Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome and proteome derived networks reveal distinct and complementary gene relationships - additional phosphoproteomics data

ABSTRACT: Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.

INSTRUMENT(S): LTQ Velos

ORGANISM(S): Zea Mays (ncbitaxon:4577)

SUBMITTER: Steven P. Briggs

PROVIDER: MSV000079303 | MassIVE |

SECONDARY ACCESSION(S): PXD002877

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome and proteome derived networks reveal distinct and complementary gene relationships

Project description:Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.

| MSV000079290 | MassIVE

Complementary peptides (cPEPs) modulate protein translation

Project description:MicroRNAs (miRNAs) are small regulatory RNAs that control plant and animal development by regulating post-transcriptional gene expression. Primary transcripts of miRNAs contain small ORFs that can be translated into small peptides (miPEPs). MiPEPs specifically enhance the expression of their cognate miRNA in a positive feedback loop. Here, by addressing the molecular bases of miPEP specificity, we identified an unanticipated mechanism modulating coding gene expression. We found that the miORF itself constitutes a prerequisite for the miPEP to specifically control the expression of its miRNA. We extended this property to any coding gene through the design of artificial peptides. We called these peptides « complementary peptides » (cPEPs) as their external application modulates the translation of their corresponding protein. We discovered here a yet undescribed mechanism of post-transcriptional regulation, opening new promising avenues in fundamental research and applied biology. Quantitative proteomics using LC-MS/MS after co-immunoprecipitation with a HA-tagged cPEP or scrambled peptide was performed to identify interactors of the cPEP or scrambled peptide in co-eluates of plants.

2023-01-09 | PXD017404 | Pride

Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species

Project description:Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species

| PRJNA957804 | ENA

RNA-Seq of chicken embryonic feather/scale recombination skin explants

Project description:The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major more modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze the transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered chromatin opening sites, and they are distributed around. When a key gene is perturbed, many other co-expressed genes in the same module also will be influenced. These findings suggest that these feather / scale fate specification genes form an interconnected network, and rewiring of the gene network can lead to changes of appendage phenotypes. This work shows the key hub positions of Beta catenin and retinoic acid signaling in the hierarchy of the scale / feather fate specification gene networks, opening up new possibilities to understand the control switches of multi-component organ phenotypes.

2018-10-15 | GSE111099 | GEO

ATAC-Seq of chicken embryonic metatarsal skin treated with RCAS-CTNNB1, RCAS-GFP, and retinoic acid

2018-10-15 | GSE111098 | GEO

A proteomic atlas of the common wheat

Project description:Integration of multi-omics data can provide information on biomolecules from different layers to illustrate the complex biology systematically. Here, we built the first global quantitative atlas containing transcriptomes, proteomes, phospho-proteomes and acetyl-proteomes of 20 tissues in common wheat. We identified 132,570 transcripts, 32,256 proteins, 69,364 phosphorylation sites, and 34,974 acetylation sites across wheat development stages. Our data demonstrated that homoeolog expression bias exists divergence at different omics layers. Regulatory networks dissected critical proteins or genes controlling important biology processes. Four wheat trait-gene families refer to timely flowering, disease resistance, starch biosynthesis-related genes, and seed storage proteins were used as examples to verify our data and shed novel inlight on the importance of post-translational modifications in wheat previously unknown. Importantly, a novel Fusarium crown rot (FCR) resistant gene delta-1-pyrroline-5-carbo

2023-04-20 | PXD041703 |

A multi-omics atlas of common wheat

2023-05-25 | PXD042492 |

Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy

Project description:This data is for the manuscript "Investigating the differential structural organization and gene expression regulatory networks of lamin A Ig fold domain mutants of muscular dystrophy."

2024-10-21 | MSV000096145 | MassIVE

Transcriptional profiling of Triticea seed and vegetative tissues

Project description:Despite their importance, there remains to be few large scale expression-based studies of tissue-specific expression information in the species belonging to the Triticeae. We used the 55K Affymetrix GeneChip® Wheat Genome Array to generate a gene expression atlas of triticale tissues. The global transcriptional profiles of seed tissues (embryo, endosperm, crease, pericarp and epiderm) and vegetative tissues (root, coleoptile, stem and leaf) were analyzed and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae tissue development and function.

2014-12-24 | GSE43127 | GEO

Developmental transcriptional profiling of Triticeae reproductive development

Project description:Despite their importance, there remains a paucity of large scale expression-based studies of reproductive development in the species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip® Wheat Genome Array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages and co-regulated as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function.

2012-11-01 | GSE41984 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data