of Substituents: meta-Directing Groups

5.9K
Substituents on the benzene ring that direct an incoming electrophile to undergo substitution at the meta position are called meta directors. All meta directors either have a positive charge on the atom directly bonded to the ring or a partial positive charge. These groups function by withdrawing electrons from the ring through inductive and resonance effects. Consider the carbocation intermediates formed upon the addition of an electrophile on nitrobenzene at the...
5.9K
Performing a Simple Data Analysis using MS-Excel Function01:17

Performing a Simple Data Analysis using MS-Excel Function

1.0K
Microsoft Excel offers a suite of functions and tools ideal for statistical analysis, making it accessible to students and researchers. This article outlines fundamental Excel functions pivotal for data analysis.
SUM: This function calculates the total sum of a range of values. It's the foundation for aggregating data, essential for determining overall trends and totals in datasets.
AVERAGE: It computes the mean value of a given set of numbers, providing a quick insight into the central...
1.0K
Simple Pendulum01:10

Simple Pendulum

8.0K
A simple pendulum consists of a small diameter ball suspended from a string, which has negligible mass but is strong enough to not stretch. In our daily life, pendulums have many uses, such as in clocks, on a swing set, and on a sinker on a fishing line. 
The period of a simple pendulum depends on two factors: its length and the acceleration due to gravity. The period is completely independent of any other factors, such as mass or maximum displacement. For small displacements, a pendulum is...
8.0K
Simple Trusses01:21

Simple Trusses

2.9K
A truss is a structural framework consisting of slender members connected at joints, designed to support external loads while minimizing material usage and weight. Simple trusses are a type of planar truss where all members lie within a single two-dimensional plane.
The most basic planar truss is a simple truss with three members arranged in a triangular formation. This triangular truss is inherently stable and rigid due to its geometry, making it an ideal starting point for creating more...
2.9K
meta-Directing Deactivators: –NO2, –CN, –CHO, –⁠CO2R, –COR, –CO2H01:13

meta-Directing Deactivators: –NO2, –CN, –CHO, –⁠CO2R, –COR, –CO2H

6.7K
All meta-directing substituents are deactivating groups. These substituents withdraw electrons from the aromatic ring, making the ring less reactive toward electrophilic substitution. For example, the nitration of nitrobenzene is 100,000 times slower than that of benzene because of the deactivating effect of the nitro group. The first step in an electrophilic aromatic substitution is the addition of an electrophile to form a resonance-stabilized carbocation. The energy diagrams for...
6.7K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Plant growth-promoting abilities of Methylobacterium sp. 2A involve auxin-mediated regulation of the root architecture.

Plant, cell & environment·2024
Same author

Arabidopsis hypocotyl growth in darkness requires the phosphorylation of a microtubule-associated protein.

The Plant journal : for cell and molecular biology·2024
Same author

Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits.

Plants (Basel, Switzerland)·2023
Same author

Calcium-dependent protein kinase 2 plays a positive role in the salt stress response in potato.

Plant cell reports·2021
Same author

Neighbour signals perceived by phytochrome B increase thermotolerance in Arabidopsis.

Plant, cell & environment·2019
Same journal

RETRACTED: Wang et al. Integrated Analysis of Physiological and Transcriptional Mechanisms in Response to Drought Stress in <i>Scaevola taccada</i> Seedlings. <i>Plants</i> 2026, <i>15</i>, 970.

Plants (Basel, Switzerland)·2026
Same journal

RETRACTED: Russo et al. Chamazulene-Rich <i>Artemisia arborescens</i> Essential Oils Affect the Cell Growth of Human Melanoma Cells. <i>Plants</i> 2020, <i>9</i>, 1000.

Plants (Basel, Switzerland)·2026
Same journal

Correction: Terletskaya et al. Soil-Climatic Drivers of Anatomical and Metabolic Plasticity in <i>Rheum tataricum</i> L.f. Across Arid Landscapes of Kazakhstan. <i>Plants</i> 2026, <i>15</i>, 1025.

Plants (Basel, Switzerland)·2026
Same journal

Correction: Damásio et al. Can Grapevine Leaf Water Potential Be Modelled from Physiological and Meteorological Variables? A Machine Learning Approach. <i>Plants</i> 2023, <i>12</i>, 4142.

