Integrated Transcriptomic and Proteomic Analysis

Service Details
Case Study

The transcriptome is the complete collection of information transcribed by a cell at a particular stage of development or under physiological conditions. It represents the intermediate state of gene expression. Proteins are the direct executors of life functions, and the proteome is the entire set of proteins expressed by a cell or organism. Both proteomics and transcriptomics are critical tools for obtaining gene expression information. The comprehensive analysis of proteomics and transcriptomics data can compensate for problems caused by the lack of single-omics data, noise interference and other factors. It can also reduce false positives brought about by single-omics analysis. Comprehensive analysis of proteomics and transcriptomics data can be used to explain biological problems from a holistic point of view, explore organism physiological and disease mechanisms. It is conducive to the study of the multilevel regulation of gene expression, and obtains more comprehensive information on gene expression, which can provide more comprehensive information for biomedical research, drug research and development, and agricultural research and application. It can make up for the problems caused by single-omics data, noise interference and other factors. It can also reduce false positives brought on by single histology analyses.

Creative Proteomics has many years of experience in multi-omics integrative services. We combine high-throughput transcriptome sequencing platform and advanced mass spectrometry platform with customizable bioinformatics methods for integration, aiming to provide customers with one-stop transcriptomics and proteomics integrated analysis services.

Integrating transcriptomics and proteomics to decipher disease biology (Kumar D, et al,. 2016)

What are the main analyses we provide?

Shared gene analysis.
Qualitative association analysis.
Transcriptome and proteome quantitative association analysis.
Pathway analysis of genes with consistent mRNA and protein expression trends.
Analysis of gene pathways with opposite trends in mRNA and protein expression.
Pathway analysis of genes corresponding to differentially expressed mRNAs with no change in protein expression.
Pathway analysis of genes corresponding to differentially expressed proteins with no change in mRNA expression.
Transcriptome and proteome expression pattern analysis.
Protein interaction network analysis.

Purpose and advantages of integrated transcriptomics and proteomics analysis

The integration of the two groups can provide a "panoramic view" of expression profiles and realize the complementarity of the two groups to analyze the expression levels of mRNAs and proteins in a specific state of an organism.
Integration of transcriptome and proteome analysis can provide in-depth understanding of differential expression profiles, uncover key mRNAs or proteins subject to post-transcriptional regulation, and identify and validate important regulatory pathways.
For species for which protein databases are lacking or poorly annotated, the number of protein identifications can be substantially increased by constructing protein search libraries from transcriptome data.

Applications of integrated transcriptomics and proteomics analyses

Agroforestry field. Research on plant biotic stress mechanisms, research on plant abiotic stress mechanisms, research on plant growth and development mechanisms, and research on breeding and conservation.
Animal research. Animal genetic breeding, animal nutritional quality research, animal disease research.
Medical research. Tumor development mechanism, complex disease molecular mechanism research, biomarkers, disease typing, personalized treatment, etc.
Biomedicine. Research on drug action target and mechanism, evaluation of drug efficacy, drug development, etc.
Microbiology. Pathogenesis, drug resistance mechanism, pathogen-host interaction research, etc.
Food nutrition. Optimization of food storage and processing conditions, identification of food components and quality, functional food development, food safety monitoring and testing, etc.

Our service workflow

What do we offer?

Creative Proteomics will provide you with a detailed technical report on the following.

Experimental steps.
Relevant experimental parameters.
Mass spectrometry images.
Raw data.
Transcriptomics and proteomics analysis results.

Creative Proteomics has rich experience in multi-omics co-analysis. The transcriptomics and proteomics co-analysis services we provide are designed to help researchers analyze gene expression and other organism-related issues in a more comprehensive manner. If you are interested in us, please feel free to contact us.

