Transcriptome and Proteome Integration Analysis



Protein is the ultimate function of the organism, and its content changes with the growth of organisms, environmental stress response, and the development of diseases. Therefore, the analysis of proteins is of great significance. The transcriptome is an intermediate module connecting the genome and the proteome. The process of transcribing DNA into mRNA and then translating into protein involves a complete set of fine expression regulation mechanisms, such as transcription regulation, post-transcriptional regulation, translation regulation, and post-translational regulation, etc. Studies have shown that the correlation coefficient between the transcriptome and the proteome is not high, indicating that in this process, translation and post-translational regulation have a very important regulatory effect on protein expression.

Transcriptome and proteome integration analysis is to mine the expression levels of mRNA and protein through joint analysis of transcriptome data and proteome data, make full use of the differences and complementarities of transcriptome and proteome research, measure the expression level of genes in an all-around way, obtain a panoramic view of the expression and regulation of each step of gene expression, and discover new results that conventional single omics have not found, and then comprehensively explore the biological disease mechanism, growth and development mechanism, etc.

Rb Phosphorylation as a Driver and Therapeutic Target in Colon Cancer.Figure1. Rb Phosphorylation as a Driver and Therapeutic Target in Colon Cancer. (Y Suhas V, et al. 2019)

Application Fields

Transcriptome and proteome integration analysis is used in various fields of biomedical research, such as:

  • Basic medicine research: biomarker discovery, disease mechanism research, drug action mechanism, drug efficacy evaluation, drug development.
  • Clinical diagnosis: disease classification, personalized treatment.

What We Offer

As one of the experienced biomedical data analysis service providers, we offer established, cost-efficient and rapid turnaround analysis services for transcriptome and proteome integration analysis. The raw input RNA data and proteome data can be produced from different sequencing platforms or mass spectrometers. In addition, we can use various formats of data for analysis such as raw data files, or other intermediate data formats. We provide our clients with the following services:

  • Data analysts evaluate and filter raw data.
  • Develop suitable analysis strategies according to the data situation.
  • Perform transcriptome and proteome integration analysis.
  • An analysis report includes analysis methods and interpretation of biological significance.
  • Experienced bioinformatics engineers complete all analysis content in a short period of time.

Data Analysis Technical Route

Flow chart showing transcriptome and proteome integration analysis. - CD Genomics.Fig 2. Flow chart showing transcriptome and proteome integration analysis.

Analysis Content Includes:

Based on different types of transcriptome data (such as denovo sequencing, reference sequencing, DGE and microarray data) and proteome data (such as iTRAQ, label-free, etc.), we first perform differential expression and functional analysis of each omics data, and then conduct integration analysis.

  • Quantitative association analysis of transcriptome and proteome.
  • Gene pathway analysis with consistent mRNA and protein expression trends.
  • Gene pathway analysis of the opposite trend of mRNA and protein expression.
  • No change in protein expression, pathway analysis of genes corresponding to differentially expressed mRNA.
  • No change in mRNA expression, pathway analysis of genes corresponding to differentially expressed protein.
  • Transcriptome and proteome expression pattern analysis.
  • Protein interaction network analysis.

Data Ready

Before data analysis, the first thing is to get your data ready. The input data can be obtained from the following channels:

Channels of transcriptome and proteome input data. - CD Genomics.

In order to process data more efficiently, we prefer to receive data files in the raw format, but we can also accept pre-normalized files.  In addition, if you have any questions about the data analysis cycle, analysis content and price, please click online inquiry.

What's More

For transcriptome and proteome integration analysis, if you have not generated the raw data, CD Genomics can help by arranging for the generation of your data. Alternatively, we are able to provide services for obtaining and mining data from available databases. For more questions, please feel free to contact us. We have a professional technical support team to serve you.


  1. Suhas V, et al. Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities[J]. Cell, 2019, 177, 1-15.

* For research use only. Not for use in clinical diagnosis or treatment of humans or animals.

Online Inquiry

Please submit a detailed description of your project. Our industry-leading scientists will review the information provided as soon as possible. You can also send emails directly to for inquiries.