Plants (Basel, Switzerland)·2026
Same journal

Apple Leaf Disease Detection Based on Improved YOLOv11 with DSSA Mechanism.

Plants (Basel, Switzerland)·2026
Same journal

New Pollen Morphological Perspectives into <i>Vernonia</i> (Compositae-Vernonieae) from Madagascar.

Plants (Basel, Switzerland)·2026
See all related articles

Related Experiment Video

Updated: Jan 29, 2026

Building a Simple and Versatile Illumination System for Optogenetic Experiments
06:41

Building a Simple and Versatile Illumination System for Optogenetic Experiments

Published on: January 12, 2021

4.4K

OmicIntegrator: A Simple and Versatile Tool for Meta-Analysis.

Iván Federico Berco Gitman1, Cecilia Eugenia María Grossi1, Denise Soledad Arico1,2,3

  • 1Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Vuelta de Obligado 2490, 2do piso, Ciudad Autónoma de Buenos Aires 1428, Argentina.

Plants (Basel, Switzerland)
|January 28, 2026
PubMed
Summary
This summary is machine-generated.

OmicIntegrator standardizes multi-omics data for plant development studies. It identified key protein kinases, like CPK3 and CPK9, crucial for seedling survival in darkness (skotomorphogenesis).

Keywords:
Arabidopsis thalianaprotein kinasesprotein phosphatasesproteomic and phosphoproteomic integrative meta-analysisskotomorphogenesistranscriptomic

More Related Videos

Meta-Analysis of the Effectiveness and Safety of Shugan Jieyu Capsules for the Treatment of Insomnia
04:34

Meta-Analysis of the Effectiveness and Safety of Shugan Jieyu Capsules for the Treatment of Insomnia

Published on: February 17, 2023

1.6K
Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images SDM-PSI
06:26

Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images SDM-PSI

Published on: November 27, 2019

77.4K

Related Experiment Videos

Last Updated: Jan 29, 2026

Building a Simple and Versatile Illumination System for Optogenetic Experiments
06:41

Building a Simple and Versatile Illumination System for Optogenetic Experiments

Published on: January 12, 2021

4.4K
Meta-Analysis of the Effectiveness and Safety of Shugan Jieyu Capsules for the Treatment of Insomnia
04:34

Meta-Analysis of the Effectiveness and Safety of Shugan Jieyu Capsules for the Treatment of Insomnia

Published on: February 17, 2023

1.6K
Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images SDM-PSI
06:26

Meta-analysis of Voxel-Based Neuroimaging Studies using Seed-based d Mapping with Permutation of Subject Images SDM-PSI

Published on: November 27, 2019

77.4K

Area of Science:

  • Plant developmental biology
  • Molecular signaling networks
  • Multi-omics data integration

Background:

  • Skotomorphogenesis is critical for seedling survival in darkness, relying on complex signaling.
  • Understanding gene and protein regulation during this phase is essential.

Purpose of the Study:

  • To develop a pipeline (OmicIntegrator) for standardizing and integrating transcriptomic, proteomic, and phosphoproteomic data.
  • To identify protein kinases and phosphatases involved in Arabidopsis thaliana skotomorphogenesis.
  • To reveal post-transcriptional and post-translational regulatory mechanisms.

Main Methods:

  • Development of the OmicIntegrator pipeline for multi-omics data standardization and integration.
  • Application of the pipeline to Arabidopsis thaliana etiolated seedling datasets.
  • Meta-analysis of transcriptomic, proteomic, and phosphoproteomic data.
  • Motif enrichment analysis to identify regulatory patterns.

Main Results:

  • Revealed discrepancies between transcript and protein abundance, indicating complex regulation.
  • Identified distinct phosphorylation patterns across protein kinase families.
  • Highlighted RxxS motifs, suggesting regulation by calcium-dependent protein kinases (CPKs).
  • CPK3 and CPK9 emerged as key candidate genes for skotomorphogenesis.

Conclusions:

  • OmicIntegrator is a flexible framework for contextualizing signaling and identifying robust patterns from multi-omics data.
  • The study provides valuable insights into the molecular mechanisms of skotomorphogenesis.
  • Identified CPK3 and CPK9 as high-priority targets for future functional studies in plant development.