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Integrative Analysis of Transcriptomics - Proteomics - Metabolomics

Creative Proteomics provides comprehensive analysis services of transcriptomics - proteomics - metabolomics to mine the correlation and mutual verification of transcriptome, proteome and metabolome levels; screen key genes / proteins / metabolites / metabolic pathways from massive data to provide powerful insights into the mechanism of complex life activities evidence. Then analyze the development of biological system processes, explain the complexity and integrity of biological processes.

Why Do Integrative Analysis of Transcriptomics - Proteomics - Metabolomics?

The transcriptome represents the intermediate state of gene expression and can reflect mechanisms such as transcriptional regulation and post-transcriptional regulation; the proteome represents the direct function execution state of the organism and can reflect the actual expression of transcripts; and the metabolome can reflect the phenotype of the organism status change. Multi-omics analysis of transcriptome – proteome - metabolome can simultaneously realize the process from "cause" to "result" to explore biological problems; to verify each other; to screen out key genes, proteins and metabolic pathways from massive data ; explain the complexity and integrity of biological processes.

Our Integrative analysis services of Transcriptomics - Proteomics - Metabolomics

Creative Proteomics provides you with one-stop proteome detection, metabolome detection and transcriptome sequencing services. In addition, we offer integrative analysis services of transcriptomics - proteomics - metabolomics to seamlessly connect your experiments upstream and downstream.

Bioinformatics Analysis

Through the expression trend analysis of differential genes and differential proteins, gene-protein sets with different/same/opposite expression trends can be obtained. The functional enrichment analysis of different gene sets can further explore the key genes and proteins that regulate biological phenotypes. Based on the integrated analysis of transcriptome-proteome, combined with metabolomic analysis, molecular changes and phenotypic changes can be linked, so that the regulatory process from genes to proteins to metabolism can be systematically described. In this way, key proteins, key metabolites and key regulatory pathways can be mined, making the entire research content richer and more complete.

Bioinformatics Analysis

Our analysis content and analysis ideas are constantly being updated, so if you would like to learn more, please contact our technical engineers today.

Why Choose Us?

  • We have a complete multi-omics technology service system from genome, transcriptome, epigenome to proteome and metabolome.
  • We continue to carry out technology development, process optimization, introduction of excellent equipment, gathering of excellent talents, and continuous improvement of management, and have established a first-class technical platform in the industry to provide quality technical services to our clients.
  • Excellent bioinformatics analysis - our bioinformatics center brings together many high-level information analysis talents from home and abroad, and has many years of practical experience in the field of bioinformatics research and development.
  • We understand the needs of our customers, accompany them for in-depth scientific interaction, take care of every detail, and continue to provide good service.

Case Study

Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish

Journal: PNAS
Impact factor: 9.504
Published: 2017


Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified.

Materials & Methods

  • Using the adult zebrafish fish tail as a study model, the uninjured and modeled fish tails along the spatial axis (proximal, middle, distal) were used.
  • Transcriptome, proteome, and metabolome for quantitative analysis and combined analysis.
Type There were significant differential expression changes at the transcriptional / protein / metabolite levels in different caudal fin positions.
Transcriptomic GO analysis and transmembrane receptor analysis found that 53 of the 693 mRNAs encoding transcription factors were differentially expressed in the anterior and terminal regions of the caudal fin; and 12/13/10 corresponding signaling in the RA/WNT/FGF signaling pathway genes have opposite transcriptional gradients.
Proteomic GO analysis of the proteome identified proteins involved in amino acid metabolism and lipid transport, suggesting that in addition to genetically encoded cues, metabolites may also contribute to location memory.
Transcriptomic + Proteomic The combined transcription-proteomic analysis of different positions of the caudal fin showed that: the proximal region has 66 transcripts and 54 proteins highly expressed; the distal region has 51 transcripts and 29 proteins highly expressed; of which 32 is the transcript and protein association. It shows that there are extensive post-translational modification regulatory mechanisms in organisms.
Metabolomic Metabolomics analysis found that 26 were highly expressed in the proximal caudal fin (including arginine, glutamine, leucine, etc.), and 16 were highly expressed in the proximal caudal fin.
Transcriptomic + Proteomic + Metabolomic Metabolomics research, as the complement of transcriptome and proteome, qualitatively and quantitatively analyzes metabolites at different positions in the near and far caudal fins, making the dynamic changes of the whole organism more comprehensive, and realizing the integration of molecular regulation and phenotypic changes.


Complex overlapping expression patterns of hundreds of molecules involved in diverse cellular functions reveal candidate effector molecules for place memory with roles in adult appendages for regeneration and control of organ size.

Transcriptomic and proteomic mapping of positional information in uninjured caudal fins.Fig.1 Transcriptomic and proteomic mapping of positional information in uninjured caudal fins. (Rabinowitz JS, et al., 2017)

Creative Proteomics relies on advanced platforms and cutting-edge technologies to provide omics services to customers around the world, and provide accurate and detailed analysis reports. In addition, we also provide multi-omics integrated analysis services. You can discuss with our technical engineers to customize solutions or build new methods to meet your specific needs. If you have any questions, you can tell us through the inquiry form, and our technicians will communicate with you. Please don't hesitate to contact us, Creative Proteomics can be trusted.


  1. Rabinowitz JS, Robitaille AM, Wang Y, Ray CA, Thummel R, Gu H, Djukovic D, Raftery D, Berndt JD, Moon RT. Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):E717-E726. doi: 10.1073/pnas.1620755114. Epub 2017 Jan 17. PMID: 28096348; PMCID: PMC5293114.
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