Reference

Kumar D, Bansal G, Narang A, et al. Integrating transcriptome and proteome profiling: Strategies and applications. Proteomics. 2016 ;16(19):2533-2544.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Journal: Cell Syst

Published: 2015

Abstract

Aging is a multifactorial process associated with progressive loss of physiological integrity, leading to functional decline and increased morbidity. Current studies have found that aging is associated with protein, cellular, and organ decline. The authors utilized an integrated transcriptomic and proteomic analysis approach to study gene expression, bulk translation, and cell biology in the brain and liver of aged old rats, which was used to better explain aging at the organismal level.

Results

In this study, the authors combined birdshot mass spectrometry with subcellular isolation, RNA sequencing, and ribosome analysis to study physiological changes in the liver and brain of young and old rats (Figure 1). This integrated analysis provides a system-wide comparison between the brain, which has limited cellular renewal capacity, and the liver, which has a greater capacity for renewal, enabling the identification of specific alterations, such as protein kinases and signaling mediators in the brain, metabolic processes in the brain, and common responses that differentiate between the organs of young and old animals.

Figure 1

The characterization of affected transcripts and proteins also suggests organ-specific differences between young and old animals. Of the 1,099 altered transcript abundances, only 48 were significantly lower than expected and were common in the brain and liver, of which 37 (77%) were consistently changed (Figure 2).

Figure 2

Conclusion

By comparing two organs with different physiological and regenerative capacities, the authors distinguish between organ-specific effects and systemic effects of aging. Intuitively, this study suggests that age-specific organ-specific effects are closely related to organ function. In the liver, most age-related changes are driven by alterations in transcript abundance, suggesting age-related changes in transcriptional regulation. In contrast, the brain is affected by age primarily at the translational level. Overall, the study suggests that age-related remodeling of the brain's translational machinery may ultimately lead to changes in the translation efficiency of a subset of transcripts in older animals. Specifically, the authors found that 15% of brain transcripts were affected by translation changes (compared to 2% in the liver).

The authors did this by quantifying the molecular changes between two organs, the brain and the liver, in young and old rats. By integrating transcriptomic and proteomic analyses, they reveal that translation changes are the main cause of altered protein levels during aging. However, they also identified other levels of regulation, such as protein localization and phosphorylation. These levels are involved in proteome modification in older animals.

Reference

Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Syst. 2015.

* For Research Use Only. Not for use in diagnostic procedures.

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"I recently used their proteomics service for a project analyzing protein interactions in yeast models. The team was very responsive and helped clarify the methodology they employed, which made me feel confident in the results. The data quality was solid, with clear identification of several key proteins involved in our study. Their thorough analysis enabled me to pinpoint specific interactions that I hadn't considered before, which significantly improved the direction of my research. I appreciate their professionalism and support throughout the process."

Sarah Thompson, University of California, Berkeley

"Our lab collaborated with them on a project studying cancer biomarkers. The proteomics analysis provided was detailed and focused, specifically highlighting the differential expression of proteins between healthy and tumor samples. Their clear explanations of the data helped my team understand the biological implications. I also appreciated their willingness to revise the reports based on our feedback, ensuring that we had everything we needed for our publication. This collaborative spirit was invaluable."

Emily Rodriguez, Stanford University

"Our lab worked with them on a project studying the effects of diet on gut microbiota using proteomics. They used a label-free quantification method to analyze proteins in fecal samples before and after dietary intervention. The results showed significant changes in protein expression linked to microbial activity. This was pivotal for our hypothesis about diet-microbiota interactions. The clarity of their data presentation made it easy for our team to integrate these findings into our ongoing research."

Dr. Lisa Wong, University of Toronto

"My experience with Creative Proteomics during the mass spectrometry analysis was excellent. We sent in human saliva and mouse brain tissue samples, which they expertly analyzed using both LC-MS and GC-MS techniques. The results were invaluable, revealing key metabolites in the saliva and identifying biomarkers linked to brain function in the brain tissue."

Dr. Emily Carter, Senior Research Scientist

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Dr. Laura Henderson, Plant Physiologist

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Dr. Sarah Mitchell, Research Scientist

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